http://rosbnet.org/wiki/wiki/api.php?action=feedcontributions&feedformat=atom&user=MarkChangRoSBNet - User contributions [en]2026-05-11T16:33:58ZUser contributionsMediaWiki 1.35.1http://rosbnet.org/wiki/wiki/index.php?title=Member_List&diff=1041Member List2013-01-26T01:11:37Z<p>MarkChang: /* Biology/Biochemistry Researchers */</p>
<hr />
<div>= RoSBNet Members =<br />
<br />
Below you will find a list of RoSBNet members, with links to their websites for more information.<br />
<br />
== Engineering/Mathematics Researchers == <br />
{| border="1"<br />
! Member !! Affiliation !! Research Interests !!<br />
<br />
|-<br />
| [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou] || University of Oxford || Systems and synthetic biology, nonlinear systems, automatic control systems, synchronization, complex networks<br />
|-<br />
| [http://www.ist.uni-stuttgart.de/allgower/allgower.shtml Frank Allgower] || Institute for Systems Theory and Automatic Control, University of Stuttgart || Automatic control, systems biology<br />
|-<br />
|[http://www3.imperial.ac.uk/people/m.barahona Mauricio Barahona] || Imperial College London || Applied mathematics in biological, physical and engineering systems<br />
|-<br />
| [http://www.eee.strath.ac.uk/~hongyue/ Hong Yue] || University of Strathclyde || Modelling and system analysis of biological networks; optimal/robust experimental design; Process control <br />
|-<br />
| [http://www.eee.manchester.ac.uk/aboutus/staff/show.html?ea=William.Heath William Heath] || University of Manchester || System Identification: in particular identification of signals and dynamic models associated with biological homeostasis<br />
|-<br />
| [http://biology.st-andrews.ac.uk/vannesmithlab/ Anne Smith] || University of St Andrews || Complex biological networks (molecular, neuronal, ecological), network evolution<br />
|-<br />
| [http://www.rdg.ac.uk/icmr/about/staff/icmr-m-tindall.asp Marcus Tindall] || University of Reading || Mathematical modelling, multi-scale modelling, multicellular systems biology, bacterial chemotaxis , non-linear ordinary and partial differential equations<br />
|-<br />
| [http://www.montefiore.ulg.ac.be/~bullinger/ Eric Bullinger] || Université de Liège || Systems Biology, from data analysis over modelling to model analysis as well as the development of system theoretical methodologies<br />
|-<br />
| [http://www.gla.ac.uk/departments/aerospace/staff/academicstaff/jongraekim Jongrae Kim] || University of Glasgow || Stochastic dynamics; System identification; Robustness analysis; Large-scale network analysis<br />
|-<br />
| [http://control.ee.ethz.ch/~auguste/ Elias August] || Swiss Federal Institute of Technology || Systems biology<br />
|-<br />
| [http://www.sbs.ox.ac.uk/faculty/Reed-Tsochas+Felix/ Felix Reed-Tsochas] || University of Oxford || <br />
|-<br />
| [http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Jotun Hein] || University of Oxford || Bioinformatics<br />
|-<br />
| [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:James_Anderson James Anderson] || University of Oxford || Control and dynamical systems, systems biology, synthetic biology<br />
|-<br />
| [http://www.eng.ox.ac.uk/samp/people.html Patrick McSharry] || University of Oxford || Signal processing, systems biology, complex adaptive systems, operations research and forecasting<br />
|-<br />
| [http://www.ist.uni-stuttgart.de/~waldherr/ Steffen Waldherr] || Institute for Systems Theory and Automatic Control Universität Stuttgart || Applications of approaches from control engineering and dynamical systems theory to systems biology and biological networks<br />
|-<br />
| [http://www3.imperial.ac.uk/people/r.tanaka Reiko Tanaka] || Imperial College London || Biological control, systems biology<br />
|-<br />
| [http://www.comlab.ox.ac.uk/people/Jonathan.Whiteley/ Jonathan Whiteley] || University of Oxford || Mathematical modelling and scientific computing related to multiscale, multiphysics problems arising in physiology and biology<br />
|-<br />
| [http://www.physics.ox.ac.uk/users/kapanidis/ Achillefs Kapanidis] || University of Oxford || Single-molecule studies of DNA-processing biomachines<br />
|-<br />
|[http://www.staff.ncl.ac.uk/d.j.wilkinson/ Darren Wilkinson] || Newcastle University || Applications of Bayesian statistics to a variety of problems in Molecular biology, Bioinformatics and Systems Biology<br />
|-<br />
| [http://www.comlab.ox.ac.uk/people/David.Gavaghan/ David Gavaghan] || University of Oxford || Computational biology<br />
|-<br />
| [http://emps.exeter.ac.uk/staff/dgb208 Declan Bates] || University of Exeter || Robustness and feedback control in cellular and physiological systems <br />
|-<br />
| [http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves] || University of Cambridge || Systems Biology: modelling, analysis, and control of biological systems like circadian rhythms and gene regulatory networks.<br />
|-<br />
| [http://www.mit.edu/~ddv/ Domitilla del Vecchio] || MIT || Control and dynamical systems, biomolecular networks<br />
|-<br />
| [http://biochemistry.ucsf.edu/labs/elsamad/people/Hana_El_Samad/hana_el_samad.html Hana El-Samad] || University of California, San Francisco || Interface between biology, mathematics, dynamical systems, and control theory<br />
|-<br />
| [http://www.bionanotechnology.ox.ac.uk/index.php?option=com_content&task=view&id=24&Itemid=50 John Ryan] || University of Oxford ||Molecular motors, membrane proteins, single-molecule electronics and photonics<br />
|-<br />
| [http://www.engineering.ucsb.edu/~khammash/ Mustafa Khammash ] || University of California, Santa Barbara || Control theory and its applications to engineering and to biological systems<br />
|-<br />
| [http://people.maths.ox.ac.uk/~maini/ Philip Maini] || University of Oxford || Mathematical and computational modelling of temporal and spatiotemporal phenomena in a number of areas in the life sciences, including developmental biology, wound healing, cancer biology and bacterial chemotaxis<br />
|- <br />
| [http://www2.imperial.ac.uk/~nsjones/ Nick Jones] || Imperial College London || Cellular fluctuations and cellular energy variability, Principles of Natural networks<br />
|-<br />
| [http://www.eng.ox.ac.uk/control/peopleSD.shtml Steve Duncan] || University of Oxford || Control theory, biological systems, epidemiology<br />
|-<br />
| [http://www3.imperial.ac.uk/people/g.stan Guy-Bart Stan] || Imperial College London || Nonlinear dynamical systems and control, complex networks, synthetic biology, systems biology<br />
|-<br />
| [http://melykuti.web.elte.hu/index.htm Bence Melykuti] || University of California, Santa Barbara || The interfaces of mathematical (esp. probabilistic) modelling, stochastic processes, control theory, systems biology, operations research<br />
|-<br />
| [http://www-control.eng.cam.ac.uk/~aoh21/ Abdullah Hamadeh] || University of Waterloo || Modelling and analysis of nonlinear dynamical systems with applications to automatic control, process control and systems biology<br />
|-<br />
| [http://www.eng.ox.ac.uk/~stcman/people.shtml Edward Hancock] || University of Oxford || Nonlinear dynamical systems, systems biology<br />
|-<br />
| [http://www.st-hildas.ox.ac.uk/index.php/fellowsandlecturers/alubansky.html Alex Lubansky] || University of Oxford || Microfluidics, Rheology, Synthetic Biology<br />
|-<br />
|[http://www3.imperial.ac.uk/people/natalja.strelkowa06 Natalja Strelkowa] || Imperial College London || Stochastic analysis of gene regulatory networks and applications of control theory and theoretical aspects of population dynamical models <br />
|-<br />
| [http://www.multidisciplinary.soton.ac.uk/profile/ajc6/#information Andrew Chipperfield] || University of Southampton || Control systems engineering, biomedical modelling, signal processing <br />
|-<br />
| [http://people.exeter.ac.uk/oss203/ Orkun Soyer] || University of Exeter || Evolutionary systems biology, synthetic biology, signalling networks, metabolic networks, bacterial communities<br />
|-<br />
| [http://www.enm.bris.ac.uk/anm/staff/enmdb/home.html Mario Di Bernardo] || University of Bristol || Analysis, synchronization and control of complex networks, systems and synthetic Biology <br />
|-<br />
| [http://users.ox.ac.uk/~dpag0022/index.htm Eric Werner] || University of Oxford || <br />
|-<br />
| [http://mpf.biol.vt.edu/lab_website/people/Tongli_Zhang/ Tongli Zhang] || University of Oxford ||Modelling signal transduction pathways in mammalian cells<br />
|-<br />
| [http://www.montefiore.ulg.ac.be/~sepulch/ Rodolphe Sepulchre] || Université de Liège || Nonlinear control and optimization<br />
|}<br />
<br />
== Biology/Biochemistry Researchers == <br />
<br />
{| border="1"<br />
! Member !! Affiliation !! Research Interests !!<br />
<br />
|-<br />
| [http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=565 Judy Armitage] || University of Oxford || Bacterial networks and protein dynamics<br />
|-<br />
| [http://www.abdn.ac.uk/ims/staff/details.php?id=i.stansfield Ian Stansfield] || University of Aberdeen || The mechanism of protein synthesis in eukaryote cells, and in the control of gene expression at the level of mRNA translation, both using the yeast Saccharomyces as a model system<br />
|-<br />
| [http://www.brookes.ac.uk/res/experts/profiles/david_fell David Fell] || Oxford Brookes University || General principles governing the organization, regulation and control of metabolism<br />
|-<br />
| [http://www.plantsci.cam.ac.uk/research/alexwebb.html Alex Webb] || University of Cambridge || The physiological benefits of the circadian clock and the signalling mechanisms by which the circadian clock regulates cell physiology<br />
|-<br />
| [http://swainlab.bio.ed.ac.uk/details.php Peter Swain] || University of Edinburgh || Systems biology<br />
|-<br />
| [http://www.eng.ox.ac.uk/~cheit/ Ian Thompson] || University of Oxford || <br />
|-<br />
| [http://dps.plants.ox.ac.uk/plants/Staff/LeeSweetlove.aspx Lee Sweetlove] ||University of Oxford ||Regulation and engineering of the plant metabolic network<br />
|-<br />
| [http://www.lincoln.ox.ac.uk/content/view/832/40/ Mark Roberts] || University of Oxford/BBSRC || Biological signalling circuits, bacterial transcription<br />
|-<br />
| [http://www.pmb.ox.ac.uk/Fellows_Staff/Fellow_and_Staff_Profiles.php?profile=146 Steve Porter]|| University of Exeter|| Chemosensory signal transduction pathway in the photosynthetic bacterium, Rhodobacter sphaeroides <br />
|-<br />
| [http://my2.tmu.edu.tw/markchang Yo-Cheng (Mark) Chang] ||Taipei Medical University, Taiwan || Systems and synthetic biology<br />
|-<br />
| [http://waterfall.union.edu/Staff_Directory/Union/Electrical__Computer_Engineering/Hooshangi_Sara_.php Sara Hooshangi]|| Union College, NY ||<br />
