Along a 40-year scientific career, I published over 110 primary articles, most of them as the senior author. These include over 70 papers in computational biology between 2000 and 2016. These articles were cited 4000 times, one was cited over 800 times.
I also wrote or edited 26 scientific books; wrote 15 book chapters; and edited 7 special issues of scientific journals.
In addition, I annually organised 2-7 international conferences/schools between 2002 and 2017.
I organised, chaired or was an invited speaker at a total of 60 scientific meetings in synthetic biology between 2005 and 2018.
Selected publications
- Képès, F. (2018). Biologie de synthèse et agronomie. Concepts et outils du génie génétique.
- Le Treut, G., Képès, F. and Orland, H. (2018). A Polymer Model for the Quantitative Reconstruction of Chromosome Architecture from HiC and GAM Data. Biophys J., 115, 2286-94.
- Le Treut, G., Képès, F. and Orland, H. (2016). Phase behavior of DNA in the presence of DNA-binding proteins. Biophys J., 110, 51-62.
- Bouyioukos, C., Elati, M. and Képès, F. (2016). GREAT:SCAN, tools for the analysis of genome layout and regulation. BMC Bioinformatics 17(Suppl 5), 191.
- Boldt, K. et al. (2016). An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature Commun. 7, 11491.
- Bouyioukos, C., Bucchini, F., Elati, M. and Képès, F. (2016). GREAT: a web portal for Genome REgulatory Architecture Tools. Nucleic Acids Research (Web Server issue). Advance Access published on May 5, 2016.
- Bouyioukos, C., Reverchon, S. and Képès, F. (2016). From multiple pathogenicity islands to a unique organized pathogenicity archipelago. Scientific Reports (NPG) 6, 27978.
- Bouyioukos, C., Elati, M. and Képès F. (2016). Protocols for probing genome architecture of regulatory networks in hydrocarbon and lipid microorganisms. In McGenity, Timmis & Nogales (eds.), Hydrocarbon and Lipid Microbiology Protocols, Springer Protocols Handbooks, p. 119-134 (Springer-Verlag Berlin Heidelberg).
- Lepage, T., Képès, F. and Junier, I. (2015). Thermodynamics of Long Supercoiled Molecules: Insights from Highly Efficient Monte Carlo Simulations. Biophys J. 109, 135-43.
- Elati, M., Nicolle, R., Junier, I., Fernandez, D., Fekih, R., Font, J. and Képès, F. (2013). PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION. Nucleic Acids Res. 41, 1406-15.
- Képès, F., Jester, B.C., Lepage, T., Rafiei, N., Rosu, B. and Junier, I. (2012). The layout of a bacterial genome. FEBS Lett. 586, 2043-2048. Synthetic Biology special issue.
- Junier, I., Hérisson, J. and Képès, F. (2012). Genomic Organization of Evolutionarily Correlated Genes in Bacteria: Limits and Strategies. J. Mol. Biol. 419, 369-86.
- Junier, I., Martin, O., and Képès, F. (2010). Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Computational Biology 6, 2.
- Poudret, M., Arnould, A., Comet, J.-P., Le Gall, P., Meseure, P. and Képès, F. (2008). Topology-based abstraction of complex biological systems: Application to the Golgi apparatus. Theory in Biosciences 127, 79-88.
- Banzhaf, W., Beslon, G., Christensen, S., Foster, J.A., Képès, F., Lefort, V., Miller, J.F., Radman, M. and Ramsden, J.J. (2006). From Artificial Evolution to Computational Evolution: a research agenda. Nature Reviews Genetics 7, 729-735.
- Képès, F. (2004). Periodic transcriptional organization of the E. coli genome. J Mol Biol 340, 957-964.
- Képès, F. and Vaillant, C. (2003). Transcription-based solenoidal model of chromosomes. ComPlexUs 1, 171-180.
- Képès, F. (2003). Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites. J Mol Biol 329, 859-865.
- Carbone A, Zinovyev A and Képès F (2003). Codon adaptation index as a measure of dominating codon bias. Bioinformatics 19(16), 2005-2015.
- Guelzim N, Bourgine P and Képès F (2002). Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics 31(1), 60-63.
