Clémence Frioux

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Ph.D student, Inria

Dyliss team, Irisa / Inria Rennes-Bretagne Atlantique,
Campus de Beaulieu, 35042 Rennes Cedex, France.
Office: A102 (Orange Floor)
Tel: +33 (0) 2 99 84 73 90
Fax: +33 (0) 2 99 84 71 71
Research GateLinkedingGithub


Ph.D  thesis (2015 present): Using preferences in Answer Set Programming to decipher interaction within the species of an ecosystem at the genomic scale Supervisor: Anne Siegel

I focus my research on topological or hybrid modeling of metabolism based on Answer Set Programming and the solving of combinatorial problems. I contributed to the meneco project, a tool dedicated to gap-fill models by selecting a minimal number of reactions from a database, in order to topologically produce compounds of interest. I then collaborated to the creation of a hybrid method for metabolism gap-filling, enabling to optimize not only the topological producibility of metabolites, but also the reaction of interest with the Flux Balance Analysis framework. I now focus on the prediction of interactions within communities.


Journal articles

2018 – Aite* M, Chevallier* M, Frioux* C, Trottier* C, et al. – Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models, PLoS Computational Biology, 2018, 14(5): e1006146

2017 – Laniau J, Frioux C, Nicolas J, Cortés MP, Got J, Trottier C, Eveillard D, Siegel A Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks, PeerJ 5:e3860

2017 Prigent S, Frioux C, Dittami SM, Thiele S, Larhlimi A, Collet G, Gutknecht F, Got J, Eveillard D, Bourdon J, Plewniak F, Tonon T, Siegel A Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, PLoS Computational Biology, 2017, 13(1), pp.32. <10.1371/journal.pcbi.1005276> hal-01449100

2014 Haikarainen T, Frioux C, Zhnag LQ, Li DC, Papageorgiou AC. Crystal structure and biochemical characterization of a manganese superoxide dismutase from Chaetomium thermophilum - Biochimica Et Biophysica Acta, Vol. 1844, Number 2. February 2014. doi: 10.1016/j.bbapap.2013.11.014

International conferences with proceedings

2017 Frioux C, Schaub T, Schellhorn S, Siegel A and Wanko P Hybrid Metabolic Network Completion. In Balduccini,M., Janhunen,T. (eds), Logic Programming and Nonmonotonic Reasoning: 14th International Conference, LPNMR 2017, Espoo, Finland, July 3-6, 2017, Proceedings. Springer International Publishing, Cham, pp. 308321. Best student paper of the Conference

International conferences

2015 Dittami SM, Gobet A, Duboscq-Bidot L, Perennou M, Corre E, Frioux C, et al. Microbiomes impact algal acclimation: the example of a freshwater strain of Ectocarpus. European Journal of Phycology. 50, 44–44. August 2015

National conferences

2016 Chevallier M, Aite M, Got J, Collet G, Loira N, Cortes MP, Frioux C, Laniau J, Trottier C, Maas A, Siegel A Handling the heterogeneity of genomic and metabolomic networks data within flexible workflows with the PADMet Toolbox Journées Ouvertes de Biologie Informatique et Mathématiques, JOBIM 2016. June 2016

International Collaboration

University of Potsdam Institute for Computer Science, Knowledge Processing and Information System Group October to December, 2016. Development of hybrid LP-ASP modeling of metabolic networks. Joint work with Sebastian Schellhorn, Philipp Wanko and supervised by Torsten Schaub.

Scientific Communication


2017 Poster at International Conference on Holobionts April 19th-21st 2017. Topology to elucidate the respective roles of species in a symbiotic community.

2016 Poster at École Jeunes Chercheurs CNRS 3ème École thématique de modélisation formelle des réseaux de régulation biologique "Bioregul". Combinatorial gap-filling for genome-scale metabolic networks using taxonomy and pathway information.

Poster Bioregul 2016





2017 – 4ème Colloque du GDR de Génomique Environnementale Marseille, September 13-15th 2017. Toward the study of metabolic functions in algal-bacterial holobionts

2017 3ème édition des Journées annuelles du GDR BIOSS Montpellier, March 13-14th 2017. Hybrid gap-filling to reconcile qualitative and quantitative abstractions of metabolism

Scientific Popularisation

2016 Very Short Films Festival "Sciences en Court[s]", Une petite histoire de Symbiose(s), 2nd jury prize

2016 Short Films Festival "Bioinfuse" JOBIM 2016, Une petite histoire de Symbiose(s)


2017 Claire Lippold (Master 1 Bio-Informatique et Génomique, Université de Rennes 1) Exploration and characterization of the microbiome associated to Ectocarpus subulatus str. BFT.


2017/2018 École Nationale de la Statistique et de l'Analyse de l'Information (ENSAI)

2016/2017 University of Rennes 1

  • Bureautique 12h
  • Programmation Scientifique (Python) 20h