|-<br />
| [http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=593 Bela Novak] || University of Oxford ||<br />
|-<br />
| [http://www.sysbio.ox.ac.uk/People/GW.html George Wadhams] || University of Oxford || Quantitative analysis of bacterial signalling pathways. Rewiring two component signal transduction pathways. Manipulation of protein-protein interactions within signalling pathways. The effect of host cell choice on the input-output characteristics of biological pathways<br />
|-<br />
|[http://sbcb.bioch.ox.ac.uk/sansom.php Mark Sansom]|| University of Oxford ||<br />
|-<br />
|[http://www.sheffield.ac.uk/civil/staff/academic/wh.html Wei Huang] || University of Sheffield || Single cell Raman tweezers technology (e.g. study genetic functions of non-culturable microorganisms in ecosystem). Microbial evolution (e.g. the role of gene transformation in evolution). Synthetic biology (e.g. gene trapping & screening, biosensors and bioenergy) <br />
|-<br />
|[http://www2.le.ac.uk/departments/engineering/ William Bryant] ||University of Leicester || <br />
|-<br />
|[http://www.shef.ac.uk/materials/staff/claeyssens.html Frederik Claeyssens]|| University of Sheffield ||<br />
|-<br />
|[http://www.cs.ncl.ac.uk/people/j.s.hallinan Jennifer Hallinan] ||Newcastle University||Complex Systems and analysis of biological networks<br />
|-<br />
| [http://www3.imperial.ac.uk/people/k.polizzi Karen Polizzi] || Imperial College London || Biopharmaceutical processing, neurodegeneration and ageing, tools for synthetic biology<br />
|-<br />
|[http://www2.warwick.ac.uk/fac/sci/whri/about/staff/kdenby/ Katherine Denby] || University of Warwick||<br />
|-<br />
|[http://www.ceas.manchester.ac.uk/aboutus/staff/show.html?ea=hans.westerhoff Hans Westerhoff] || University of Manchester ||Integrative systems biology<br />
|-<br />
| [http://www.eda.kent.ac.uk/school/staff_detail.aspx?id=330 Najl Valeyev] || University of Kent ||<br />
|-<br />
| [http://www.dpag.ox.ac.uk/research/cardiac_science/peter_robbins/robbins_members Nayia Petousi]|| University of Oxford ||<br />
|-<br />
| [http://www.mib.manchester.ac.uk/postgraduate/DTC/ Victoria Jackson] || University of Manchester || Integrative Systems Biology <br />
|}<br />
<br />
== Researchers from the Ethical, Legal and Social Sciences == <br />
<br />
{| border="1"<br />
! Member !! Affiliation !! Research Interests !!<br />
<br />
|-<br />
| [http://web.comlab.ox.ac.uk/Annamaria.Carusi/ Annamaria Carusi] || University of Oxford || Philosophical issues relating to synthetic biology; ethics, science and technology studies<br />
|-<br />
| [http://www.sbs.ox.ac.uk/insis/people/sugden+chris.htm Chris Sugden] || University of Oxford || Contemporary ideas of novelty and innovation<br />
|-<br />
| [http://www.ethox.org.uk/people/michael-parker Michael Parker] || University of Oxford ||<br />
|-<br />
| [http://people.bath.ac.uk/ak280/ Alexander Kelle] || University of Bath ||<br />
|-<br />
| [http://www.ifom-ieo-campus.it/research/boniolocv.php Giovanni Boniolo]|| European Institute of Oncology||<br />
|-<br />
| [http://www.practicalethics.ox.ac.uk/nstaff.htm Julian Savulescu] || University of Oxford ||<br />
|-<br />
| [http://www.philosophy.ox.ac.uk/members/marianne_talbot Marianne Talbot] || University of Oxford || <br />
|-<br />
| [http://www.bep.ox.ac.uk/our%20people.html Mark Sheehan] || University of Oxford || Research ethics, ethics of emerging technologies, ethics of resource allocation, the ethics and justification of public engagement, ethics and social science methodology<br />
|-<br />
| [http://www.neuroethics.ox.ac.uk/node/19 Steve Clarke] || University of Oxford ||<br />
|-<br />
| [http://www.ethox.org.uk/people/jane-kaye Jane Kaye] ||University of Oxford ||The role of law in the global regulation of innovative technologies in medicine, with particular focus on biobanks and standardisation<br />
|-<br />
| [http://www.practicalethics.ox.ac.uk/nstaff.htm#staff Thomas Douglas] || University of Oxford || The ethics of enhancing or modifying moral capacities, the nature of moral improvement, and the ethics of producing and disseminating dangerous knowledge<br />
|-<br />
| [http://helex.medsci.ox.ac.uk/staff/researchers/liam-curren Liam Curren] || ||<br />
|-<br />
| [http://www.sussex.ac.uk/Units/spru/hsp/People/James%20Revill.html James Revill] || University of Sussex ||<br />
|}</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=1040Yo-Cheng (Mark) Chang2013-01-26T01:08:33Z<p>MarkChang: Replacing page with '[http://my2.tmu.edu.tw/markchang]http://my2.tmu.edu.tw/markchang<br>'</p>
<hr />
<div>[http://my2.tmu.edu.tw/markchang]http://my2.tmu.edu.tw/markchang<br></div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Second_RoSBNet_Workshop&diff=659Second RoSBNet Workshop2010-03-11T21:31:36Z<p>MarkChang: </p>
<hr />
<div>{{RoSBNet template}}<br />
<br />
<center><br />
<br />
</center><br />
<br />
=== Second RoSBNet Synthetic Biology Workshop 12th-14th July 2010 ===<br />
<br />
The second RoSBNet Synthetic Biology workshop will be held on the 12th, 13th and 14th of July 2010 at [http://www.st-annes.ox.ac.uk St Annes' College], University of Oxford. <br />
<br />
[[Image:Small oxford.jpg|thumb|350px|right]]<br />
<br />
== Topics ==<br />
<br />
*''<B>Biology Theme:</B>'' Constructing and modifying signal transduction, protein-protein and metabolic networks.<br />
<br />
*''<B>Electrical/Computer Engineering Theme:</B>'' Interconnecting parts to create circuits that perform efficiently and reliably.<br />
<br />
*''<B>Control/Systems Engineering Theme:</B>'' Interconnection of subsystems to design robust super-systems; modularity in design.<br />
<br />
Ethical, economical, philosophical, legal and societal issues as well as measurement methods will form ''<B>underlying themes</B>''.<br />
<br />
== Confirmed Speakers ==<br />
<br />
*Professor Murat Arcak (University of California Berkeley, USA)<br />
*Professor Giovanni Boniolo (IFOM—IEO, Italy)<br />
*Dr Stuart Dunbar (Syngenta, UK)<br />
*Professor Michael Hecht (University of Princeton, USA)<br />
*Professor Andrew Hopkins (University of Dundee, UK)<br />
*Professor Béla Novák (University of Oxford, UK)<br />
*Professor Michael Savageau (University of California Davis, USA)<br />
*Professor Christina Smolke (Stanford University, USA)<br />
*Dr Susan Soulsby (EPSRC, UK)<br />
*Dr Dirk Stemerding (Rathenau Institute, The Netherlands)<br />
*Professor Peter Swain (University of Edinburgh, UK)<br />
*Professor Ian Thompson (University of Oxford, UK)<br />
*Professor Hans Westerhoff (University of Manchester, UK)<br />
<br />
== Location of the Workshop ==<br />
<br />
St Anne’s is located within easy walking distance from the centre of Oxford and is situated within 5 acres of tranquil leafy grounds. The workshop will take place in the new conference facilities of the Ruth Deach Building and Tsuzuki Lecture Theatre. The conference brochure, which includes a map on page 6, is available [http://www.st-annes.ox.ac.uk/fileadmin/STA/Documents/Conference_brochure.pdf here].<br />
<br />
== Travel Information ==<br />
<br />
Directions to Oxford can be found [http://www.oxford.gov.uk/PageRender/decTS/How_to_get_to_Oxford_occw.htm here]. It is within easy reach of [http://www.bhx.co.uk Birmingham Airport], [http://www.heathrowairport.com Heathrow Airport], [http://www.gatwickairport.com Gatwick Airport] and [http://www.southamptonairport.com Southampton International Airport]. Information on the best way to travel to Oxford can be found [http://www.eng.ox.ac.uk/contact/travel.html here]. A map of St Anne’s College can be viewed [http://www.st-annes.ox.ac.uk/about/how-to-find-us.html here]. Car Parking within Oxford is extremely limited and expensive. If you are coming by car it is recommended that you use the Pear Tree or Water Eaton [http://www.oxford.gov.uk/PageRender/decTS/Park_and_Ride_occw.htm Park and Ride facilities].<br />
<br />
== Flyer and Registration Form ==<br />
<br />
[[Media:RoSBNet2010_Flyer.pdf|RoSBNet 2010 workshop flyer]] <br><br />
[[Media:RoSBNet2010_Registration_Form.pdf|RoSBNet 2010 workshop Registration Form in PDF format]] <br><br />
[[Media:RoSBNet2009_Registration_Form.doc|RoSBNet 2010 workshop Registration Form in MS Word format]] <br></div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=649Welcome to RoSBNet wiki2010-03-03T23:58:51Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php/Second_RoSBNet_Workshop <span style="color:#FF00FF; font-size: 150%;"> ''Our Second Workshop will be held on the 12th-14th July 2010'' </span>]<br><br />
<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
London - [http://www.selectbiosciences.com/conferences/ASB2010/ The 3rd annual Advances in Synthetic Biology]<br />
<br />
- 04 - 05 March, 2010<br><br />
- London, UK<br />
<br />
<br />
Institut Pasteur - [http://elsevier.dmsx.net/c/r?EMID=09601CR1O34NFKSNO014MF4019506VG Systems Biology of Microorganisms]<br />
<br />
- 22 - 24 March, 2010<br><br />
- Paris, France<br />
<br />
<br />
Dublin - [http://www.selectbiosciences.com/conferences/SCAC2010/ Single Cell Analysis Congress]<br />
<br />
- 25 - 26 May, 2010<br><br />
- Dublin, Ireland<br />
<br />
<br />
Boston - [http://www.selectbiosciences.com/conferences/RNAiWC2010/ RNAi & miRNA World Congress]<br />
<br />
- 05 - 07 May, 2010<br><br />
- Boston, USA<br />
<br />
<br />
UCL - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- London, UK<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
Edinburgh - [http://www.selectbiosciences.com/conferences/CTS2010/ Cellular Therapy Summit]<br />
<br />
- 24 - 25 August, 2010<br><br />
- Edinburgh, Scotland<br />
<br />
<br />
ICSB - [http://www.icsb2010.org.uk/welcome/ 11th International Conference on Systems Biology]<br />
<br />
- 10 - 15 October, 2010<br><br />
- Edinburgh, Scotland, UK<br />
<br />
<br />
Italy - [http://www.selectbiosciences.com/conferences/AMP2010/ Advances in Metabolic Profiling]<br />
<br />
- 9 - 10 November, 2010<br><br />
- Florence, Italy<br />
<br />
<br />
China - [http://www.selectbiosciences.com/conferences/IFSC2010/ International Forum on Stem Cells]<br />
<br />
- 12 - 13 November, 2010<br><br />
- Tianjin, China<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 12th-14th July 2010 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=648Welcome to RoSBNet wiki2010-03-03T23:57:56Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php/Second_RoSBNet_Workshop <span style="color:#FF00FF; font-size: 150%;"> ''Our Second Workshop will be held on the 12th-14th July 2010'' </span>]<br><br />
<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
London - [http://www.selectbiosciences.com/conferences/ASB2010/ The 3rd annual Advances in Synthetic Biology]<br />