All publications
ISI Web of Science (log in first !)
Conferences / meetings since 2004
| Year | Conference | Role | Location | |
| 2004 | Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Evry, France | |
| Société Francophone de Biologie Théorique « Biologie théorique, philosophie des sciences et épistémologie » | Invited Speaker | Lyon, France | ||
| JOBIM Congress | Brief presentation * | Montréal, Canada | ||
| École Interdisciplinaire de Berder | Invited Speaker | Berder, France | ||
| Computational Methods in Systems Biology | Program Committee | Paris, France | ||
| Déterminismes et complexités: de la physique à l’éthique | Invited Speaker | Cerisy, France | ||
| European Conference on Complex Systems | Organiser & Tutorial | Turin, Italy | ||
| ISMB / ECCB | Poster * | Glasgow, UK | ||
| 2005 | Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Montpellier, France | |
| Computational Methods in Systems Biology | Program C & Tutorial | Edinburgh, UK | ||
| Bio-Info-Math Workshop | Conference & Tutorial | Tehran, Iran | ||
| ESF Workshop on Functional Genomics | Invited Speaker | Madrid, Spain | ||
| Biostatistics Special Course | Conference & Tutorial | Florence, Italy | ||
| Complexity Advanced Course : Functional Genomics | Organiser & Tutorial | Évry, France | ||
| Santa Fe Institute Workshop on Complex Systems | Invited Speaker | Santa Fe, NM, USA | ||
| Thematic Institute on Combinatorial optimization | Invited Speaker | Turin, Italy | ||
| « Geometry of Genome » Congress | Invited Speaker | Leicester, UK | ||
| First European Conference on Complex Systems 2005 (ECCS’05) | Conference Chair | Paris, France | ||
| First European Conference on Complex Systems 2005 (ECCS’05) | Conference* & Poster* | Paris France | ||
| ECCS’05 Satellite Workshop on « Reverse modeling of regulatory biological networks: expectations and limitations » | Organiser | Évry, France | ||
| Integrative Post-Genomics 2005 (IPG’05) | Program Committee | Lyon, France | ||
| RIAMS (satellite of IPG’05) | Program Committee | Lyon, France | ||
| Workshop LIX 2005 | Invited Speaker | Palaiseau, France | ||
| ISMB’05 Congress | Poster * | Detroit, USA | ||
| 2006 | Journée thématique INRA | Invited Speaker | Jouy, France | |
| Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Bordeaux, France | ||
| Colloque du Centre d’Alembert « Démarches intégratives dans les sciences aujourd’hui » | Invited Speaker | Orsay, France | ||
| « Complex Systems & Biology » Workshop | Invited Speaker | Lyon, France | ||
| ISCOM (European Commission) final meeting | Session Chair | Venice, Italy | ||
| Symposium « The Making Up of Organisms: Mapping the Future of Biological Models » | Invited Speaker | Paris, France | ||
| Bioinformatics Meeting | Invited Speaker | TIFR, Bangalore, India | ||
| JOBIM Congress | Program Committee | Bordeaux, France | ||
| JOBIM Congress | Brief presentation * | Bordeaux, France | ||
| Second European Conference on Complex Systems 2006 (ECCS’06) | Steering Committee | Oxford, UK | ||
| SFG Conference « Genetics meets Systems Biology: Theory and Practice » | Organiser | Paris, France | ||
| Integrative Post-Genomics 2006 (IPG’06) | Program Committee | Lyon, France | ||
| RIAMS (satellite of IPG’06) | Program Committee | Lyon, France | ||
| Computational Methods in Systems Biology | Program Committee | Trento, Italy | ||
| Colloque ‘Microbiologie’ PRES Universud Paris | Program Committee | Orsay, France | ||
| EuroBio 2006, Bio-IT Symposium | Chair | Paris, France | ||
| 2007 | Colloque de Biologie et Philosophie « À quoi sert la modélisation » | Invited Speaker | Paris, France | |
| ENFIN Euro-conference on Systems Biology | Invited Speaker | Evry, France | ||
| Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Evry, France | ||
