User:Alexis Courbet

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 automatize the implementation of logic circuits in biological substrate (i.e. synthetic genes circuits and biochemical circuits). I developped 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

• The Baker Laboratory, Institute for Protein Design
  

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

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

• DIYbio
• Aeon
• Registry of biological parts
• The Biochemical Abstract Machine BIOCHAM
• The stochastic automaton HSIM
• Less Wrong