<br />
- 04 - 05 March, 2010<br><br />
- London, UK<br />
<br />
<br />
Institut Pasteur - [http://elsevier.dmsx.net/c/r?EMID=09601CR1O34NFKSNO014MF4019506VG Systems Biology of Microorganisms]<br />
<br />
- 22 - 24 March, 2010<br><br />
- Paris, France<br />
<br />
<br />
Dublin - [http://www.selectbiosciences.com/conferences/SCAC2010/ Single Cell Analysis Congress]<br />
<br />
- 25 - 26 May, 2010<br />
- Dublin, Ireland<br />
<br />
<br />
Boston - [http://www.selectbiosciences.com/conferences/RNAiWC2010/ RNAi & miRNA World Congress]<br />
<br />
- 05 - 07 May, 2010,<br />
- Boston, USA<br />
<br />
<br />
UCL - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- London, UK<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
Edinburgh - [http://www.selectbiosciences.com/conferences/CTS2010/ Cellular Therapy Summit]<br />
<br />
- 24 - 25 August, 2010,<br />
- Edinburgh, Scotland<br />
<br />
<br />
ICSB - [http://www.icsb2010.org.uk/welcome/ 11th International Conference on Systems Biology]<br />
<br />
- 10 - 15 October, 2010<br><br />
- Edinburgh, Scotland, UK<br />
<br />
<br />
Italy - [http://www.selectbiosciences.com/conferences/AMP2010/ Advances in Metabolic Profiling]<br />
<br />
- 9 - 10 November, 2010<br />
- Florence, Italy<br />
<br />
<br />
China - [http://www.selectbiosciences.com/conferences/IFSC2010/ International Forum on Stem Cells]<br />
<br />
- 12 - 13 November, 2010<br />
- Tianjin, China<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 12th-14th July 2010 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=645Welcome to RoSBNet wiki2010-02-19T15:56:03Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php/Second_RoSBNet_Workshop <span style="color:#FF00FF; font-size: 150%;"> ''Our Second Workshop will be held on the 12th-14th July 2010'' </span>]<br><br />
<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
London - [http://www.selectbiosciences.com/conferences/ASB2010/ The 3rd annual Advances in Synthetic Biology]<br />
<br />
- 04 - 05 March, 2010<br><br />
- London, UK<br />
<br />
<br />
Institut Pasteur - [http://elsevier.dmsx.net/c/r?EMID=09601CR1O34NFKSNO014MF4019506VG Systems Biology of Microorganisms]<br />
<br />
- 22 - 24 March, 2010<br><br />
- Paris, France<br />
<br />
<br />
UCL - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- London, UK<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
ICSB - [http://www.icsb2010.org.uk/welcome/ 11th International Conference on Systems Biology]<br />
<br />
- 10 - 15 October, 2010<br><br />
- Edinburgh, Scotland, UK<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 12th-14th July 2010 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=644Welcome to RoSBNet wiki2010-01-28T10:56:14Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php/Second_RoSBNet_Workshop <span style="color:#FF00FF; font-size: 150%;"> ''Our Second Workshop will be held on the 12th-14th July 2010'' </span>]<br><br />
<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
London - [http://www.selectbiosciences.com/conferences/ASB2010/ The 3rd annual Advances in Synthetic Biology]<br />
<br />
- 04 - 05 March, 2010<br><br />
- London, UK<br />
<br />
<br />
UCL - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- London, UK<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
ICSB - [http://www.icsb2010.org.uk/welcome/ 11th International Conference on Systems Biology]<br />
<br />
- 10 - 15 October, 2010<br><br />
- Edinburgh, Scotland, UK<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 12th-14th July 2010 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=625Welcome to RoSBNet wiki2010-01-10T20:06:12Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
RoSBNet - [http://www.eng.ox.ac.uk/control/RoSBNet RoSBNet Synthetic Biology Network Meeting]<br />
<br />
- 14 January, 2010<br><br />
- Oxford, UK<br />
<br />
<br />
London - [http://www.selectbiosciences.com/conferences/ASB2010/ The 3rd annual Advances in Synthetic Biology]<br />
<br />
- 04 - 05 March, 2010<br><br />
- London, UK<br />
<br />
<br />
UCL - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- London, UK<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
ICSB - [http://www.icsb2010.org.uk/welcome/ 11th International Conference on Systems Biology]<br />
<br />
- 10 - 15 October, 2010<br><br />
- Edinburgh, Scotland, UK<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 14th-16th September 2009 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=572Yo-Cheng (Mark) Chang2009-09-06T05:19:36Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|150px]]<br />
<B><I>D.Phil. student<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I></B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Control Group, Department of Engineering Science, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Genome Analysis and Bioinformatics Group, Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: D.Phil. student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=571Yo-Cheng (Mark) Chang2009-09-06T05:18:26Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|150px]]<br />
<B><I>D.Phil. student<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I></B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Control Group, Department of Engineering Science, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Genome Analysis and Bioinformatics Group, Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: D.Phil student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=570Yo-Cheng (Mark) Chang2009-09-06T05:17:55Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|150px]]<br />
<B><I>D.Phil. student<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I></B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Control Group, Department of Engineering Science, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Genome Analysis and Bioinformatics Group, Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=569Yo-Cheng (Mark) Chang2009-09-06T05:14:50Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|150px]]<br />
<B><I>D.Phil. candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I></B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Oxford Centre for Integrative Systems Biology, Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Control Group, Department of Engineering Science, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Genome Analysis and Bioinformatics Group, Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=568Welcome to RoSBNet wiki2009-09-06T05:11:17Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br><br />
<br><br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php/Current_events <span style="color:#0000FF; font-size: 200%;"> '' Register Now for the Synthetic Biology Workshop'' </span>]<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
RoSBNet - [http://www.rosbnet.org/ Network in Synthetic Biology]<br />
<br />
- 14 - 16 September, 2009<br><br />
- Oxford, England<br />
<br />
<br />
Keck Foundation - [http://www.keckfutures.org/site/PageServer?pagename=Upcoming_Conferences_Synthetic_Biology_2009 Synthetic Biology: Building on Nature's Inspiration]<br />
<br />
- 18 - 21 November, 2009<br><br />
- Irvine, CA<br />
<br />
<br />
UCL - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- London, England<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 14th-16th September 2009 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=RoSBNet:Community_Portal&diff=567RoSBNet:Community Portal2009-09-06T05:07:25Z<p>MarkChang: </p>
<hr />
<div>== Network Resources ==<br />
[[Image:RoSBlogos.jpg|thumb|right|300px]]<br />
<br />
[[Media:RoSBNet flyer.pdf|RoSBNet Flier for distribution.pdf]]<br />
<br />
[[Media:RoSBNet flyer AP4 -Compatibility Mode-.pdf|RoSBNet Flier A5]]<br />
<br />
[[Media:RoSBNet poster draft2.pdf|RoSBNet Poster for Community Awareness.pdf]]<br />
<br />
<br />
== Synthetic biology resources ==<br />
<br />
[[Media:Synthetic biology flyer.pdf|BBSRC Synthetic Biology Brochure.pdf]]<br />
<br />
[http://kn.theiet.org/communities/biology/ IET Systems and Synthetic Biology Network]<br />
<br />
[http://www.genomicsnetwork.ac.uk/egenis/research/sciencetechnologyandinnovation/projecttitle,2370,en.html New directions in genomics: Philosophical considerations in synthetic biology]<br />
<br />
[http://www.synbiosafe.eu/ SYNBIOSAFE: Safety and Ethical Aspects of Synthetic Biology]<br />
<br />
[http://www.synbiosafe.eu/index.php?page=other-sb-projects Other European Synthetic Biology Projects]<br />
<br />
[http://partsregistry.org/Main_Page MIT: Registry of Standard Biological Parts]<br />
<br />
[http://igem.org/ The International Genetically Engineered Machine Competition (iGEM)]<br />
<br />
[http://biobricks.org/ The BioBricks Foundation]<br />
<br />
[http://openwetware.org/wiki/Main_Page OpenWetWare]<br />
<br />
<br />
== Links to other Synthetic Biology Networks ==<br />
[http://www.synbio.org.uk/ Synthetic Biology in Cambridge]<br />
<br />
[http://www.smb.ucl.ac.uk/synbion/ Synbion: The UCL Network in Synthetic Biology]<br />
<br />
[http://www.bris.ac.uk/scn/ University of Bristol - 'Synthetic components network: towards synthetic biology from the bottom up']<br />
<br />
[http://www.synbiont.org/ University of Nottingham - 'SynBioNT: a synthetic biology network for modelling and programming cell-chell interactions']<br />
<br />
[http://www.sppi-net.org/links.php University of Durham - 'SPPI-NET: a network for synthetic plant products for industry']<br />
<br />
[http://oasis.bbsrc.ac.uk/netans-bin/gate.exe?f=doc&state=3c11m5.1.4 University of Sheffield - 'MATEs - Microbial Applications to Tissue Engineering: An Exemplar of Synthetic Biology']<br />
<br />
[http://oasis.bbsrc.ac.uk/netans-bin/gate.exe?f=doc&state=3c11m5.1.7 University of Edinburgh - 'Standards for the Design and Engineering of Modular Biological Devices']</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=544Welcome to RoSBNet wiki2009-08-05T10:16:45Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
ISMB/ECCB - [http://www.iscb.org/ismbeccb2009/ 17th Annual Conference on Intelligent Systems for Molecular Biology and 8th Annual European conference on Computational Biology]<br />
<br />
- 27 June - 2 July, 2009<br><br />
- Stockholm, Sweden<br />
<br />
<br />
UBC - [http://www.math.ubc.ca/Research/MathBio/SMB2009/ International Conference on Mathematical Biology and Annual Meeting of The Society for Mathematical Biology]<br />
<br />
- 27 - 30 July, 2009<br><br />
- Vancouver, Canada<br />
<br />
<br />
FOSBE - [http://www.fosbe.org/ Foundations of Systems Biology in Engineering]<br />
<br />
- 9 - 12 August, 2009<br><br />
- Denver, Colorado<br />
<br />
<br />
ICSB - [http://www.icsb-2009.org/ 10th International Conference on Systems Biology]<br />