| ERASysBio Strategy Conference | Organiser | Oxford, UK | ||
| Séminaire sur les interfaces géométrie-physique-biologie et sur la biologie des systèmes | Invited Speaker | EHESS, Paris, France | ||
| Complexity of biological networks Advanced Course | Organiser | Evry, France | ||
| First International Conference on Living Technology | Session Chair | Venice, Italy | ||
| ACI VicAnne final meeting « Modélisation stochastique à des échelles mésoscopiques » | Invited Speaker | Bordeaux, France | ||
| Statistical Mechanics & Biological Information | Organiser & Conference | Turin, Italy | ||
| CNRS-MPG joint meeting on Systems Biology | Organiser & Conference | Berlin, Germany | ||
| Third European Conference on Complex Systems (ECCS’07) | Steering Committee | Dresden, Germany | ||
| Integrative Post-Genomics 2007 (IPG’07) | Program Committee | Lyon, France | ||
| RIAMS (satellite of IPG’07) | Program Committee | Lyon, France | ||
| 2008 | iGEM in Europe Teacher’s Workshop | Organiser | Evry, France | |
| French Workshop on Synthetic Biology | Panelist | Paris, France | ||
| Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Lille, France | ||
| Gennetec Int’l Conf « Gene regulatory networks: Dynamics, spatial organization & inference » | Organiser & Conference * | Turin, Italy | ||
| Colloque « Biologie systémique et synthétique » du PRES UniverSud Paris « Approches quantitatives de la complexité biologique » | Organiser | Orsay, France | ||
| Think tank on « Statistical Semantics of Genomes: from sequence to function » | Organiser | Evry, France | ||
| International Solvay Institutes Conference on « The logic of gene regulatory networks » | Session Chair | Brussels, Belgium | ||
| ENFIN Workshop on « Systems modeling » | Invited Speaker | Cachan, France | ||
| Fourth European Conference on Complex Systems (ECCS’08) | Poster * | Jerusalem, Israel | ||
| Fourth European Conference on Complex Systems (ECCS’08) | Invited Speaker | Jerusalem, Israel | ||
| Think tank on Complexity | Invited Speaker | Jerusalem, Israel | ||
| Genopole® 10 year Symposium | Session Chair | Evry, France | ||
| BioComplex 2008 Workshop (with Nobel awardee) | Invited Speaker | Trentino, Italy | ||
| Integrative Post-Genomics 2008 (IPG’08) | Program Committee | Lyon, France | ||
| TESSY (Towards a European Strategy in Synthetic Biology) meeting | Organiser | Evry, France | ||
| iGEM-international « Education » Committee meeting | Chair | Boston, USA | ||
| 2009 | GENNETEC Training Course | Course | Paris, France | |
| Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Nice, France | ||
| Collège de France Int’l Conf « From synthetic chemistry to synthetic biology » (with Nobel awardee) | Invited Speaker | Paris, France | ||
| « OGM face aux nouveaux paradigmes de biologie » Conference | Invited Speaker | Paris, France | ||
| Journée Biologie Systémique de Paris-Descartes | Invited Speaker | Paris, France | ||
| Tasters in complex systems, MIR@W | Invited Speaker | Warwick, UK | ||
| Gennetec – ICTP International School | Organiser & Course | Trieste, Italy | ||
| Gennetec – ICTP International Workshop | Organiser | Trieste, Italy | ||
| CNRS-MPG Workshop « Experimental data integration within genome-scale metabolic models » | Organiser | Paris, France | ||
| Fifth European Conference on Complex Systems 2009 (ECCS’09) | Program Chair | Warwick, UK | ||
| Fifth European Conference on Complex Systems 2009 (ECCS’09) | Poster * | Warwick, UK | ||
| EuroBIO 2009 Conference | Invited Speaker | Lille, France | ||
| CNRS-MPG annual meeting | Organiser | Leipzig, Germany | ||
| European Conference on Synthetic Biology | Invited Speaker | Sant Feliu, Spain | ||
| OECD, NAS USA, UK Royal Society « Opportunities and Challenges in the Emerging Field of Synthetic Biology » | Invited Speaker | Washington DC, USA | ||
| Integrative Post-Genomics 2009 (IPG’09) | Program Committee | Lyon, France | ||
| 2010 | Symposium « Top-Down, Bottom-Up and Computational Approaches in Synthetic Biology » | Plenary Speaker | Nottingham, UK | |
| Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Evry, France | ||
| Thematic School on « Modelling complex biological systems in the context of genomics » | Poster * | Evry, France | ||
| EC Synthetic Biology Workshop: from science to governance | Invited Speaker | Brussels, Belgium | ||
| EC-US Task Force on Biotechnology Research Workshop on Standards in Synthetic Biology | Invited Speaker | Segovia, Spain | ||
| Séminaire « Technologies convergentes » | Invited Speaker | Paris, France | ||
| LANL Q-Bio conference | Speaker * | Santa Fe, NM, USA | ||
| Genopole Int’l Conf « Synthetic Biology: Bottom-up, Top-down and Cell-free approaches » | Organiser | Evry, France | ||
| CSynBI/LSE Workshop on Synthetic Biology and open source | Opening Speaker | London, UK | ||
| OECD Conference on Better Health through Bio-Medicine Innovative Governance | Keynote Speaker | Berlin, Germany | ||
| Ecole d’automne sur la toxicologie prédictive (CEA) | Invited Speaker | Giens, France | ||
| CNRS-MPG Workshop | Organiser | Leipzig, Germany | ||
| OECD Conference on Delivering Global Promise Through the Life Sciences | Invited Speaker | Paris, France | ||
| CNRS-MPG annual meeting | Organiser | Paris, France | ||
| IoSSB 4th Symposium at Imperial College London | Plenary Speaker | London, UK | ||
| Integrative Post-Genomics 2010 (IPG’10) | Program Committee | Lyon, France | ||
| ERASysBio Synthetic Biology Workshop | Co-Organiser | Bath, UK | ||
| 2011 | Aviesan ITMO BMSV Inaugural Symposium | Round-table Panelist | Paris, France | |
| Annual seminar of INRA CEPIA Department | Plenary Speaker | Anglet, France | ||
| Workshop of the EVOSYS European Project on Embodied Artificial Evolution | Invited Panelist | Mallorca, Spain | ||
| BioVision plenary on « Reconstructing Life: which Biology for the future? » (with Nobel awardees) | Plenary Speaker | Lyon, France | ||
| 6 Academies (US, UK, China) Conference on Synthetic Biology | Plenary Speaker | London, UK | ||
| Franco-American Symposium on « Synthetic Biology for learning and doing » | Chair & Speaker | Paris, France | ||
| Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Sophia Antipolis, France | ||
| C’Nano School | Invited Course | Porquerolles, France | ||
| Physics and Biological Systems Conference | Organiser | Orsay, France | ||
| International Conference on « Synthetic Biology at the interface of science and policy » | Invited Speaker | Ottawa, Canada | ||
| 2012 | Journée d’étude du CREA sur la biologie de synthèse | Organiser | Paris, France | |
| Thematic School on « Modelling complex biological systems in the context of genomics » | Chair | Evry, France | ||
| 6 Academies (US, UK, China) Conference on Synthetic Biology | Speaker | Washington DC, USA | ||
| Santorini Conference on Systems Biology and Translation | Plenary speaker | Thira, Greece | ||
| Colloquium IFRIS – Genopole « Science en Société » | Invited Speaker | Paris, France | ||
| Seminar « Maladies Infectieuses Émergentes » | Co-Chair | Paris, France | ||
| Colloquium Aviesan/Allenvi « Perspectives en biologie de synthèse » | Co-Organiser and co-Chair | Paris, France | ||
| 2013 | Conference on « Freedom in Biological Research » | Co-Organiser and co-Chair | Veyrier-du-Lac, France | |
| BioVision Prospective Session | Plenary Speaker | Lyon, France | ||
| Thematic School on « advances in Systems & Synthetic Biology » | Chair | La Colle sur Loup, France | ||
| School on « Epigenetics of Civilization Diseases » | Invited Speaker | Leipzig, Germany | ||
| Meeting of the European Synthetic Biology Centres | Chair | London, UK | ||
