GECO Génomique Computationnelle et Evolutive

Minimal Cut Sets of a Consortium Model of P. aeruginosa and S. aureus Reveal New Cross-Feeding Interactions

Maxime Mahout, Sabine Peres

Metabolic Pathway Analysis 2023 .

2023

Acte de congrès

voir la publication

A General Framework for Enumerating Equivalence Classes of Solutions

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Algorithmica . 85 ( 10 ) : 3003-3023

DOI: 10.1007/s00453-023-01131-1

2023

Article dans une revue

voir la publication

Look4LTRs: A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony Garza, Emmanuelle Lerat, Hani Girgis

DOI: 10.1101/2023.07.28.551030

2023

Pré-publication

voir la publication

Phylogenomic analysis of protein‐coding genes resolves complex gall wasp relationships

Jack Hearn, Erik Gobbo, José Luis Nieves-Aldrey, Antoine Branca, James Nicholls, Georgios Koutsovoulos...

Systematic Entomology .

DOI: 10.1111/syen.12611

2023

Article dans une revue

voir la publication

How genomics can help biodiversity conservation

Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul Berg, Christoph Bleidorn...

Trends in Genetics .

DOI: 10.1016/j.tig.2023.01.005

2023

Article dans une revue

voir la publication

Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis : a model based exploration of the PRDM9 intra-genomic Red Queen

Alice Genestier, Laurent Duret, Nicolas Lartillot

PLoS Genetics . 20 ( 5 ) : e1011274

DOI: 10.1371/journal.pgen.1011274

2023

Article dans une revue

voir la publication

Compositionally Constrained Sites Drive Long-Branch Attraction

Lénárd L Szánthó, Nicolas Lartillot, Gergely J Szöllősi, Dominik Schrempf

Systematic Biology . 72 ( 4 ) : 767 - 780

DOI: 10.1093/sysbio/syad013

2023

Article dans une revue

voir la publication

Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?

Nicolas Lartillot

Systematic Biology . 72 : 616 - 638

DOI: 10.1093/sysbio/syad004

2023

Article dans une revue

voir la publication

Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

Thibault Latrille, Nicolas Rodrigue, Nicolas Lartillot

Proceedings of the National Academy of Sciences of the United States of America . 120 ( 11 ) : e2214977120

DOI: 10.1073/pnas.2214977120

2023

Article dans une revue

voir la publication

Deciphering evolutionary trajectories of lactate dehydrogenases provides new insights into allostery.

Adeline Robin, Céline Brochier-Armanet, Quentin Bertrand, Caroline Barette, Eric Girard, Dominique Madern

Molecular Biology and Evolution . msad223

DOI: 10.1093/molbev/msad223

2023

Article dans une revue

voir la publication

The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

Sophie Mathieu, Mélanie Touvrey, Laurent Poulet, Sophie Drouillard, Thirumalai Selvi Ulaganathan, Laure Ségurel...

DOI: 10.1101/2023.03.30.534863

2023

Pré-publication

voir la publication

Proposed mechanism for the selection of lactase persistence in childhood

Alexandre Fabre, Anne Fabre, Céline Bon, Paul Guerry, Laure Ségurel

BioEssays . 45 ( 7 )

DOI: 10.1002/bies.202200243

2023

Article dans une revue

voir la publication

Bradyrhizobium commune sp. nov., isolated from nodules of a wide range of native legumes across the Australian continent

Bénédicte Lafay, Elina Coquery, Phil M. Oger

International Journal of Systematic and Evolutionary Microbiology . 73 ( 7 ) : 005971

DOI: 10.1099/ijsem.0.005971

2023

Article dans une revue

voir la publication

Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

Blerina Sinaimeri, Laura Urbini, Marie-France Sagot, Catherine Matias

Systematic Biology . : syad058

DOI: 10.1093/sysbio/syad058

2023

Article dans une revue

voir la publication

Hybrid modelling to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Sabine Peres

BIOSTEC 2023 .

2023

Acte de congrès

voir la publication

Population designations in biomedical research: limitations and perspectives

Caroline Gombault, Guillaume Grenet, Laure Ségurel, Laurent Duret, François Gueyffier, Pascal Cathébras...

HLA: Immune Response Genetics . 101 ( 1 ) : 3-15

DOI: 10.1111/tan.14852

2023

Article dans une revue

voir la publication

ICEscreen: a valuable tool for automatic detection of ICEs and IMEs in Firmicutes

Nathalie N. Leblond-Bourget, Julie Lao, Sophie Payot, Thomas Lacroix, Gérard Guédon, Charles Coluzzi...

Réunion du GDR3546 Eléments transposables .

2022

Acte de congrès

voir la publication

ICEscreen: a tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures

Julie Lao, Thomas Lacroix, Gérard Guédon, Charles Coluzzi, Sophie Payot, Nathalie Leblond-Bourget...

NAR Genomics and Bioinformatics . 4 ( 4 ) : lqac079

DOI: 10.1093/nargab/lqac079

2022

Article dans une revue

voir la publication

NAR Breakthrough Article Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

Manuel Ares-Arroyo, Charles Coluzzi, Eduardo P.C. Rocha

Nucleic Acids Research . 51 ( 7 ) : 3001–3016

DOI: 10.1093/nar/gkac1079

2022

Article dans une revue

voir la publication

Streptococcus suis as a reservoir of antibiotic resistance genes carried by Mobile Genetic Elements transferring by conjugation

Sophie Payot, Virginie Libante, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon...

5th International Caparica Congress in Antibiotic Resistance (IC2AR 2022) .