<br />
- 30 August - 4 September, 2009<br><br />
- Stanford, California<br />
<br />
<br />
RoSBNet - [http://www.rosbnet.org/ Network in Synthetic Biology]<br />
<br />
- 14 - 16 September, 2009<br><br />
- Oxford, England<br />
<br />
<br />
Keck Foundation - [http://www.keckfutures.org/site/PageServer?pagename=Upcoming_Conferences_Synthetic_Biology_2009 Synthetic Biology: Building on Nature's Inspiration]<br />
<br />
- 18 - 21 November, 2009<br><br />
- Irvine, CA<br />
<br />
<br />
UCL - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- London, England<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 14th-16th September 2009 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=543Welcome to RoSBNet wiki2009-08-05T10:15:37Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
ISMB/ECCB - [http://www.iscb.org/ismbeccb2009/ 17th Annual Conference on Intelligent Systems for Molecular Biology and 8th Annual European conference on Computational Biology]<br />
<br />
- 27 June - 2 July, 2009<br><br />
- Stockholm, Sweden<br />
<br />
<br />
UBC - [http://www.math.ubc.ca/Research/MathBio/SMB2009/ International Conference on Mathematical Biology and Annual Meeting of The Society for Mathematical Biology]<br />
<br />
- 27 - 30 July, 2009<br><br />
- Vancouver, Canada<br />
<br />
<br />
FOSBE - [http://www.fosbe.org/ Foundations of Systems Biology in Engineering]<br />
<br />
- 9 - 12 August, 2009<br><br />
- Denver, Colorado<br />
<br />
<br />
ICSB - [http://www.icsb-2009.org/ 10th International Conference on Systems Biology]<br />
<br />
- 30 August - 4 September, 2009<br><br />
- Stanford, California<br />
<br />
<br />
RoSBNet - [http://www.rosbnet.org/ Network in Synthetic Biology]<br />
<br />
- 14 - 16 September, 2009<br><br />
- Oxford, England<br />
<br />
<br />
Keck Foundation - [http://www.keckfutures.org/site/PageServer?pagename=Upcoming_Conferences_Synthetic_Biology_2009 Synthetic Biology: Building on Nature's Inspiration]<br />
<br />
- 18 - 21 November, 2009<br><br />
- Irvine, CA<br />
<br />
<br />
The Physical Cell - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- UCL, London<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 14th-16th September 2009 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Welcome_to_RoSBNet_wiki&diff=542Welcome to RoSBNet wiki2009-08-05T10:15:11Z<p>MarkChang: </p>
<hr />
<div><center><br />
<br />
[http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php?title=Special:Userlogin&type=signup <span style="color:#FF0000; font-size: 200%;"> ''Please sign up to create a login in order to add information to the Wiki'' </span>]<br><br />
<br />
</center><br />
<br />
<br />
<br />
[[Image:RoSBlogos.jpg|thumb|left|300px]]<br />
== Upcoming Events ==<br />
{{scrollable<br />
|height=140<br />
|content=<br />
<br />
ISMB/ECCB - [http://www.iscb.org/ismbeccb2009/ 17th Annual Conference on Intelligent Systems for Molecular Biology and 8th Annual European conference on Computational Biology]<br />
<br />
- 27 June - 2 July, 2009<br><br />
- Stockholm, Sweden<br />
<br />
<br />
UBC - [http://www.math.ubc.ca/Research/MathBio/SMB2009/ International Conference on Mathematical Biology and Annual Meeting of The Society for Mathematical Biology]<br />
<br />
- 27 - 30 July, 2009<br><br />
- Vancouver, Canada<br />
<br />
<br />
FOSBE - [http://www.fosbe.org/ Foundations of Systems Biology in Engineering]<br />
<br />
- 9 - 12 August, 2009<br><br />
- Denver, Colorado<br />
<br />
<br />
ICSB - [http://www.icsb-2009.org/ 10th International Conference on Systems Biology]<br />
<br />
- 30 August - 4 September, 2009<br><br />
- Stanford, California<br />
<br />
<br />
RoSBNet - [http://www.rosbnet.org/ Network in Synthetic Biology]<br />
<br />
- 14 - 16 September, 2009<br><br />
- Oxford, England<br />
<br />
<br />
Keck Foundation - [http://www.keckfutures.org/site/PageServer?pagename=Upcoming_Conferences_Synthetic_Biology_2009 Synthetic Biology: Building on Nature's Inspiration]<br />
<br />
- 18 - 21 November, 2009<br><br />
- Irvine, CA<br />
<br />
<br />
The Physical Cell - [http://www.ucl.ac.uk/PhysCell2010/ The Physical Cell - In search of the design principles of life]<br />
<br />
- 28 - 30 June, 2010<br><br />
- UCL, London<br />
<br />
<br />
ISMB/ECCB - [http://www.iscb.org/about-ismb 18th Annual International Conference on Intelligent Systems for Molecular Biology and 9th Annual European conference on Computational Biology] <br />
<br />
- 10 - 14 July, 2010<br><br />
- Boston, Massachusetts<br />
<br />
Bio-bricks foundation - Synthetic Biology 5.0<br />
<br />
- Date not confirmed<br><br />
- location not confirmed<br />
<br />
<br />
}}<br />
<br />
== Introduction to RoSBNet ==<br />
RoSBNet brings together people working in [[:Category:Synthetic Biology|'''Synthetic''']] and Systems Biology as well as Systems/Control Engineers, electrical, chemical, computer engineers, Physicists and Mathematicians to address the theoretical and practical challenges of designing new robust biological networks or modifying already existing ones, which have to function inside uncertain biological environments, all the way from parts to whole systems. The network will focus on the Ethical, Legal and Societal Issues that are raised by advances in Synthetic Biology, aiming to create a fruitful discussion on how such concerns can be balanced by the potential usefulness of the many applications, such as environmental cleanup, fuel generation and healthcare. The objective is to transfer knowledge and develop a fruitful discussion and cross-fertilization of ideas on ''modelling, analysis, design and construction of synthetic biological networks'' creating a mobility and communication between control/electrical/computer engineering, biology, mathematics and the social sciences as well as with Industry. The goal is to create a cohesive community that can respond effectively to research challenges, funding opportunities and international activities. <br/><br />
<br />
Synthetic Biology is a new research field which aims in designing new or modifying existing biological pathways in order to produce systems with superior or different properties, usually for a novel application. In the related field of systems biology, it is recognized that it is impossible to infer the biological network behaviour by just listing its components but rather the whole feedback mechanism linking them needs to be considered; the same is true in every Synthetic Biology design. However, these designs need to be implemented inside a cellular environment and a major challenge that synthetic biology has to face is that the effect of the interactions of the new pathways with the cellular environment need to be taken into account during the design or redesign process. This is unlike any other engineering design procedure, such as electrical circuit or computer engineering design, where the behaviour of simple parts (e.g., resistors), of more complicated components (e.g., transistors) or even of whole systems (e.g., complete circuits) can be predicted (and eventually measured and verified) efficiently after implementation. This unique feature to Synthetic Biology design poses new challenges to engineering and mathematics. At the same time, many engineering disciplines, such as control and computer engineering, have for years been dealing with the analysis and design of complex systems that have to operate robustly in uncertain environments and therefore have a lot to contribute towards constructing biological modules, whether these are parts, pathways, artificial cells or cultures/tissues with performance guarantees within an uncertain environment. <br/><br />
<br />
== Organisation of the Network ==<br />
It is important to emphasise that the objectives of this network are difficult to achieve by individuals alone – instead, an integrated collaboration between members of the whole network would be required. RoSBNet creates these necessary collaborative links. The activities aim to benefit not only the network as a whole, but also the individuals who will widen their research outreach through the network interactions. <br/><br />
<br />
The figure below shows the topics that will be investigated in the following three years. The challenge is to exchange views and expertise on how to construct robust biological networks at different organisational scales. From the '''Biology''' side, in the first year we will look at the gene regulatory network level, in the second year at signal transduction/metabolic/protein-protein interaction pathways and in the third year at how whole cells can be constructed. At the same time, every year we will be looking at paradigms from '''Electrical and Computer engineering''' that are directly related to the biological scale – resistors/capacitors/inductors and small circuits (op-amps, transistors etc) in the first year, larger circuits in the second year and computer networks and protocols/modularity/architecture in the third year. In parallel to these there will be a '''control/mathematical''' direction which will discuss modelling for design at these different organizational levels. Two common themes for all three years will be measurement – i.e., how one can build devices that evaluate the performance of designs – and '''ELSI''', i.e., what are the ethical, legal, social, philosophical, economical and other issues that are raised by Synthetic Biology research.<br/><br />
<br />
[[Image:SB2_color_small.png||thumb|1000px|centre]]<br />
<br />
== RoSBNet will network in 3 ways: ==<br />
# Via a series of [[Current events| yearly, multi-day, workshops]] with the next hosted on 14th-16th September 2009 in Oxford.<br />
# Via this online [[Main Page|Wiki]]<br />
# Via an email-based [mailto:rosbnet-subscribe@maillist.ox.ac.uk newsletter mailing list]. To self-subscribe please send a blank mail to: [mailto:rosbnet-subscribe@maillist.ox.ac.uk rosbnet-subscribe@maillist.ox.ac.uk]<br />
<br />
__NOTOC__</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Member_List&diff=529Member List2009-07-22T18:49:09Z<p>MarkChang: </p>
<hr />
<div>== Engineering/Mathematics Researchers == <br />
* [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]<br><br />
* [http://www.ist.uni-stuttgart.de/allgower/allgower.shtml Frank Allgower]<br><br />
* [http://www3.imperial.ac.uk/people/m.barahona Mauricio Barahona]<br><br />
* [http://www.eee.strath.ac.uk/~hongyue/ Hong Yue]<br><br />
* [http://biology.st-andrews.ac.uk/vannesmithlab/ Anne Smith]<br><br />
* [http://www.rdg.ac.uk/icmr/about/staff/icmr-m-tindall.asp Marcus Tindall]<br><br />
* [http://www.montefiore.ulg.ac.be/~bullinger/ Eric Bullinger] <br> <br />
* [http://www.gla.ac.uk/departments/aerospace/staff/academicstaff/jongraekim Jongrae Kim]<br> <br />
