2023
Journal articles
Jiménez, N. E., Acuña, V., Cortés, M. P., Eveillard, D., and Maass, A. E. (2023). Unveiling abundance-dependent metabolic phenotypes of microbial communities. mSystems, e00492-23. https://doi.org/10.1128/msystems.00492-23
Belcour, A., Got, J., Aite, M., Delage, L., Collén, J., Frioux, C., Leblanc, C., Dittami, S. M., Blanquart, S., Markov, G. V., and Siegel, A. (2023). Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe. Genome Research. https://doi.org/10.1101/gr.277056.122
Frioux, C., Ansorge, R., Özkurt, E., Nedjad, C. G., Fritscher, J., Quince, C., Waszak, S. M., and Hildebrand, F. (2023). Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host & Microbe. https://doi.org/10.1016/j.chom.2023.05.024
2022
Journal articles
Preprints and submitted articles
Arnaud Belcour, Baptiste Ruiz, Clémence Frioux, Samuel Blanquart, Anne Siegel. EsMeCaTa: Estimating metabolic capabilities from taxonomic affiliations. 2022. ⟨hal-03697249⟩
Arnaud Belcour, Jeanne Got, Méziane Aite, Ludovic Delage, Jonas Collen, et al.. AuCoMe: inferring and comparing metabolisms across heterogeneous sets of annotated genomes. 2022. ⟨hal-03778267⟩
Thesis
Arnaud Belcour. Combining knowledge-based and sequence comparison approaches to elucidate metabolic functions, from pathways to communities. Univ. Rennes, 2022.
Book chapter
Clémence Frioux, Anne Siegel. Problèmes d’optimisation combinatoire pour l’étude du métabolisme. Approches symboliques de la modélisation et de l’analyse des systèmes biologiques, ISTE éditions, 2022, Encyclopédie Sciences, 9781789480290. ⟨10.51926/ISTE.9029.ch2⟩. ⟨hal-03885249⟩
Conferences
Maxime Lecomte, David James Sherman, Hélène Falentin, Clémence Frioux. Reasoning approaches for the characterization of cooperation and competition in large-scale microbial communities. Journée GT Bioss 2022, Nov 2022, Nantes, France. ⟨hal-03857781⟩
Posters
Coralie Muller, Arie Wortsman, Pablo Ugalde-Salas, Clémence Frioux, Simon Labarthe. Modelling the dynamics of Salmonella infection in the gut at the bacterial and the host level. Microbial communities: current approaches and open challenges, Oct 2022, Cambridge, United Kingdom. ⟨hal-03839405⟩
Maxime Lecomte, David James Sherman, Hélène Falentin, Clémence Frioux. Characterising competition and cooperation potentials in microbial communities using discrete models of metabolism. An exploratory analysis. JOBIM 2022 – JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES, Jul 2022, Rennes, France.
Coralie Muller, Arie Worstman, Pablo Ugalde-Salas, Clémence Frioux, Simon Labarthe. Modelling the dynamics of Salmonella infection in the gut at the bacterial and host levels. JOBIM 2022 – Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. ⟨hal-03839374⟩
2021
Journal articles
Falk Hildebrand, Toni Gossmann, Clémence Frioux, Ezgi Özkurt, Pernille Myers, et al.. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell host & microbe, 29(7), 1167–1176.e9, 2021. <10.1016/j.chom.2021.05.008>.
Preprints and submitted articles
A. Di Genova, G. Nardocci, R. Maldonado-Agurto, C. Hodar, C. Valdivieso, P. Morales, F. Gajardo, R. Marina, R. Gutiérrez, A. Orellana, V. Cambiazo, M. González, A. Glavic, M. Mendez, A. Maass, M. Allende, M. Montecino, Genome sequencing and transcriptomic analysis of the Atacama Desert fish Orestias ascotanensis reveals adaptation to high-altitude aquatic life. Submitted.
M. González, J. Maldonado, F. Maza, C. Hodar, M. P. Cortés, R. Palma, C. Andreani, A. Gaete, J. Vásquez-Dean, V. Acuña, M. C. Aguado, D. Mandakovic, M. Latorre, A. Orellana, R. A. Gutiérrez, M. Montecino, M. Allende, A. Maass, V. Cambiazo, Genomic analysis provides insights into the functional capacity of soil bacterial communities inhabiting an altitudinal gradient in the Atacama Desert. Submitted.
2020
Journal articles
Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife, eLife Sciences Publication, 2020, 9, ⟨10.1101/803056⟩. ⟨hal-02395024v2⟩
Dinka Mandakovic, Ángela Cintolesi, Jonathan Maldonado, Sebastián Mendoza, Méziane Aite, et al.. Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment. Scientific Reports, Nature Publishing Group, 2020, 10 (1), pp.1-12. ⟨10.1038/s41598-020-62130-8⟩. ⟨hal-02524471⟩
Clémence Frioux, Simon Dittami, Anne Siegel. Using automated reasoning to explore the metabolism of unconventional organisms: a first step to explore host–microbial interactions. Biochemical Society Transactions, Portland Press, 2020, 48 (3), pp.901-913. ⟨10.1042/BST20190667⟩. ⟨hal-02569935⟩
Dante Travisany, Eric Goles, Mauricio Latorre, María-Paz Cortés, Alejandro Maass, Generation and robustness of boolean networks to model Clostridium difficile infection. Natural Computing (19) 2020, 111-134. <10.1007/s11047-019-09730-0>.
Arnaud Belcour, Jean Girard, Méziane Aite, Ludovic Delage, Camille Trottier, et al.. Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift. iScience, Elsevier, 2020, 23 (2), pp.100849. ⟨10.1016/j.isci.2020.100849⟩. ⟨hal-01943880v2⟩
María-Paz Cortés, Vicente Acuña, Dante Travisany, Anne Siegel, Alejandro Maass and Mauricio Latorre. Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways. Front. Mol. Biosci. 6:155, 2020. <10.3389/fmolb.2019.00155>.
Conference papers
Nayat Sanchez-Pi, Luis Marti, André Abreu, Olivier Bernard, Colomban de Vargas, et al.. Artificial Intelligence, Machine Learning and Modeling for Understanding the Oceans and Climate Change. NeurIPS 2020 Workshop – Tackling Climate Change with Machine Learning, Dec 2020, Santiago / Virtual, Chile. ⟨hal-03138712⟩
