User:Alexis Courbet: Difference between revisions

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==Research interests==
[[Image:Alexis_Courbet.jpg|thumb|right|Alexis Courbet]]
 
* Cellular/molecular engineering
* Biocomputing & Biosensing
* Synthetic biological circuits
* CAD & computational design for synthetic biology
* Autonomous & programmable biosystems
* Protocells & minimal systems
* Microfluidics
* Biomolecular prosthetics, diagnostics & theranostics
* Medical sciences, translational medicine
* Multidisciplinary science
 
 
I am interested in the engineering of complex biological systems through synthetic biology to achieve programmable information and energy processing.
 
During my PhD I engineered bacterial cells and protocellular structures as autonomous and programmable biosensors-biocomputers capable of multiplexed biomolecular signal integration and processing. I developed CAD tools, microfluidic and molecular biology strategies to automate the implementation of logic circuits in biological substrate (i.e. synthetic genes circuits and biochemical circuits). I established concepts, systematic methods, computational tools and biological standards to:
 
*1. Engineer next-generation diagnostics. I engineered autonomous and programmable biosensors integrating multiplexed pathological biomarker detection and complex biological signal processing as ''intelligent'' diagnostic devices.
 
*2. Engineer novel biocomputing devices that solve complex problems and process/interface biological information at the microscale. I developed microfluidic and computer assisted methodologies to program these synthetic biosystems from the bottum-up (e.g. protocells).
 
 
I recently joined the Baker laboratory and am now focusing on computational protein design to develop novel bio-electronic interfaceable, ultra low power and self assembling nanoscale biocomputers. <br>
 
 
I believe that collaboration between scientists and promotion of interdisciplinarity is the key to understand and engineer biology.


==Contact Info==
==Contact Info==
[[Image:OWWEmblem.png|thumb|right|Alexis Courbet (an artistic interpretation)]]


*Alexis Courbet
*[https://www.bakerlab.org/ The Baker Laboratory], [http://www.ipd.uw.edu/ Institute for Protein Design]<br>
*Sysdiag laboratory, CNRS-Biorad
Washington Research Foundation Innovation Postdoctoral Fellow<br>
CAP DELTA
University of Washington, Seattle, USA<br>
1682 Rue de la Valsiere
CS 61003
34184 Montpellier CEDEX 4
*Montpellier, France
*[[Special:Emailuser/Alexis Courbet|Email me through OpenWetWare]]


I work in the SysDiag laboratory. I learned about [[OpenWetWare]] when doing research on synthetic biology, and looking for protocols. I've joined because I am a PhD student in synthetic biology, and I have always supported open and free entreprises, especially when it has to do with educational, scientific, and intellectual purposes. I believe that collaboration between scientists and promotion of interdisciplinarity is the key to understand and engineer biology.
Formerly at:<br>
*[https://www.sys2diag.cnrs.fr/ Sys2diag Laboratory], [http://www.cnrs.fr/en/aboutCNRS/overview.htm CNRS] ''Complex biological systems modelling and engineering for diagnosis''<br>
PhD Student <br>
University of Montpellier, France <br>
 
 
[[Special:Emailuser/Alexis Courbet|Email me through OpenWetWare]]


==Education==
==Education==
<!--Include info about your educational background-->
<!--Include info about your educational background-->
* 2012, 1st Year of PhD at Sysdiag laboratory, CNRS-Biorad
* 2012-2015, PhD at The National Center for Scientific Research (CNRS)&Bio-Rad/Stanford University
* 2012, MS in Molecular and Cellular Biophysics, Université Montpellier 1
* 2012, MS in Molecular and Cellular Biophysics, University of Montpellier
* 2011-2015, Residency in Clinical Toxicology, Pharmaceutical innovation and Biomedical Research
* 2011, MS in Cellular and Molecular Biology, University Paris Sud 11
* 2011, MS in Cellular and Molecular Biology, University Paris Sud 11
* 2010, BS, University Paris Sud 11
* 2010, BS, University of Paris Sud 11
* 2010, BMSc, University of Paris Sud 11


==Research interests==
==Publications==
<!-- Feel free to add brief descriptions to your research interests as well -->
'''Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates'''<br>
# Bacterial Biosensing systems
''Science Translational Medicine'', 2015 May 27;7(289):289ra83<br>
# Logical biochemical molecular networks
'''Alexis Courbet''', Drew Endy, Eric Renard, Franck Molina, and Jérôme Bonnet
# ''Ex vivo'' biologicaly based logic systems
[http://www.ncbi.nlm.nih.gov/pubmed/26019219 Abstract]  [[Media:Courbet_STM.pdf|PDF]]<br>
[[Media:Courbet_STM_SM.pdf|Supplementary Materials]]
 