* [http://www.ml.inf.ethz.ch/people/postgrads/auguste Elias August] <br><br />
* [http://www.sbs.ox.ac.uk/faculty/Reed-Tsochas+Felix/ Felix Reed-Tsochas] <br><br />
* [http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Jotun Hein] <br><br />
* [http://www.eng.ox.ac.uk/control/peopleJA.shtml James Anderson] <br><br />
* [http://www.eng.ox.ac.uk/samp/people.html Patrick McSharry] <br><br />
* [http://www.comlab.ox.ac.uk/people/Jonathan.Whiteley/ Jonathan Whiteley] <br> <br />
* [http://www.physics.ox.ac.uk/users/kapanidis/ Achillefs Kapanidis] <br> <br />
* [http://www.staff.ncl.ac.uk/d.j.wilkinson/ Darren Wilkinson] <br> <br />
* [http://www.comlab.ox.ac.uk/people/David.Gavaghan/ David Gavaghan] <br> <br />
* [http://www.le.ac.uk/eg/dgb3/ Declan Bates] <br><br />
* [http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves] <br><br />
* [http://www.eecs.umich.edu/~ddv/ Domitilla del Vecchio] <br><br />
* [http://biochemistry.ucsf.edu/labs/elsamad/people/Hana_El_Samad/hana_el_samad.html Hana El-Samad] <br><br />
* [http://www.bionanotechnology.ox.ac.uk/index.php?option=com_content&task=view&id=24&Itemid=50 John Ryan] <br><br />
* [http://www.me.ucsb.edu/dept_site/people/khammash_page.htm Mustafa Khammash ]<br><br />
* [http://people.maths.ox.ac.uk/~maini/ Philip Maini] <br><br />
* [http://www.physics.ox.ac.uk/cm/cmt/jones/ Nick Jones] <br><br />
* [http://www.eng.ox.ac.uk/control/peopleSD.shtml Steve Duncan] <br><br />
* [http://www-control.eng.cam.ac.uk/Homepage/officialweb.php?id=232 Guy-Bart Stan] <br><br />
* [http://melykuti.web.elte.hu/index.htm Bence Melykuti] <br><br />
<br />
== Biology/Biochemistry Researchers == <br />
* [http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=565 Judy Armitage] <br> <br />
* [http://www.abdn.ac.uk/ims/staff/details.php?id=i.stansfield Ian Stansfield]<br><br />
* [http://www.brookes.ac.uk/res/experts/profiles/david_fell David Fell]<br><br />
* [http://www.plantsci.cam.ac.uk/research/alexwebb.html Alex Webb] <br><br />
* [http://swainlab.bio.ed.ac.uk/details.php Peter Swain] <br><br />
* [http://dps.plants.ox.ac.uk/plants/Staff/LeeSweetlove.aspx Lee Sweetlove] <br><br />
* [http://www.lincoln.ox.ac.uk/content/view/832/40/ Mark Roberts] <br><br />
* [http://www.pmb.ox.ac.uk/Fellows_Staff/Fellow_and_Staff_Profiles.php?profile=146 Steve Porter] <br><br />
* [http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php/User:MarkChang Yo-Cheng (Mark) Chang] <br><br />
* Sara Hooshangi <br><br />
* [http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=593 Bela Novak] <br><br />
* [http://www.sysbio.ox.ac.uk/People/GW.html George Wadhams] <br><br />
* [http://sbcb.bioch.ox.ac.uk/sansom.php Mark Sansom] <br><br />
<br />
== Researchers from the Ethical, Legal and Social Sciences == <br />
* [http://web.comlab.ox.ac.uk/Annamaria.Carusi/ Annamaria Carusi]<br><br />
* [http://www.sbs.ox.ac.uk/insis/people/sugden+chris.htm Chris Sugden]<br><br />
* [http://www.ethox.org.uk/people/michael-parker Michael Parker]<br><br />
* [http://people.bath.ac.uk/ak280/ Alexander Kelle] <br><br />
* [http://www.ifom-ieo-campus.it/research/boniolocv.php Giovanni Boniolo] <br><br />
* [http://www.practicalethics.ox.ac.uk/nstaff.htm Julian Savulescu] <br><br />
* [http://www.philosophy.ox.ac.uk/members/marianne_talbot Marianne Talbot] <br><br />
* [http://www.bep.ox.ac.uk/our%20people.html Mark Sheehan] <br><br />
* Steve Clarke <br><br />
* [http://www.ethox.org.uk/people/jane-kaye Jane Kaye] <br></div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=References&diff=507References2009-06-15T11:06:49Z<p>MarkChang: </p>
<hr />
<div><center><br />
<span style="color:#0000FF; font-size: 200%;"><u>Please share references by adding links into this page</u></span><br />
</center><br />
<br />
<br />
[[Image:route.png|thumb|ACS Chem. Biol., 2008, 3 (1), pp 38–50|right|300px]]<br />
== General Principles of Synthetic Biology ==<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04335.html Reconstruction of genetic circuits]<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/16711359 Engineering life: building a fab for biology]<br />
<br />
[http://www.bioinfo.de/isb/2006/06/0038/ Engineering life through Synthetic Biology]<br />
<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=32f32f9adee8425380015b935a6eadf8 Systems biology as a foundation for genome-scale synthetic biology]<br />
<br />
== Parts Standardization/Construction ==<br />
[http://openwetware.org/images/9/99/Nbt1413.pdf Refinement and standardization of synthetic biological parts and devices]<br />
<br />
[http://www.jbioleng.org/content/2/1/5 Engineering BioBrick vectors from BioBrick parts]<br />
<br />
== Mathematical/Computational Methods ==<br />
[http://www.weizmann.ac.il/mcb/UriAlon/Papers/Shinar_Alon_Feinberg_SIAM_2009.pdf Sensitivity and robustness in chemical reaction networks]<br />
<br />
== New Designs/Design Principles ==<br />
[http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]<br />
<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200843.html The incoherent feed-forward loop can generate non-monotonic input functions for genes]<br />
<br />
== In-vivo/vitro Chassis ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4GS4TTH-C&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=05e4ed6bd00339746d790a93c7a96ef2 Protein synthesis by pure translation systems]<br />
<br />
[http://www.pnas.org/content/100/22/12672 Principles of cell-free genetic circuit assembly]<br />
<br />
== Applications ==<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic Escherichia coli predator–prey ecosystem]<br />
<br />
[http://www.nature.com/nature/journal/v434/n7037/full/nature03461.html A synthetic multicellular system for programmed pattern formation]<br />
<br />
== Software Packages/Tools ==<br />
[http://www.mathworks.co.uk/access/helpdesk/help/toolbox/simbio/index.html?/access/helpdesk/help/toolbox/simbio/ MATLAB SimBiology]<br />
<br />
== Measurement Methods ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4P3DWNX-S&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=179a5617e3cd099a11a4ec40f9b85780 Single-cell analysis of gene expression by fluorescence microscopy]<br />
<br />
== Ethical, Legal, and Social Issues (ELSI) ==<br />
[http://www.synbiosafe.eu/uploads///pdf/Diffusion_of_synthetic_biology.pdf Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthic Biology]<br />
<br />
[http://www.sciencemag.org/cgi/content/summary/286/5447/2087 Ethical Considerations in Synthesizing a Minimal Genome]</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=503Yo-Cheng (Mark) Chang2009-06-05T12:33:06Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|150px]]<br />
<B><I>D.Phil. candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I></B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Science, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=502Yo-Cheng (Mark) Chang2009-06-05T07:40:02Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]]<br />
<B><I>D.Phil. candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I></B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Science, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=500Yo-Cheng (Mark) Chang2009-06-04T23:48:01Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]]<br />
<B><I>D.Phil. candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I></B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=References&diff=499References2009-06-04T23:43:04Z<p>MarkChang: </p>
<hr />
<div><center><br />
<span style="color:#0000FF; font-size: 200%;"><u>Please share references by adding links into this page</u></span><br />
</center><br />
<br />
<br />
[[Image:route.png|thumb|ACS Chem. Biol., 2008, 3 (1), pp 38–50|right|300px]]<br />
== General Principles of Synthetic Biology ==<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04335.html Reconstruction of genetic circuits]<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/16711359 Engineering life: building a fab for biology]<br />
<br />
[http://www.bioinfo.de/isb/2006/06/0038/ Engineering life through Synthetic Biology]<br />
<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=32f32f9adee8425380015b935a6eadf8 Systems biology as a foundation for genome-scale synthetic biology]<br />
<br />
== Parts Standardization/Construction ==<br />
[http://openwetware.org/images/9/99/Nbt1413.pdf Refinement and standardization of synthetic biological parts and devices]<br />
<br />
[http://www.jbioleng.org/content/2/1/5 Engineering BioBrick vectors from BioBrick parts]<br />
<br />
== Mathematical/Computational Methods ==<br />
[http://www.weizmann.ac.il/mcb/UriAlon/Papers/Shinar_Alon_Feinberg_SIAM_2009.pdf Sensitivity and robustness in chemical reaction networks]<br />
<br />
== New Designs/Design Principles ==<br />
[http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]<br />
<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200843.html The incoherent feed-forward loop can generate non-monotonic input functions for genes]<br />
<br />
== In-vivo/vitro Chassis ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4GS4TTH-C&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=05e4ed6bd00339746d790a93c7a96ef2 Protein synthesis by pure translation systems]<br />
<br />
[http://www.pnas.org/content/100/22/12672 Principles of cell-free genetic circuit assembly]<br />
<br />
== Applications ==<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic Escherichia coli predator–prey ecosystem]<br />
<br />
== Software Packages/Tools ==<br />
[http://www.mathworks.co.uk/access/helpdesk/help/toolbox/simbio/index.html?/access/helpdesk/help/toolbox/simbio/ MATLAB SimBiology]<br />
<br />
== Measurement Methods ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4P3DWNX-S&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=179a5617e3cd099a11a4ec40f9b85780 Single-cell analysis of gene expression by fluorescence microscopy]<br />
<br />
== Ethical, Legal, and Social Issues (ELSI) ==<br />
[http://www.synbiosafe.eu/uploads///pdf/Diffusion_of_synthetic_biology.pdf Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthic Biology]<br />
<br />
[http://www.sciencemag.org/cgi/content/summary/286/5447/2087 Ethical Considerations in Synthesizing a Minimal Genome]</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=498Yo-Cheng (Mark) Chang2009-06-04T23:27:09Z<p>MarkChang: </p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]]<br />
<B>D.Phil. candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=497User:MarkChang2009-06-04T23:25:36Z<p>MarkChang: Redirecting to Yo-Cheng (Mark) Chang</p>
<hr />
<div>#REDIRECT [[Yo-Cheng_(Mark)_Chang]]</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Yo-Cheng_(Mark)_Chang&diff=496Yo-Cheng (Mark) Chang2009-06-04T23:17:29Z<p>MarkChang: New page: [[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]] <br> <B>D.Phil. candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface...</p>
