User:Alexis Courbet: Difference between revisions
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[[Image:Alexis_Courbet.jpg|thumb|right|Alexis Courbet]] | [[Image:Alexis_Courbet.jpg|thumb|right|Alexis Courbet]] | ||
* Cellular/molecular engineering | * Cellular/molecular engineering | ||
* Biosensing | * Biocomputing & Biosensing | ||
* Synthetic biological circuits | * Synthetic biological circuits | ||
* CAD for synthetic biology | * CAD & computational design for synthetic biology | ||
* Autonomous & programmable biosystems | * Autonomous & programmable biosystems | ||
* Protocells & minimal systems | * Protocells & minimal systems | ||
* Microfluidics | * Microfluidics | ||
* Medical sciences, translational medicine | * Biomolecular prosthetics, diagnostics & theranostics | ||
* Medical sciences, translational medicine | |||
* Multidisciplinary science | * Multidisciplinary science | ||
During my PhD, | 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. | *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). | *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. | I believe that collaboration between scientists and promotion of interdisciplinarity is the key to understand and engineer biology. | ||
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==Contact Info== | ==Contact Info== | ||
* | *[https://www.bakerlab.org/ The Baker Laboratory], [http://www.ipd.uw.edu/ Institute for Protein Design]<br> | ||
*Sys2diag | Washington Research Foundation Innovation Postdoctoral Fellow<br> | ||
''Complex biological systems modelling and engineering for diagnosis'' | University of Washington, Seattle, USA<br> | ||
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== | ||
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* 2012-2015, PhD at The National Center for Scientific Research (CNRS)&Bio-Rad/Stanford University | * 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 | * 2012, MS in Molecular and Cellular Biophysics, University of Montpellier | ||
* 2011-2015, Residency in Clinical Toxicology, Pharmaceutical innovation and Research | * 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 of Paris Sud 11 | * 2010, BS, University of Paris Sud 11 | ||
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''Acta Biotheor.'', 2015 May 13;<br> | ''Acta Biotheor.'', 2015 May 13;<br> | ||
'''Alexis Courbet''', Patrick Amar, and Franck Molina | '''Alexis Courbet''', Patrick Amar, and Franck Molina | ||
[http://www.ncbi.nlm.nih.gov | [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> | '''Engineering next generation diagnostics through synthetic biology'''<br> | ||
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'''Alexis Courbet''' | '''Alexis Courbet''' | ||
[[Media:Courbet_Thesis.pdf|PDF]]<br> | [[Media:Courbet_Thesis.pdf|PDF]]<br> | ||
'''Bringing next‐generation diagnostics to the clinic through synthetic biology''' <br> | |||
''EMBO Molecular Medicine'' 2016 July 11; DOI: 10.15252/emmm.201606541<br> | |||
'''Alexis Courbet''', Eric Renard, and Franck Molina | |||
[http://www.ncbi.nlm.nih.gov/pubmed/27402339 Abstract] [[Media:Courbet_EMM.pdf|PDF]]<br> | |||
==Useful links== | ==Useful links== | ||
*[[ | *[http://diybio.org/ DIYbio] | ||
*[[ | *[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
- 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:
- Sys2diag Laboratory, CNRS Complex biological systems modelling and engineering for diagnosis
PhD Student
University of Montpellier, France
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
