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Carole Knibbe

Associate Professor in Computational Biology

My name is Carole Knibbe. I am an Associate Professor in Computational Biology at Université Claude Bernard Lyon 1, Lyon, France. I build mathematical and computational models of biological systems, with applications in molecular evolution, and, more recently, in lipid metabolism. I am a member of the LIRIS laboratory and of the Inria Beagle team.

I am involved in the Master program in Bioinformatics, and in the Bachelor and Master programs in Computer Science. I teach imperative programming, object-oriented programming, web programming, scientific methods for computer scientists, and bio-inspired computing.

On my free time, I write a blog on evidence-based information for parents.

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Contact


Address 1

INRIA Antenne Lyon la Doua
Bâtiment CEI-2
56, Boulevard Niels Bohr
CS 52132
69603 Villeurbanne
France

You can get there with the T1 tramway line, stop at IUT-Feyssine and walk to the CEI-2 building. Here is a map.


Phone 1
+33 4 72 43 75 02

Email 1
Replace every 8 by the appropriate letter to get my second email address:
carole.kni88e [X] inria.fr

Address 2

Université C. Bernard Lyon 1
LIRIS / Dept. Informatique
Bâtiment Nautibus
43 bd du 11 novembre 1918
69622 Villeurbanne cedex
France

You can get there with the T1 tramway line, stop at Université Lyon 1 and walk to the Nautibus building. Here is a map.


Phone 2
+33 4 72 43 16 35

Email 2
Replace every 8 by the appropriate letter to get my second email address:
carole.kni88e [X] liris.cnrs.fr



Publications

  • C. Rocabert, C. Knibbe, J. Consuegra, D. Schneider, G. Beslon. (2017). Beware Batch Culture: Seasonality and Niche Construction Predicted to Favor Bacterial Adaptive Diversification. PLoS Computational Biology, in press.
  • P. Biller, L. Gueguen, C. Knibbe, E. Tannier. (2016). Breaking good: accounting for fragility of genomic regions in rearrangement distance estimation. Genome Biology and Evolution, 8(5): 1427-1439.
  • P. Biller, C. Knibbe, G. Beslon, E. Tannier. (2016). Comparative genomics of artificial life. In L. Bienvenu and N. Jonoska (ed.), CiE 2016 (Computability in Europe), Paris, France, volume 9709 of Lecture Notes in Computer Science, pp. 35-44, Springer.
  • S. Fischer, S. Bernard, G. Beslon, C. Knibbe. (2014). A model for genome size evolution. Bulletin of Mathematical Biology 76(9):2249-91.[Full text]
  • B. Batut, C. Knibbe, G. Marais, V. Daubin. (2014). Reductive genome evolution at both ends of bacterial population size spectrum. Nature Reviews Microbiology 12(12) pp. 841-850. [Full text]
  • C. Knibbe, D.P. Parsons. (2014). What happened to my genes? Insights on gene family dynamics from digital genetics experiments. In ALIFE 14 (14th Intl. Conf. on the Synthesis and Simulation of Living Systems), Sayama, H. et al. (ed.) New York, NY. MIT Press, Cambridge, Massachusetts, pp. 33-40. [Full text]
  • B. Batut, D.P. Parsons, S. Fischer, G. Beslon, C. Knibbe. (2013). In silico experimental evolution: a tool to test evolutionary scenarios. In Eleventh Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics , Macha Nikolski, Yves Van de Peer (ed.), Lyon, France, BMC Bioinformatics 14 (S15): S11.
    [Full text]
  • G. Beslon, B. Batut, D. Parsons, D. Schneider, C. Knibbe. (2013). An alife game to teach evolution of antibiotic resistance. In European Conference on Artificial Life, Taormina. pp. 43-50. MIT Press.[Full text]
  • C. Knibbe. (2013). L'évolution expérimentale in silico. In Modéliser et simuler - Epistémologies et pratiques de la modélisation et de la simulation - Tome 1, edited by F. Varenne and M. Silberstein, Editions Matériologiques, pp. 581–610. [Full text]
  • T. Hindré, C. Knibbe, G. Beslon, D. Schneider. (2012). New insights into bacterial adaptation through in vivo and in silico experimental evolution. Nature Reviews Microbiology 10:352–365. [Full text]
  • D.P. Parsons, C. Knibbe, G. Beslon. (2012). The Paradoxical Effects of Allelic Recombination on Fitness. In Artificial Life XIII, East Lansing, Michigan (USA). [Full text]
  • D.P. Parsons, C. Knibbe, G. Beslon. (2011). Homologous and nonhomologous rearrangements: Interactions and effects on evolvability. In European Conference on Artificial Life (ECAL), T. Lenaerts, M. Giacobini, H. Bersini, P. Bourgine, M. Dorigo, R. Doursat ed. Paris. pp. 622-629. MIT Press. [Full text]
  • C. Knibbe, D.P. Parsons, G. Beslon. (2011). Parsimonious modeling of scaling laws in genomes and transcriptomes. In European Conference on Artificial Life (ECAL), T. Lenaerts, M. Giacobini, H. Bersini, P. Bourgine, M. Dorigo, R. Doursat ed. Paris. pp. 414-415. MIT Press. [Full text]
  • G. Beslon, D. P. Parsons, Y. Sanchez-Dehesa, J.-M. Pena, C. Knibbe. (2010). Scaling Laws in bacterial genomes: A side-effect of selection of mutational robustness? Biosystems 102: 32–40.[Full text]
  • D. P. Parsons, C. Knibbe, G. Beslon. (2010). Importance of the rearrangement rates on the organization of transcription. In Artificial Life XII, MIT Press, pp. 479–486. [ Full text ]
  • G.Beslon, C. Knibbe. (2010). Petits bricolages en évolution. In Des mondes bricolés? Arts et sciences à l'épreuve de la notion de bricolage, edited by F. Odin and C. Thuderoz, Presses Polytechniques et Universitaires Romandes.[Full text]
  • C. Knibbe, J.M. Fayard, G. Beslon. (2008). The Topology of the Protein Network Influences the Dynamics of Gene Order : From Systems Biology to a Systemic Understanding of Evolution. Artificial Life 14(1):149–156.[ Full text]
  • C. Knibbe, A. Coulon, O. Mazet, J.-M. Fayard and G. Beslon (2007). A long-term Evolutionary Pressure on the Amount of Non-coding DNA. Molecular Biology and Evolution, 24(10):2344–2353.[Full text]
  • C. Knibbe, O. Mazet, F. Chaudier, J.-M. Fayard and G. Beslon (2007). Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences. Journal of Theoretical Biology, 244(4): 621–630. [Full text]
  • C. Knibbe (2006). Structuration des génomes par sélection indirecte de la variabilité mutationnelle : une approche de modélisation et de simulation. Doctoral thesis, 174 pages (in French). [Full text]
  • C. Knibbe, G. Beslon, V. Lefort, F. Chaudier and J.-M. Fayard (2005). Self-adaptation of genome size in artificial organisms. In Proceedings of ECAL 2005 (European Conference on Artificial Life), volume 3630 of Lecture Notes in Artificial Intelligence, Springer, pp. 423-432.[Full text]