2022

Acte de congrès

voir la publication

Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids

Charles Coluzzi, Maria Pilar Garcillán-Barcia, Fernando de la Cruz, Eduardo P.C. Rocha

Molecular Biology and Evolution . 39 ( 6 ) : msac115

DOI: 10.1093/molbev/msac115

2022

Article dans une revue

voir la publication

Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium

Helit Cohen, Claire Hoede, Felix Scharte, Charles Coluzzi, Emiliano Cohen, Inna Shomer...

PLoS Pathogens . 18 ( 4 ) : 35 p.

DOI: 10.1371/journal.ppat.1010425

2022

Article dans une revue

voir la publication

ICEscreen

Hélène Chiapello, Charles Coluzzi, Nathalie N. Leblond-Bourget, Thomas Lacroix, Julie Lao, Gérard Guédon

2022

Logiciel

voir la publication

The assembly of the rice weevil Sitophilus oryzae is dominated by transposable elements and shades light on the evolution of endosymbiosis in a major crop pest.

Nicolas Parisot, Carlos Vargas-Chávez, Clément Goubert, Patrice Baa-Puyoulet, Severine Balmand, Louis Beranger...

Arthropod Genomics Symposium 2022 .

2022

Acte de congrès

voir la publication

Geographic origin and social status of the Gallic warriors from Ribemont‐sur‐Ancre (France) studied through isotope systematics of bone remains

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Gilles Prilaux, Jeremy Martin, Romain Amiot...

International Journal of Osteoarchaeology .

DOI: 10.1002/oa.3172

2022

Article dans une revue

voir la publication

Modelling the spatiotemporal spread of beneficial alleles using ancient genomes

Rasa Muktupavela, Martin Petr, Laure L. Segurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo

DOI: 10.1101/2021.07.21.453231

2022

Pré-publication

voir la publication

Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan)

Leonardo Arias, Nicholas Q Emlen, Sietze Norder, Nora Julmi, Magdalena Lemus Serrano, Thiago Chacon...

Interface Focus . 13

DOI: 10.1098/rsfs.2022.0056

2022

Article dans une revue

voir la publication

Ethical challenges in genetic research among Philippine Indigenous Peoples: Insights from fieldwork in Zamboanga and the Sulu Archipelago

Jae Joseph Russell B Rodriguez, John Meldwin D Cuales, Michael James B Herrera, Louward Allen M Zubiri, Richard N. Muallil, Altan I. Ishmael...

Frontiers in Genetics . 13 : 901515

DOI: 10.3389/fgene.2022.901515

2022

Article dans une revue

voir la publication

The transmission of human mitochondrial DNA in four‐generation pedigrees

Qi Liu, Muhammad Faaras Iqbal, Tahir Yaqub, Sehrish Firyal, Yiqiang Zhao, Mark Stoneking...

Human Mutation . 43 : 1259-1267

DOI: 10.1002/humu.24390

2022

Article dans une revue

voir la publication

The social lives of isolates (and small language families): the case of the Northwest Amazon

Rik van Gijn, Sietze Norder, Leonardo Arias, Nicholas Q Emlen, Matheus C B C Azevedo, Allison Caine...

Interface Focus . 13 ( 1 ) : 20220054

DOI: 10.1098/rsfs.2022.0054

2022

Article dans une revue

voir la publication

GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Minimal Cut Sets of a Consortium Model of P. aeruginosa and S. aureus Reveal New Cross-Feeding Interactions

A General Framework for Enumerating Equivalence Classes of Solutions

Look4LTRs: A Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Phylogenomic analysis of protein‐coding genes resolves complex gall wasp relationships

How genomics can help biodiversity conservation

Bridging the gap between the evolutionary dynamics and the molecular mechanisms of meiosis : a model based exploration of the PRDM9 intra-genomic Red Queen

Compositionally Constrained Sites Drive Long-Branch Attraction

Identifying the Best Approximating Model in Bayesian Phylogenetics: Bayes Factors, Cross-Validation or wAIC?

Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

Deciphering evolutionary trajectories of lactate dehydrogenases provides new insights into allostery.

The porphyran degradation system of the human gut microbiota is complete, phylogenetically diverse and geographically structured across Asian populations

Proposed mechanism for the selection of lactase persistence in childhood

Bradyrhizobium commune sp. nov., isolated from nodules of a wide range of native legumes across the Australian continent

Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

Hybrid modelling to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling

Population designations in biomedical research: limitations and perspectives

ICEscreen: a valuable tool for automatic detection of ICEs and IMEs in Firmicutes

ICEscreen: a tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures

NAR Breakthrough Article Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

Streptococcus suis as a reservoir of antibiotic resistance genes carried by Mobile Genetic Elements transferring by conjugation

Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids

Intracellular Salmonella Paratyphi A is motile and differs in the expression of flagella-chemotaxis, SPI-1 and carbon utilization pathways in comparison to intracellular S. Typhimurium

ICEscreen

The assembly of the rice weevil Sitophilus oryzae is dominated by transposable elements and shades light on the evolution of endosymbiosis in a major crop pest.

Geographic origin and social status of the Gallic warriors from Ribemont‐sur‐Ancre (France) studied through isotope systematics of bone remains

Modelling the spatiotemporal spread of beneficial alleles using ancient genomes

Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan)

Ethical challenges in genetic research among Philippine Indigenous Peoples: Insights from fieldwork in Zamboanga and the Sulu Archipelago

The transmission of human mitochondrial DNA in four‐generation pedigrees

The social lives of isolates (and small language families): the case of the Northwest Amazon