<hr />
<div>[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]]<br />
<br><br />
<B>D.Phil. candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</B><br><br><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=495User:MarkChang2009-06-04T22:41:34Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ Life Sciences Interface Doctoral Training Centre], University of Oxford.</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU&ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=494User:MarkChang2009-06-04T22:27:48Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal:<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference:<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=493User:MarkChang2009-06-04T22:26:51Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: [mailto:markycchang@gmail.com markycchang@gmail.com]|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=492User:MarkChang2009-06-04T22:23:30Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." <I>Genome Research</I> 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=491User:MarkChang2009-06-04T22:20:52Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChip<sup>TM</sup> for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=490User:MarkChang2009-06-04T22:12:45Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation of the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=489User:MarkChang2009-06-04T22:09:18Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics, Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=488User:MarkChang2009-06-04T22:00:02Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%"><u>Yo-Cheng (Mark) Chang</u></span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=487User:MarkChang2009-06-04T21:56:35Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%">Yo-Cheng (Mark) Chang</span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Klebsiella pneumoniae</I>, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of <I>Mycoplasma fermentans</I> M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of <I>Vibrio vulnificus</I> YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, <I>Vibrio vulnificus</I>." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen <I>Mycoplasma fermentans</I>." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=486User:MarkChang2009-06-04T21:52:28Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%">Yo-Cheng (Mark) Chang</span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Klebsiella pneumoniae, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Mycoplasma fermentans M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of Vibrio vulnificus YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, Vibrio vulnificus." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book/Article Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=485User:MarkChang2009-06-04T21:43:46Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%">Yo-Cheng (Mark) Chang</span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>[http://www.lsi.ox.ac.uk/ LSI DTC], University of Oxford</I><br><br><br />
</span><br />
<span style="font-size:110%"><br />
Supervisors:<br><br />
[http://www2.bioch.ox.ac.uk/~armitagelab/ Prof. Judith P. Armitage], Department of Biochemistry, University of Oxford.<br><br />
[http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Dr. Antonis Papachristodoulou], Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
[http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Prof. Juton Hein], Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Klebsiella pneumoniae, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Mycoplasma fermentans M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of Vibrio vulnificus YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, Vibrio vulnificus." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=484User:MarkChang2009-06-04T21:32:55Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%">Yo-Cheng (Mark) Chang</span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>LSI DTC, University of Oxford</I><br><br><br />
Supervisors:<br><br />
Prof. Judith P. Armitage, Department of Biochemistry, University of Oxford.<br><br />
Dr. Antonis Papachristodoulou, Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
Prof. Juton Hein, Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK.<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan.<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan.<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan.<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan.<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan.<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan.<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan.<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan.<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan.<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Klebsiella pneumoniae, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Mycoplasma fermentans M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of Vibrio vulnificus YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, Vibrio vulnificus." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology".<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching".<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles".<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=483User:MarkChang2009-06-04T21:30:47Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%">Yo-Cheng (Mark) Chang</span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><br />
<I>DPhil candidate<br>LSI DTC, University of Oxford</I><br><br><br />
Supervisors:<br><br />
Prof. Judith P. Armitage, Department of Biochemistry, University of Oxford.<br><br />
Dr. Antonis Papachristodoulou, Department of Engineering Sciences, University of Oxford.<br><br><br />
College supervisor:<br><br />
Prof. Juton Hein, Department of Statistics, University of Oxford.<br><br />
</span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Klebsiella pneumoniae, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Mycoplasma fermentans M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of Vibrio vulnificus YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, Vibrio vulnificus." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology"<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching"<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles"<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Member_List&diff=482Member List2009-06-04T21:20:32Z<p>MarkChang: </p>
<hr />
<div>== Engineering/Mathematics Researchers == <br />
* [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]<br><br />
* [http://www.ist.uni-stuttgart.de/allgower/allgower.shtml Frank Allgower]<br><br />
* [http://www3.imperial.ac.uk/people/m.barahona Mauricio Barahona]<br><br />
* [http://www.eee.strath.ac.uk/~hongyue/ Hong Yue]<br><br />
* [http://biology.st-andrews.ac.uk/vannesmithlab/ Anne Smith]<br><br />
* [http://www.rdg.ac.uk/icmr/about/staff/icmr-m-tindall.asp Marcus Tindall]<br><br />
* [http://www.montefiore.ulg.ac.be/~bullinger/ Eric Bullinger] <br> <br />
* [http://www.gla.ac.uk/departments/aerospace/staff/academicstaff/jongraekim Jongrae Kim]<br> <br />
* Elias August <br><br />
* [http://www.sbs.ox.ac.uk/faculty/Reed-Tsochas+Felix/ Felix Reed-Tsochas] <br><br />
* [http://www.stats.ox.ac.uk/people/academic_staff/jotun_hein Jotun Hein] <br><br />
* [http://www.eng.ox.ac.uk/control/peopleJA.shtml James Anderson] <br><br />
* [http://www.eng.ox.ac.uk/samp/people.html Patrick McSharry] <br><br />
* [http://www.comlab.ox.ac.uk/people/Jonathan.Whiteley/ Jonathan Whiteley] <br> <br />
* [http://www.physics.ox.ac.uk/users/kapanidis/ Achillefs Kapanidis] <br> <br />
* [http://www.staff.ncl.ac.uk/d.j.wilkinson/ Darren Wilkinson] <br> <br />
* [http://www.comlab.ox.ac.uk/people/David.Gavaghan/ David Gavaghan] <br> <br />
* [http://www.le.ac.uk/eg/dgb3/ Declan Bates] <br><br />
* [http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves] <br><br />
* [http://www.eecs.umich.edu/~ddv/ Domitilla del Vecchio] <br><br />
* [http://biochemistry.ucsf.edu/labs/elsamad/people/Hana_El_Samad/hana_el_samad.html Hana El-Samad] <br><br />
* John Ryan <br><br />
* [http://www.me.ucsb.edu/dept_site/people/khammash_page.htm Mustafa Khammash ]<br><br />
* [http://people.maths.ox.ac.uk/~maini/ Philip Maini] <br><br />
* [http://www.physics.ox.ac.uk/cm/cmt/jones/ Nick Jones] <br><br />
* [http://www.eng.ox.ac.uk/control/peopleSD.shtml Steve Duncan] <br><br />
* [http://www-control.eng.cam.ac.uk/Homepage/officialweb.php?id=232 Guy-Bart Stan] <br><br />
<br />
== Biology/Biochemistry Researchers == <br />
* [http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=565 Judy Armitage] <br> <br />
* [http://www.abdn.ac.uk/ims/staff/details.php?id=i.stansfield Ian Stansfield]<br><br />
* [http://www.brookes.ac.uk/res/experts/profiles/david_fell David Fell]<br><br />
* [http://www.plantsci.cam.ac.uk/research/alexwebb.html Alex Webb] <br><br />
* [http://swainlab.bio.ed.ac.uk/details.php Peter Swain] <br><br />
* [http://dps.plants.ox.ac.uk/plants/Staff/LeeSweetlove.aspx Lee Sweetlove] <br><br />
* [http://www.lincoln.ox.ac.uk/content/view/832/40/ Mark Roberts] <br><br />
* [http://www.pmb.ox.ac.uk/Fellows_Staff/Fellow_and_Staff_Profiles.php?profile=146 Steve Porter] <br><br />
* [http://sysos.eng.ox.ac.uk/control/RoSBNet/index.php/User:MarkChang Yo-Cheng (Mark) Chang] <br><br />
* Sara Hooshangi <br><br />
* [http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=593 Bela Novak] <br><br />
* [http://www.sysbio.ox.ac.uk/People/GW.html George Wadhams] <br><br />
* [http://sbcb.bioch.ox.ac.uk/sansom.php Mark Sansom] <br><br />
<br />
== Researchers from the Ethical, Legal and Social Sciences == <br />
* [http://web.comlab.ox.ac.uk/Annamaria.Carusi/ Annamaria Carusi]<br><br />
* [http://www.sbs.ox.ac.uk/insis/people/sugden+chris.htm Chris Sugden]<br><br />
* [http://www.ethox.org.uk/people/michael-parker Michael Parker]<br><br />
* [http://people.bath.ac.uk/ak280/ Alexander Kelle] <br><br />
* [http://www.ifom-ieo-campus.it/research/boniolocv.php Giovanni Boniolo] <br><br />
* [http://www.practicalethics.ox.ac.uk/nstaff.htm Julian Savulescu] <br><br />
* [http://www.philosophy.ox.ac.uk/members/marianne_talbot Marianne Talbot] <br><br />
* [http://www.bep.ox.ac.uk/our%20people.html Mark Sheehan] <br><br />
* Steve Clarke <br><br />
* [http://www.ethox.org.uk/people/jane-kaye Jane Kaye] <br></div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=481User:MarkChang2009-06-04T21:19:19Z<p>MarkChang: </p>
<hr />
<div><br><br />
