GECO Génomique Computationnelle et Evolutive

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

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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

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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

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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

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

Sabine Peres

BIOSTEC 2023 .

2023

Acte de congrès

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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

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Self-compassion and savouring buffer the impact of the first year of the COVID-19 on PhD students' mental health

Marine Paucsik, Christophe Leys, Gabriel Marais, Céline Baeyens, Rebecca Shankland

Stress and Health .

DOI: 10.1002/smi.3142

2022

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Dosage compensation evolution in plants: theories, controversies and mechanisms

Aline Muyle, Gabriel Ab Marais, Václav Bačovský, Roman Hobza, Thomas Lenormand

Philosophical Transactions of the Royal Society B: Biological Sciences . 377 ( 1850 ) : 20210222

DOI: 10.1098/rstb.2021.0222

2022

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MacSyFinder v2: An improved search engine to model and identify molecular systems in genomes

Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo Rocha, Sophie Abby

JOBIM .

2022

Poster

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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

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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

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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

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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

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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

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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

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ICEscreen

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

2022

Logiciel

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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

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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

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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

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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

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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

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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

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Assessing Human Genome-wide Variation in the Massim Region of Papua New Guinea and Implications for the Kula Trading Tradition

Dang Liu, Benjamin M Peter, Wulf Schiefenhövel, Manfred Kayser, Mark Stoneking

Molecular Biology and Evolution . 39

DOI: 10.1093/molbev/msac165

2022

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Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Sandra Oliveira, Kathrin Nägele, Selina Carlhoff, Irina Pugach, Toetik Koesbardiati, Alexander Hübner...

Nature Ecology & Evolution . 6 : 1024 - 1034

DOI: 10.1038/s41559-022-01775-2

2022

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A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Rebekka Müller, Ingemar Kaj, Carina Mugal

Genome Biology and Evolution . 14 ( 5 )

DOI: 10.1093/gbe/evac058

2022

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Hydrogen isotope measurements of bone and dental tissues from archaeological human and animal samples and their use as climatic and diet proxies

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Journal of Archaeological Science . 147 : 105676

DOI: 10.1016/j.jas.2022.105676

2022

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Climate conditions and dietary practices during the Second Iron Age studied through the multi-isotope analysis of bones and teeth from individuals of Thézy-Glimont, Picardie, France

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Archaeological and Anthropological Sciences . 14 ( 4 ) : 61

DOI: 10.1007/s12520-022-01534-1

2022

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Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

Rasa Muktupavela, Martin Petr, Laure Ségurel, Thorfinn Korneliussen, John Novembre, Fernando Racimo

eLife . 11

DOI: 10.7554/eLife.73767

2022

Article dans une revue

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Polynomial Delay Algorithm for Minimal Chordal Completions

Caroline Brosse, Vincent Limouzy, Arnaud Mary

49th International Colloquium on Automata, Languages, and Programming (ICALP) .

DOI: 10.4230/LIPIcs.ICALP.2022.33

2022

Acte de congrès

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Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex

Fatimat Almentina Ramos Shidi, Audric Cologne, Marion Delous, Alicia Besson, Audrey Putoux, Anne-Louise Leutenegger...

Nucleic Acids Research .

DOI: 10.1093/nar/gkac1182

2022

Article dans une revue

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

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

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

Self-compassion and savouring buffer the impact of the first year of the COVID-19 on PhD students' mental health

Dosage compensation evolution in plants: theories, controversies and mechanisms

MacSyFinder v2: An improved search engine to model and identify molecular systems in genomes

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.

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

Assessing Human Genome-wide Variation in the Massim Region of Papua New Guinea and Implications for the Kula Trading Tradition

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

A Nearly Neutral Model of Molecular Signatures of Natural Selection after Change in Population Size

Hydrogen isotope measurements of bone and dental tissues from archaeological human and animal samples and their use as climatic and diet proxies

Climate conditions and dietary practices during the Second Iron Age studied through the multi-isotope analysis of bones and teeth from individuals of Thézy-Glimont, Picardie, France

Modeling the spatiotemporal spread of beneficial alleles using ancient genomes

Polynomial Delay Algorithm for Minimal Chordal Completions

Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex