Selected publications
- 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.
- 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.
- 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., Dale, R., Hou, C., Képès, F. and Dean, A. (2012). CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus. Nucleic Acids Res. 40, 7718-27.
- 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.
- Junier, I., Hérisson, J., and Képès, F. (2010). Efficient detection of periodic patterns within small datasets. Algorithms for Molecular Biology 5, 31.
- Manceny, M., Aiguier, M., Le Gall, P., Hérisson, J., Junier, I., and Képès, F. (2009). "Spatial Information to Restrict the Dynamics of Genetic Regulatory Networks" - In BICoB 2009 - International Conference on BioInformatics and Computational Biology, LNBI 5462, 270-281.
- 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.
- Yartseva, A., Klaudel, H., Devillers, R. and Képès, F. (2007). Incremental and unifying modelling formalism for biological interaction networks. BMC Bioinformatics 8:433.
- 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.
- Mercier, G., Berthault, N., Touleimat, N., Képès, F., Fourel, G., Gilson, E. and Dutreix, M. (2005). A haploid-specific transcriptional response to irradiation in Saccharomyces cerevisiae. Nucleic Acids Res. 33, 6635-43.
- 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.
- Guelzim, N., Bottani, S., Bourgine, P. and Képès, F. (2002). Topological and causal structure of the yeast transcriptional regulatory network. Nature Genetics 31, 60-63.
All publications
ISI Web of Science (log in first !)
Conferences / meetings since 2005
| Year | Conference | Role | Location | ||||
| 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 | Organizer & 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" | Organizer | 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 | 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" | Organizer | 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 | Organizer | 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 | Organizer | 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 | Organizer & Conference | Turin, Italy | |||||
| CNRS-MPG joint meeting on Systems Biology | Organizer & 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 | Organizer | 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" | Organizer & Conference * | Turin, Italy | |||||
| Colloque "Biologie systémique et synthétique" du PRES UniverSud Paris "Approches quantitatives de la complexité biologique" | Organizer | Orsay, France | |||||
| Think tank on "Statistical Semantics of Genomes: from sequence to function" | Organizer | 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 | Organizer | 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 | Organizer & Course | Trieste, Italy | |||||
| Gennetec - ICTP International Workshop | Organizer | Trieste, Italy | |||||
| CNRS-MPG Workshop "Experimental data integration within genome-scale metabolic models" | Organizer | 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 | Organizer | 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" | Organizer | 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 | Organizer | Leipzig, Germany | |||||
| OECD Conference on Delivering Global Promise Through the Life Sciences | Invited speaker | Paris, France | |||||
| CNRS-MPG annual meeting | Organizer | 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-Organizer | 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 | |||||
| Physics and Biological Systems Conference | Organizer | Orsay, France | |||||
| International Conference on "Synthetic Biology at the interface of science and policy" | Speaker | Ottawa, Canada | |||||
| 2012 | Journée d'étude du CREA sur la biologie de synthèse | Organizer | 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" | Speaker | Paris, France | |||||
| Séminaire "Maladies Infectieuses Émergentes" | Co-Chair | Paris, France | |||||
| Colloquium Aviesan/Allenvi "Perspectives en biologie de synthèse" | Co-Organizer and co-Chair | Paris, France | |||||
| 2013 | Conference on "Freedom in Biological Research" | Co-Organizer 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" | Speaker | Leipzig, Germany | |||||
| Meeting of the European Synthetic Biology Centres | Chair | London, UK | |||||
| Congress of the International Union of Physiological Sciences | Speaker | Birmingham, UK | |||||
| Interdisciplinary Workshop on Synthetic Biology | Chair | Athens, Greece | |||||
| * | Co-author | ||||||