<span style="font-size:200%">Yo-Cheng (Mark) Chang</span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><I>DPhil candidate<br>LSI DTC, University of Oxford</I></span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Klebsiella pneumoniae, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Mycoplasma fermentans M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of Vibrio vulnificus YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, Vibrio vulnificus." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology"<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching"<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles"<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=480User:MarkChang2009-06-04T21:18:13Z<p>MarkChang: </p>
<hr />
<div><br><br><br />
<span style="font-size:200%">Yo-Cheng (Mark) Chang</span><br />
[[Image:MarkChang.jpg|thumb|Contact Email: markycchang@gmail.com|right|200px]]<br />
<br><br />
<span style="font-size:130%"><I>DPhil candidate<br>LSI DTC, University of Oxford</I></span><br />
<br />
<br />
== Education ==<br />
*2005.10-present: Doctoral student, Life Sciences Interface Doctoral Training Centre, University of Oxford, UK<br />
*1997.9-1999.6: M.S. in Biomedical Engineering, National Yang Ming University, Taiwan<br />
*1993.9-1997.6: B.S. in Biomedical Engineering, Chung-Yuan Christian University, Taiwan<br />
<br />
== Work Experience ==<br />
*2005.3-2005.9: Project Manager, The Taiwan Biobank Project, Institute for Information Industry, Taiwan<br />
*2000.7-2005.1: Associate Researcher, Biomedical Engineering Center, Industrial Technology Research Institute, Taiwan<br />
**Department of Nanobiotechnology (2003.1-2005.1)<br />
**Department of Genomics (2000.7-2003.1)<br />
*1999.9-2000.6: Research Assistant, Department of Biomedical Engineering, National Yang Ming University, Taiwan<br />
<br />
== Teaching Experience ==<br />
*2005.2-2005.7: Adjunct Lecturer (Course: Computational biology), Department of Biotechnology, Ming Chuan University, Taiwan<br />
*2004.9-2005.1: Adjunct Lecturer (Course: Bioinformatics), Graduate Institute of Life Sciences, Tamkang University, Taiwan<br />
*2003.3-2003.6: Instructor (Course: Special topics in bioinformatics), Graduate Program of Bioinformatics, National Yang Ming University, Taiwan<br />
*2002.12: Instructor (Course: Microarray data analysis), Tze-Chiang Foundation of Science & Technology, Taiwan<br />
<br />
== Projects ==<br />
*2007-present: Design and construction of synthetic biological components with robust performance and stability based on the bacterial two-component system, LSI DTC, Oxford.<br />
*2007-2008: A systematic, algorithmic methodology for model reduction of large-scale biochemical networks, Department of Engineering Science, Oxford.<br />
*2006: In-vitro transcription and translation in lipid-bilayer vesicles, LSI DTC, Oxford.<br />
*2006: Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles, LSI DTC, Oxford.<br />
*2004-2005: Simulation of the conjugation between mouse IgG antibody and nanoparticle, ITRI, Taiwan<br />
*2003-2004: Conservation profiling of functionally coupled gene clusters through multiple genome comparison, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Klebsiella pneumoniae, NYMU, Taiwan.<br />
*2003: Whole genome annotation and analysis of Mycoplasma fermentans M64, NYMU, Taiwan.<br />
*2002-2003: Integrated protein-protein interaction and microarray database, ITRI, Taiwan.<br />
*2002: Large-scale analysis of bacterial repeat sequences, NYMU &ITRI, Taiwan.<br />
*2002: Automated protein classification system based on machine learning methods, ITRI, Taiwan.<br />
*2001-2002: Whole genome annotation and analysis of Vibrio vulnificus YJ016, NYMU&ITRI, Taiwan.<br />
*2001-2002: Automated and object-oriented bacteria genome annotation system, ITRI, Taiwan.<br />
*2000-2001: Automated microarray probe design system, ITRI, Taiwan.<br />
<br />
== Publications ==<br />
*Journal<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for model reduction of large-scale biochemical networks." (in preparation)<br />
# Chung-Yung Chen, Keh-Ming Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Hui-Chi Tsai, Tsai-Lien Liao, Yen-Ming Liu, Hsiang-Ju Chen, Arthur Bo-Ting Shen, Jian-Chiuan Li, Teh-Li Su, Chung-Ping Shao, Chung-Te Lee, Lien-I Hor, and Shih-Feng Tsai. "Comparative genome analysis of an invasive marine pathogen, Vibrio vulnificus." Genome Research 13(12):2577-87, Dec. 2003.<br />
<br />
*Conference<br />
# <u>Yo-Cheng Chang</u>, George H. Wadhams, Judith P. Armitage, and Antonis Papachristodoulou. "RoSBNet: From Robust Synthetic Biological Parts to Whole Systems: Theoretical, Practical and Ethical Challenges." The 4th International Meeting on Synthetic Biology (Synthetic Biology 4.0), Oct. 2008, Hong Kong, China.<br />
# <u>Yo-Cheng Chang</u>, Antonis Papachristodoulou, George H. Wadhams, and Judith P. Armitage. "A new design concept for synthetic biological components with desired and robust performance based on bacterial two-component system." ESF-EMBO Symposium on Bacterial Networks 2008 (BacNet'08), Sep. 2008, Sant Feliu de Guixols, Spain.<br />
# <u>Yo-Cheng Chang</u> and Antonis Papachristodoulou. "A systematic, algorithmic methodology for reducing biochemical network models" The 9th International Conference on Systems Biology (ICSB 2008), Aug. 2008, Gothenburg, Sweden.<br />
# <u>Yo-Cheng Chang</u>, Simon Ross, Mark Wallace, Richard Berry, and Anthony Watts, "Photosynthetic-driven ATP synthesis by bacteriorhodopsin and F1Fo ATP synthase co-reconstituted in large unilamellar vesicles." EPSRC Life Sciences Interface DTC Conference, July 2006, Oxford, UK.<br />
# <u>Yo-Cheng Chang</u> and Yuh-Jiuan Lin. "Simulation of the conjugation between mouse IgG antibody and nanoparticle." 2nd ITRI Conference of Computational Nanobiotechnology, Dec. 2004, Hsin-Chu, Taiwan.<br />
# Hon-Wei Chen, <u>Yo-Cheng Chang</u>, Der-Ming Liou, and Chuan-Hsiung Chang. "Conservation profiling of functionally-coupled gene clusters through multiple genome comparison." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB), Jul.-Aug. 2004, Glasgow, UK.<br />
# Chung-Yung Chen, Keh-Min Wu, <u>Yo-Cheng Chang</u>, Chuan-Hsiung Chang, Wnsi S Hu, and Shih-Feng Tsai. "The complete genome analysis of human respiratory pathogen Mycoplasma fermentans." 2nd NHRI Conference on Bacterial Gene Regulation and Pathegenesis, Apr. 2004, Tao-Yuan, Taiwan.<br />
# Chao-Chih Pan, Ju-hwa Lin, Jeng-Dau Wu, Yao-Sung Chang, Chun-Ju Chang, Meng-Chorng Tyan, Charng-Yih Leu, <u>Yo-Cheng Chang</u>, Jie-Len Huang, and Chuan-Hsiung Chang. "FeverChipTM for fever-causing pathogen detection and identification." IBC's 8th Annual Biochip Technology Conference, Oct.-Nov. 2001, San Diego, USA.<br />
<br />
== Book Translations ==<br />
*Traditional Chinese translation for the MIT Open CourseWare, OOPS, 2005. <br />
**Layer 1 translation of "18.417 Introduction to Computational Molecular Biology"<br />
*The Traditional Chinese version of "Developing Bioinformatics Computer Skills", O'Reilly, 2002.<br />
**Chapter 7, "Sequence Analysis, Pairwise Alignment, and Database Searching"<br />
**Chapter 8, "Multiple Sequence Alignments, Trees, and Profiles"<br />
<br />
== Invited Talks ==<br />
*2004.9: "Modeling genetic networks of a living cell.", Department of Mathematics Tamkang University, Taiwan.<br />
*2004.4: "Principles, applications, and recent research topics of bioinformatics.", Graduate Institute of Life Sciences, Tamkang University, Taiwan.<br />
<br />
<br />
----</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=File:MarkChang.jpg&diff=479File:MarkChang.jpg2009-06-04T20:11:24Z<p>MarkChang: </p>
<hr />
<div></div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=User:MarkChang&diff=478User:MarkChang2009-06-04T19:59:11Z<p>MarkChang: New page: test</p>
<hr />
<div>test</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=Member_List&diff=398Member List2009-05-27T15:32:24Z<p>MarkChang: </p>
<hr />
<div>== Engineering/Mathematics Researchers == <br />
* [http://sysos.eng.ox.ac.uk/control/sysos/index.php/User:Antonis Antonis Papachristodoulou]<br><br />
* [[User:Allgower|Frank Allgower]]<br><br />
* [[User:Barahona|Mauricio Barahona]]<br><br />
* [[User:Hong|Hong Yue]]<br><br />
* [[User:Vannesmith|Anne Smith]]<br><br />
* Marcus Tindall <br><br />
* [http://www.montefiore.ulg.ac.be/~bullinger/ Eric Bullinger] <br> <br />
* Jongrae Kim <br> <br />
* Elias August <br><br />
* Felix Reed-Tsochas <br><br />
* Jotun Hein <br><br />
* James Anderson <br><br />
* Patrick McSharry <br><br />
* Jonathan Whiteley <br> <br />
* Steffen Waldherr <br> <br />
* Achillefs Kapanidis <br> <br />
* Darren Wilkinson <br> <br />
* David Gavaghan <br> <br />
* Declan Bates <br><br />
* Jorge Goncalves <br><br />
* Domitilla del Vecchio <br><br />
* Hana El-Samad <br><br />
* John Ryan <br><br />
* Mustafa Khammash <br><br />
* Philip Maini <br><br />
* Nick Jones <br><br />
* Steve Duncan <br><br />
* Guy-Bart Stan <br><br />
<br />
== Biology/Biochemistry Researchers == <br />
* Judy Armitage <br> <br />
* [[User:I.stansfield|Ian Stansfield]]<br><br />
* [[User:Davidfell|David Fell]]<br><br />
* Alex Webb <br><br />
* Peter Swain <br><br />
* Chris French <br><br />
* Lee Sweetlove <br><br />
* Mark Roberts <br><br />
* Steve Porter <br><br />
* Yo-Cheng (Mark) Chang <br><br />
* Sara Hooshangi <br><br />
* Bela Novak <br><br />
* George Wadhams <br><br />
* Mark Sansom <br><br />
* Gos Micklem <br><br />
* Jim Haseloff <br><br />
<br />
== Researchers from the Ethical, Legal and Social Sciences == <br />
* [[User:Annamaria|Annamaria Carusi]]<br><br />
* [[User:Csugden|Chris Sugden]]<br><br />
* [[User:Mparker|Michael Parker]]<br><br />
* Alexander Kelle <br><br />
* Giovanni Boniolo <br><br />
* Julian Savulescu <br><br />
* Marianne Talbot <br><br />
* Mark Sheehan <br><br />
* Steve Clarke <br><br />
* Jane Kaye <br></div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=References&diff=397References2009-05-26T18:03:51Z<p>MarkChang: </p>
<hr />
<div><center><br />
<span style="color:#0000FF; font-size: 200%;">Please share references by adding links into this page</span><br />
</center><br />
<br />
<br />
[[Image:route.png|thumb|ACS Chem. Biol., 2008, 3 (1), pp 38–50|right|300px]]<br />
== General Principles of Synthetic Biology ==<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04335.html Reconstruction of genetic circuits]<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/16711359 Engineering life: building a fab for biology]<br />
<br />
[http://www.bioinfo.de/isb/2006/06/0038/ Engineering life through Synthetic Biology]<br />
<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=32f32f9adee8425380015b935a6eadf8 Systems biology as a foundation for genome-scale synthetic biology]<br />