| C’Nano School | Invited Course | Porquerolles, France | ||
| Congress of the International Union of Physiological Sciences | Invited Speaker | Birmingham, UK | ||
| EU workshop on Synthetic Biology – IP, standard and regulatory issues | Invited Speaker | London, UK | ||
| France-UK bilateral Synthetic Biology Conference | Co-Organiser | London, UK | ||
| Colloque « Éthique des Technologies du Vivant » | Invited Speaker | Lyon, France | ||
| Synthetic Biology Symposium | Invited Speaker | Singapore, Singapore | ||
| Journée Région Aquitaine sur le Biologie de Synthèse | Opening Speaker | Bordeaux, France | ||
| Workshop « Synthetic Biology in action: from genetic engineering to engineered genetics » | Chair | Athens, Greece | ||
| 2014 | Colloque AgroParisTech sur la Biologie de Synthèse | Invited Speaker | Paris, France | |
| BioVision Prospective Session (3000 participants) | Plenary Speaker | Alexandria, Egypt | ||
| Thematic School on « advances in Systems & Synthetic Biology » | Chair | Évry, France | ||
| Meeting of the European Synthetic Biology Centres | Chair | Évry, France | ||
| Colloque « Figures de l’autotranscendance. Pour une Société de l’Ouroboros » | Invited Speaker | Cerisy, France | ||
| Flowers Conference on Synthetic Biology | Invited Speaker | London, UK | ||
| BioIntelligence Open Symposium | Chair | Paris, France | ||
| First ICTP Workshop on « Interdisciplinary Views on Chromosome Structure and Function » | Chair | Trieste, Italy | ||
| Santorini Conference on Systems Biology and Translation | Plenary Speaker | Thira, Greece | ||
| Synthetic Biology Congress | Invited Speaker | London, UK | ||
| Synthetic Biology Leadership Council | Invited Speaker | London, UK | ||
| 2015 | SMODIA conference | Speaker * | Valencia, Spain | |
| Synthetic Biology standards stakeholders meeting | Co-organiser | Valencia, Spain | ||
| Thematic School on « advances in Systems & Synthetic Biology » | Chair | Strasbourg, France | ||
| Synthetic Biology standardization meeting | Organiser | Paris, France | ||
| IHÉS « Cellular and Molecular Biotechnology » Conference | Chair | Bures, France | ||
| 2016 | Thematic School on « advances in Systems & Synthetic Biology » | Chair | Evry, France | |
| Alphy conference | Speaker * | Lyon, France | ||
| JeBIF JOBIM | Keynote Speaker | Lyon, France | ||
| Meeting « Synthetic Biology: from ideas to market » | Co-organiser & Speaker | Paris, France | ||
| Colloque « La biologie de synthèse modifie-t-elle notre conception du vivant ? » | Co-organiser | Paris, France | ||
| 2017 | Thematic School on « advances in Systems & Synthetic Biology » | Chair | Lyon, France | |
| « Genome Project—write » meeting | Consortium Member | New York City, USA | ||
| 2018 | Thematic School on « advances in Systems & Synthetic Biology » | Co-Chair | Evry, France | |
| Conférence « Chimie et biologie de synthèse : les applications » (1400 participants) | Opening Plenary Speaker | Paris, France | ||
| BioVision Prospective Session (2700 participants) | Plenary Speaker | Alexandria, Egypt | ||
| 2020 | Conférence « Biologie synthétique et Pharmaceutique » Biolabs & Servier | Opening Speaker | Paris, France | |
| Colloque « ADN, polymères et big data »; CNRS & Académie des technologies | Organiser & Speaker | Paris, France | ||
| 2022 | Conférence de lancement du PEPR molecularxiv, CNRS | Round table | Paris, France | |
| Forum Teratec Atelier A4 | Speaker | Palaiseau, France | ||
| Colloque IONIS iGEM | Speaker | Villejuif, France | ||
| 2024 | MoleculArXiv meeting | SAB member | Nice, France | |
| Séminaire du CNCB sur les recherches duales à risques, Académie des Sciences, SGDSN | Round table | Paris, France | ||
* co-author
François KEPES 
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