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Publications
GEM Team's publications
HAL publications access
Journal articles
Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria
Alejandro Couce, Larissa Viraphong Caudwell, Christoph Feinauer, Thomas Hindré, Jean-Paul Feugeas, Martin Weigt, Richard E. Lenski, Dominique Schneider, Olivier Tenaillon
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (43), pp.E9026 - E9035. ⟨10.1073/pnas.1705887114⟩. ⟨hal-01653591⟩
Conference papers
Environmental seasonality drives digital populations towards stable cross-feeding
Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon
European Conference on Artificial Life (ECAL), Sep 2017, Villeurbanne, France. ⟨hal-01569093⟩
Book sections
Modeling Bacterial DNA: Simulation of Self-avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix
Thibaut Lepage, Ivan Junier
The Bacterial Nucleoid, 2017. ⟨hal-01655027⟩
Journal articles
Genetic Basis of Exploiting Ecological Opportunity During the Long-Term Diversification of a Bacterial Population
Jessika Consuegra, Jessica Plucain, Joël Gaffé, Thomas Hindré, Dominique Schneider
Journal of Molecular Evolution, 2017, 85 (1-2), pp.26 - 36. ⟨10.1007/s00239-017-9802-z⟩. ⟨hal-01653588⟩
Journal articles
The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ
Laurent Loiseau, Cameron Fyfe, Laurent Aussel, Mahmoud Hajj Chehade, Sara B. Hernández, Bruno Faivre, Djemel Hamdane, Caroline Mellot-Draznieks, Bérengère Rascalou, Ludovic Pelosi, Christophe Velours, David Cornu, Murielle Lombard, Josep Casadesús, Fabien Pierrel, Marc Fontecave, Frédéric Barras
Journal of Biological Chemistry, 2017, 292 (28), pp.11937 - 11950. ⟨10.1074/jbc.M117.789164⟩. ⟨hal-01615493⟩
Journal articles
Isee-resistance : using in silico experimental evolution to sensitize providers on antibiotic resistance
Guillaume Beslon, Dominique Schneider
Antimicrobial Resistance and Infection Control, 2017, Abstracts from the 4th International Conference on Prevention & Infection Control (ICPIC 2017), 6(Suppl 3) (52), pp.2. ⟨hal-01569262⟩
Journal articles
Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification
Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon
PLoS Computational Biology, 2017, 13 (3), e1005459 (32 p.). ⟨10.1371/journal.pcbi.1005459.s006⟩. ⟨hal-01508751⟩
Journal articles
The COQ2 genotype predicts the severity of coenzyme Q 10 deficiency
Maria Andrea Desbats, Valeria Morbidoni, Micol Silic-Benussi, Mara Doimo, Vincenzo Ciminale, Matteo Cassina, Sabrina Sacconi, Michio Hirano, Giuseppe Basso, Fabien Pierrel, Placido Navas, Leonardo Salviati, Eva Trevisson
Human Molecular Genetics, 2017, 25 (19), pp.4256 - 4265. ⟨10.1093/hmg/ddw257⟩. ⟨hal-01635280⟩
Journal articles
Impact of Chemical Analogs of 4-Hydroxybenzoic Acid on Coenzyme Q Biosynthesis: From Inhibition to Bypass of Coenzyme Q Deficiency
Fabien Pierrel
Frontiers in Physiology, 2017, 87, pp.80 - 80. ⟨10.3389/fphys.2017.00436⟩. ⟨hal-01583835⟩
Theses
Ecological and molecular bases of adaptive diversification in Escherichia coli
Jessika Consuegra Bonilla
Microbiology and Parasitology. Université Grenoble Alpes, 2016. English. ⟨NNT : 2016GREAV090⟩. ⟨tel-01626007⟩
Journal articles
Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria
Jessica Plucain, Antonia Suau, Stéphane Cruveiller, Claudine Médigue, Dominique Schneider, Mickael Le Gac
BMC Evolutionary Biology, 2016, 16 (1), ⟨10.1186/s12862-016-0662-8⟩. ⟨hal-01653387⟩
Reports
EvoEvo Deliverable 6.8
Guillaume Beslon, Jonas Abernot, Santiago F. Elena, Dominique Schneider, Paulien Hogeweg, Susan Stepney, Christophe Rigotti
Final report. [Research Report] INRIA Grenoble - Rhône-Alpes. 2016. ⟨hal-01577187⟩
Patents
Réacteur intestinal implantable
Philippe Cinquin, Dominique Schneider, Max Maurin, Donald K Martin, Sarra El Ichi, Abdelkader Zebda, Jean-Pierre Alcaraz, Fabian Reche, Patrick Tuvignon
France, Patent n° : FR3034307. 2016. ⟨hal-02010289⟩
Reports
EvoEvo Deliverable 1.5
Dominique Schneider, Guillaume Beslon, José-Luis Carrasco, Santiago F. Elena, Otmane Lamrabet, A. Willemsen
: Analysis of evolvability (part 2). [Research Report] INRIA Grenoble - Rhône-Alpes. 2016. ⟨hal-01577130⟩
Reports
EvoEvo Deliverable 1.6
Dominique Schneider, Guillaume Beslon, Santiago F. Elena, Otmane Lamrabet
: Analysis of phenotypic innovation (part 2). [Research Report] INRIA Grenoble - Rhône-Alpes. 2016. ⟨hal-01577131⟩
Journal articles
Mechanistic Details of Early Steps in Coenzyme Q Biosynthesis Pathway in Yeast
Laurie-Anne Payet, Mélanie Leroux, John C. Willison, Akio Kihara, Ludovic Pelosi, Fabien Pierrel
Cell Chemical Biology, 2016, 23 (10), pp.1241 - 1250. ⟨10.1016/j.chembiol.2016.08.008⟩. ⟨hal-01424510⟩
Conference papers
In Silico Experimental Evolution Highlights the Influence of Environmental Seasonality on Bacterial Diversification
Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon
2nd EvoEvo Workshop, satellite workshop of CCS2016, Sep 2016, Amsterdam, Netherlands. ⟨hal-01375677⟩
Journal articles
Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions
Ludovic Pelosi, Anne-Lise Ducluzeau, Laurent Loiseau, Frédéric Barras, Dominique Schneider, Ivan Junier, Fabien Pierrel
mSystems, 2016, 1 (4), pp.00091-16. ⟨10.1128/mSystems.00091-16⟩. ⟨hal-01424513⟩
Journal articles
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.
Tobias Grosskopf, Jessica Consuegra, Joël Gaffé, John Willison, Richard E Lenski, Orkun S. Soyer, Dominique Schneider
BMC Evolutionary Biology, 2016, 16 (1), pp.163. ⟨10.1186/s12862-016-0733-x⟩. ⟨hal-01360095⟩
Journal articles
Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
Jonathan a. Stefely, Floriana Licitra, Leila Laredj, Andrew g. Reidenbach, Zachary a. Kemmerer, Anais Grangeray, Tiphaine Jaeg-Ehret, Catherine e. Minogue, Arne Ulbrich, Paul d. Hutchins, Emily m. Wilkerson, Zheng Ruan, Deniz Aydin, Alexander s. Hebert, Xiao Guo, Elyse c. Freiberger, Laurence Reutenauer, Adam Jochem, Maya Chergova, Isabel e. Johnson, Danielle c. Lohman, Matthew j.P. Rush, Nicholas w. Kwiecien, Pankaj k. Singh, Anna i. Schlagowski, Brendan j. Floyd, Ulrika Forsman, Pavel j. Sindelar, Michael s. Westphall, Fabien Pierrel, Joffrey Zoll, Matteo Dal peraro, Natarajan Kannan, Craig a. Bingman, Joshua j. Coon, Philippe Isope, Hélène Puccio, David j. Pagliarini
Molecular Cell, 2016, 63 (4), pp.608 - 620. ⟨10.1016/j.molcel.2016.06.030⟩. ⟨hal-01424495⟩
HAL publications access
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