<br />
== Parts Standardization/Construction ==<br />
[http://openwetware.org/images/9/99/Nbt1413.pdf Refinement and standardization of synthetic biological parts and devices]<br />
<br />
[http://www.jbioleng.org/content/2/1/5 Engineering BioBrick vectors from BioBrick parts]<br />
<br />
== Mathematical/Computational Methods ==<br />
[http://www.weizmann.ac.il/mcb/UriAlon/Papers/Shinar_Alon_Feinberg_SIAM_2009.pdf Sensitivity and robustness in chemical reaction networks]<br />
<br />
== New Designs/Design Principles ==<br />
[http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]<br />
<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200843.html The incoherent feed-forward loop can generate non-monotonic input functions for genes]<br />
<br />
== In-vivo/vitro Chassis ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4GS4TTH-C&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=05e4ed6bd00339746d790a93c7a96ef2 Protein synthesis by pure translation systems]<br />
<br />
[http://www.pnas.org/content/100/22/12672 Principles of cell-free genetic circuit assembly]<br />
<br />
== Applications ==<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic Escherichia coli predator–prey ecosystem]<br />
<br />
== Software Packages/Tools ==<br />
[http://www.mathworks.co.uk/access/helpdesk/help/toolbox/simbio/index.html?/access/helpdesk/help/toolbox/simbio/ MATLAB SimBiology]<br />
<br />
== Measurement Methods ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4P3DWNX-S&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=179a5617e3cd099a11a4ec40f9b85780 Single-cell analysis of gene expression by fluorescence microscopy]<br />
<br />
== Ethical, Legal, and Social Issues (ELSI) ==<br />
[http://www.synbiosafe.eu/uploads///pdf/Diffusion_of_synthetic_biology.pdf Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthic Biology]<br />
<br />
[http://www.sciencemag.org/cgi/content/summary/286/5447/2087 Ethical Considerations in Synthesizing a Minimal Genome]</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=References&diff=396References2009-05-26T18:03:13Z<p>MarkChang: </p>
<hr />
<div><center><br />
<span style="color:#0000FF; font-size: 200%;">Please share references by adding links into this page</span><br />
</center><br />
<br />
[[Image:route.png|thumb|ACS Chem. Biol., 2008, 3 (1), pp 38–50|right|300px]]<br />
== General Principles of Synthetic Biology ==<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04335.html Reconstruction of genetic circuits]<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/16711359 Engineering life: building a fab for biology]<br />
<br />
[http://www.bioinfo.de/isb/2006/06/0038/ Engineering life through Synthetic Biology]<br />
<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=32f32f9adee8425380015b935a6eadf8 Systems biology as a foundation for genome-scale synthetic biology]<br />
<br />
== Parts Standardization/Construction ==<br />
[http://openwetware.org/images/9/99/Nbt1413.pdf Refinement and standardization of synthetic biological parts and devices]<br />
<br />
[http://www.jbioleng.org/content/2/1/5 Engineering BioBrick vectors from BioBrick parts]<br />
<br />
== Mathematical/Computational Methods ==<br />
[http://www.weizmann.ac.il/mcb/UriAlon/Papers/Shinar_Alon_Feinberg_SIAM_2009.pdf Sensitivity and robustness in chemical reaction networks]<br />
<br />
== New Designs/Design Principles ==<br />
[http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]<br />
<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200843.html The incoherent feed-forward loop can generate non-monotonic input functions for genes]<br />
<br />
== In-vivo/vitro Chassis ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4GS4TTH-C&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=05e4ed6bd00339746d790a93c7a96ef2 Protein synthesis by pure translation systems]<br />
<br />
[http://www.pnas.org/content/100/22/12672 Principles of cell-free genetic circuit assembly]<br />
<br />
== Applications ==<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic Escherichia coli predator–prey ecosystem]<br />
<br />
== Software Packages/Tools ==<br />
[http://www.mathworks.co.uk/access/helpdesk/help/toolbox/simbio/index.html?/access/helpdesk/help/toolbox/simbio/ MATLAB SimBiology]<br />
<br />
== Measurement Methods ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4P3DWNX-S&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=179a5617e3cd099a11a4ec40f9b85780 Single-cell analysis of gene expression by fluorescence microscopy]<br />
<br />
== Ethical, Legal, and Social Issues (ELSI) ==<br />
[http://www.synbiosafe.eu/uploads///pdf/Diffusion_of_synthetic_biology.pdf Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthic Biology]<br />
<br />
[http://www.sciencemag.org/cgi/content/summary/286/5447/2087 Ethical Considerations in Synthesizing a Minimal Genome]</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=File:Route.png&diff=395File:Route.png2009-05-26T17:54:04Z<p>MarkChang: </p>
<hr />
<div></div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=References&diff=392References2009-05-19T13:01:17Z<p>MarkChang: </p>
<hr />
<div><center><br />
<span style="color:#0000FF; font-size: 200%;">Please share references by adding links into this page</span><br />
</center><br />
<br />
<br />
== General Principles of Synthetic Biology ==<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04335.html Reconstruction of genetic circuits]<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/16711359 Engineering life: building a fab for biology]<br />
<br />
[http://www.bioinfo.de/isb/2006/06/0038/ Engineering life through Synthetic Biology]<br />
<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=32f32f9adee8425380015b935a6eadf8 Systems biology as a foundation for genome-scale synthetic biology]<br />
<br />
== Parts Standardization/Construction ==<br />
[http://openwetware.org/images/9/99/Nbt1413.pdf Refinement and standardization of synthetic biological parts and devices]<br />
<br />
[http://www.jbioleng.org/content/2/1/5 Engineering BioBrick vectors from BioBrick parts]<br />
<br />
== Mathematical/Computational Methods ==<br />
[http://www.weizmann.ac.il/mcb/UriAlon/Papers/Shinar_Alon_Feinberg_SIAM_2009.pdf Sensitivity and robustness in chemical reaction networks]<br />
<br />
== New Designs/Design Principles ==<br />
[http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]<br />
<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200843.html The incoherent feed-forward loop can generate non-monotonic input functions for genes]<br />
<br />
== In-vivo/vitro Chassis ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4GS4TTH-C&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=05e4ed6bd00339746d790a93c7a96ef2 Protein synthesis by pure translation systems]<br />
<br />
[http://www.pnas.org/content/100/22/12672 Principles of cell-free genetic circuit assembly]<br />
<br />
== Applications ==<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic Escherichia coli predator–prey ecosystem]<br />
<br />
== Software Packages/Tools ==<br />
[http://www.mathworks.co.uk/access/helpdesk/help/toolbox/simbio/index.html?/access/helpdesk/help/toolbox/simbio/ MATLAB SimBiology]<br />
<br />
== Measurement Methods ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4P3DWNX-S&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=179a5617e3cd099a11a4ec40f9b85780 Single-cell analysis of gene expression by fluorescence microscopy]<br />
<br />
== Ethical, Legal, and Social Issues (ELSI) ==<br />
[http://www.synbiosafe.eu/uploads///pdf/Diffusion_of_synthetic_biology.pdf Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthic Biology]<br />
<br />
[http://www.sciencemag.org/cgi/content/summary/286/5447/2087 Ethical Considerations in Synthesizing a Minimal Genome]</div>MarkChanghttp://rosbnet.org/wiki/wiki/index.php?title=References&diff=391References2009-05-19T11:53:11Z<p>MarkChang: </p>
<hr />
<div><center><br />
<span style="color:#0000FF; font-size: 200%;">Please share references by adding links in this page</span><br />
</center><br />
<br />
<br />
== General Principles of Synthetic Biology ==<br />
[http://www.nature.com/nature/journal/v438/n7067/abs/nature04335.html Reconstruction of genetic circuits]<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/16711359 Engineering life: building a fab for biology]<br />
<br />
[http://www.bioinfo.de/isb/2006/06/0038/ Engineering life through Synthetic Biology]<br />
<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=32f32f9adee8425380015b935a6eadf8 Systems biology as a foundation for genome-scale synthetic biology]<br />
<br />
== Parts Standardization/Construction ==<br />
[http://openwetware.org/images/9/99/Nbt1413.pdf Refinement and standardization of synthetic biological parts and devices]<br />
<br />
[http://www.jbioleng.org/content/2/1/5 Engineering BioBrick vectors from BioBrick parts]<br />
<br />
== Mathematical/Computational Methods ==<br />
[http://www.weizmann.ac.il/mcb/UriAlon/Papers/Shinar_Alon_Feinberg_SIAM_2009.pdf Sensitivity and robustness in chemical reaction networks]<br />
<br />
== New Designs/Design Principles ==<br />
[http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators]<br />
<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200843.html The incoherent feed-forward loop can generate non-monotonic input functions for genes]<br />
<br />
== In-vivo/vitro Chassis ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WN5-4GS4TTH-C&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=05e4ed6bd00339746d790a93c7a96ef2 Protein synthesis by pure translation systems]<br />
<br />
[http://www.pnas.org/content/100/22/12672 Principles of cell-free genetic circuit assembly]<br />
<br />
== Applications ==<br />
[http://www.nature.com/msb/journal/v4/n1/full/msb200824.html A synthetic Escherichia coli predator–prey ecosystem]<br />
<br />
== Software Packages/Tools ==<br />
[http://www.mathworks.co.uk/access/helpdesk/help/toolbox/simbio/index.html?/access/helpdesk/help/toolbox/simbio/ MATLAB SimBiology]<br />
<br />
== Measurement Methods ==<br />
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4P3DWNX-S&_user=126524&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000010360&_version=1&_urlVersion=0&_userid=126524&md5=179a5617e3cd099a11a4ec40f9b85780 Single-cell analysis of gene expression by fluorescence microscopy]<br />
<br />
== Ethical, Legal, and Social Issues (ELSI) ==<br />
[http://www.synbiosafe.eu/uploads///pdf/Diffusion_of_synthetic_biology.pdf Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthic Biology]<br />
<br />
[http://www.sciencemag.org/cgi/content/summary/286/5447/2087 Ethical Considerations in Synthesizing a Minimal Genome]</div>MarkChang