'''Computing with Synthetic Protocells'''<br>
''Acta Biotheor.'', 2015 May 13;<br>
'''Alexis Courbet''', Patrick Amar, and Franck Molina
[http://www.ncbi.nlm.nih.gov/pubmed/25969126?report=abstract Abstract]  [[Media:Courbet_Acta.pdf|PDF]]<br>
 
'''Engineering next generation diagnostics through synthetic biology'''<br>
''University of Montpellier, Medical Thesis'', 2015 July 2;<br>
'''Alexis Courbet'''
[[Media:Courbet_Thesis.pdf|PDF]]<br>


==Publications==
'''Bringing next‐generation diagnostics to the clinic through synthetic biology''' <br>
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications.  You can add or remove lines as needed -->
''EMBO Molecular Medicine'' 2016 July 11; DOI: 10.15252/emmm.201606541<br>
<biblio>
'''Alexis Courbet''', Eric Renard, and Franck Molina
// leave a comment about a paper here
[http://www.ncbi.nlm.nih.gov/pubmed/27402339 Abstract] [[Media:Courbet_EMM.pdf|PDF]]<br>
</biblio>


==Useful links==
==Useful links==
*[[OpenWetWare:Welcome|Introductory tutorial]]
*[http://diybio.org/ DIYbio]
*[[Help|OpenWetWare help pages]]
*[http://aeon.co/magazine/ Aeon]
*[http://parts.igem.org/Main_Page?title=Main_Page Registry of biological parts]
*[https://lifeware.inria.fr/biocham/ The Biochemical Abstract Machine BIOCHAM]
*[https://www.lri.fr/~pa/Hsim/ The stochastic automaton HSIM]
*[http://lesswrong.com/ Less Wrong]
*[https://fold.it/portal/ Foldit]
*[https://www.rosettacommons.org/ Rosetta]

Revision as of 12:20, 3 August 2016

Research interests

Alexis Courbet
  • Cellular/molecular engineering
  • Biocomputing & Biosensing
  • Synthetic biological circuits
  • CAD & computational design for synthetic biology
  • Autonomous & programmable biosystems
  • Protocells & minimal systems
  • Microfluidics
  • Biomolecular prosthetics, diagnostics & theranostics
  • Medical sciences, translational medicine
  • Multidisciplinary science


I am interested in the engineering of complex biological systems through synthetic biology to achieve programmable information and energy processing.

During my PhD I engineered bacterial cells and protocellular structures as autonomous and programmable biosensors-biocomputers capable of multiplexed biomolecular signal integration and processing. I developed CAD tools, microfluidic and molecular biology strategies to automate the implementation of logic circuits in biological substrate (i.e. synthetic genes circuits and biochemical circuits). I established concepts, systematic methods, computational tools and biological standards to:

  • 1. Engineer next-generation diagnostics. I engineered autonomous and programmable biosensors integrating multiplexed pathological biomarker detection and complex biological signal processing as intelligent diagnostic devices.
  • 2. Engineer novel biocomputing devices that solve complex problems and process/interface biological information at the microscale. I developed microfluidic and computer assisted methodologies to program these synthetic biosystems from the bottum-up (e.g. protocells).


I recently joined the Baker laboratory and am now focusing on computational protein design to develop novel bio-electronic interfaceable, ultra low power and self assembling nanoscale biocomputers.


I believe that collaboration between scientists and promotion of interdisciplinarity is the key to understand and engineer biology.

Contact Info

Washington Research Foundation Innovation Postdoctoral Fellow
University of Washington, Seattle, USA

Formerly at:

PhD Student
University of Montpellier, France


Email me through OpenWetWare

Education

  • 2012-2015, PhD at The National Center for Scientific Research (CNRS)&Bio-Rad/Stanford University
  • 2012, MS in Molecular and Cellular Biophysics, University of Montpellier
  • 2011-2015, Residency in Clinical Toxicology, Pharmaceutical innovation and Biomedical Research
  • 2011, MS in Cellular and Molecular Biology, University Paris Sud 11
  • 2010, BS, University of Paris Sud 11
  • 2010, BMSc, University of Paris Sud 11

Publications

Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates
Science Translational Medicine, 2015 May 27;7(289):289ra83
Alexis Courbet, Drew Endy, Eric Renard, Franck Molina, and Jérôme Bonnet Abstract PDF
Supplementary Materials

Computing with Synthetic Protocells
Acta Biotheor., 2015 May 13;
Alexis Courbet, Patrick Amar, and Franck Molina Abstract PDF

Engineering next generation diagnostics through synthetic biology
University of Montpellier, Medical Thesis, 2015 July 2;
Alexis Courbet PDF

Bringing next‐generation diagnostics to the clinic through synthetic biology
EMBO Molecular Medicine 2016 July 11; DOI: 10.15252/emmm.201606541
Alexis Courbet, Eric Renard, and Franck Molina Abstract PDF

Useful links

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