GECO Génomique Computationnelle et Evolutive

Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors

Emmanuelle Lerat, Nelly Burlet, Vincent Navratil, Camilles Noûs

DOI: 10.1101/2021.07.16.452652

2021

Pré-publication

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A new tool to cross and analyze TE and gene annotations

Emmanuelle Lerat

Peer Community In Genomics . : 100010

DOI: 10.24072/pci.genomics.100010

2021

Autre publication

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A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Nicolas Rodrigue, Thibault Latrille, Nicolas Lartillot

Molecular Biology and Evolution . 38 ( 3 ) : 1199-1208

DOI: 10.1093/molbev/msaa265

2021

Article dans une revue

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Universal probabilistic programming offers a powerful approach to statistical phylogenetics

Fredrik Ronquist, Jan Kudlicka, Viktor Senderov, Johannes Borgström, Nicolas Lartillot, Daniel Lundén...

Communications Biology . 4 ( 1 ) : 244

DOI: 10.1038/s42003-021-01753-7

2021

Article dans une revue

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Reconstructing the History of Variation in Effective Population Size along Phylogenies

Mathieu Brevet, Nicolas Lartillot

Genome Biology and Evolution . 13 ( 8 )

DOI: 10.1093/gbe/evab150

2021

Article dans une revue

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Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

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

WABI 2021 - 21st International Workshop on Algorithms in Bioinformatics . : 1-18

DOI: 10.4230/LIPIcs.WABI.2021.3

2021

Acte de congrès

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Climatic change and diet of the pre-Hispanic population of Gran Canaria (Canary Archipelago, Spain) during the Medieval Warm Period and Little Ice Age

Christophe Lécuyer, Jean Goedert, Johanne Klee, Thibault Clauzel, Pascale Richardin, François Fourel...

Journal of Archaeological Science . 128 : 105336

DOI: 10.1016/j.jas.2021.105336

2021

Article dans une revue

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Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

Virginie Libante, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon, Marcelo Gottschalk...

Pathogens . 9 ( 1 ) : 22

DOI: 10.3390/pathogens9010022

2020

Article dans une revue

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Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism

Maxime Mahout, Ross Carlson, Sabine Peres

Processes . 8 ( 12 ) : 1649

DOI: 10.3390/pr8121649

2020

Article dans une revue

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Ancient DNA from Guam and the peopling of the Pacific

Irina Pugach, Alexander Hübner, Hsiao-Chun Hung, Matthias Meyer, Mike Carson, Mark Stoneking

Proceedings of the National Academy of Sciences of the United States of America . 118 ( 1 ) : 1-12

DOI: 10.1073/pnas.2022112118

2020

Article dans une revue

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Expanding the Geographic Characterisation of Epstein–Barr Virus Variation through Gene-Based Approaches

Marco Telford, David Hughes, David Juan, Mark Stoneking, Arcadi Navarro, Gabriel Santpere

Microorganisms . 8 ( 11 ) : 1686

DOI: 10.3390/microorganisms8111686

2020

Article dans une revue

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Ancient DNA indicates human population shifts and admixture in northern and southern China

Melinda Yang, Xuechun Fan, Bo Sun, Chungyu Chen, Jianfeng Lang, Ying-Chin Ko...

Science . 369 ( 6501 ) : 282-288

DOI: 10.1126/science.aba0909

2020

Article dans une revue

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Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand

Wibhu Kutanan, Rasmi Shoocongdej, Metawee Srikummool, Alexander Hübner, Thanatip Suttipai, Suparat Srithawong...

European Journal of Human Genetics . 28 : 1563 - 1579

DOI: 10.1038/s41431-020-0693-x

2020

Article dans une revue

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Papuan mitochondrial genomes and the settlement of Sahul

Nicole Pedro, Nicolas Brucato, Verónica Fernandes, Mathilde André, Lauri Saag, William Pomat...

Journal of Human Genetics .

DOI: 10.1038/s10038-020-0781-3

2020

Article dans une revue

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The paternal and maternal genetic history of Vietnamese populations

Enrico Macholdt, Leonardo Arias, Nguyen Thuy Duong, Nguyen Dang Ton, Nguyen Van Phong, Roland Schröder...

European Journal of Human Genetics . 28 ( 5 ) : 636-645

DOI: 10.1038/s41431-019-0557-4

2020

Article dans une revue

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Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity

Dang Liu, Nguyen Thuy Duong, Nguyen Dang Ton, Nguyen van Phong, Brigitte Pakendorf, Nong van Hai...

Molecular Biology and Evolution . 37 ( 9 ) : 2503 - 2519

DOI: 10.1093/molbev/msaa099

2020

Article dans une revue

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Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F 1 hybrids

Carina Mugal, Mi Wang, Niclas Backström, David Wheatcroft, Murielle Ålund, Marie Sémon...

Genome Research . 30 ( 12 ) : 1727-1739

DOI: 10.1101/gr.254508.119

2020

Article dans une revue

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Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species

Carina Mugal, Verena Kutschera, Fidel Botero-Castro, Jochen Wolf, Ingemar Kaj

Molecular Biology and Evolution . 37 ( 1 ) : 260-279

DOI: 10.1093/molbev/msz203

2020

Article dans une revue

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Cancer and Alzheimer’s disease: intracellular pH scales the metabolic disorders

Laurent Schwartz, Sabine S. Peres, Mario Jolicoeur, Jorgelindo da Veiga Moreira

Biogerontology . 21 ( 6 ) : 683-694

DOI: 10.1007/s10522-020-09888-6

2020

Article dans une revue

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Thermodynamic Approaches in Flux Analysis

Sabine S. Peres, Vincent Fromion

Metabolic Flux Analysis in Eukaryotic Cells . : 359-367

DOI: 10.1007/978-1-0716-0159-4_17

2020

Chapitre d'ouvrage

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Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity

Dominik Schrempf, Nicolas Lartillot, Gergely Szöllősi

Molecular Biology and Evolution . 37 : 3616 - 3631

DOI: 10.1093/molbev/msaa145

2020

Article dans une revue

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Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA

Laure Ségurel, Perle Guarino-Vignon, Nina Marchi, Sophie Lafosse, Romain Laurent, Céline Bon...

PLoS Biology . 18 ( 6 ) : e3000742

DOI: 10.1371/journal.pbio.3000742

2020

Article dans une revue

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Response of the human gut and saliva microbiome to urbanization in cameroon

Ana Lokmer, Sophie Aflalo, Norbert N. Amougou, Sophie Lafosse, Alain Froment, Francis Ekwin Tabe...

Scientific Reports . 10 ( 1 )

DOI: 10.1038/s41598-020-59849-9

2020

Article dans une revue

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How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?

Marie Cariou, Hélène Henri, Sonia Martinez, Laurent Duret, Sylvain Charlat

Molecular Ecology Resources . 20 ( 5 ) : 1294-1298

DOI: 10.1111/1755-0998.13178

2020

Article dans une revue

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Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Natalia Sawka-Gądek, Alexey Potekhin, Deepankar Pratap Singh, Inessa Grevtseva, Olivier Arnaiz, Simon Penel...

Genome Biology and Evolution . ( evaa258 )

DOI: 10.1093/gbe/evaa258

2020

Article dans une revue

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Efficient hybrid de novo assembly of human genomes with WENGAN

Alex Di Genova, Elena Buena-Atienza, Stephan Ossowski, Marie-France Sagot

Nature Biotechnology . 39 : 422–430

DOI: 10.1038/s41587-020-00747-w

2020

Article dans une revue

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MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Ricardo Andrade, Mahdi Doostmohammadi, João Santos, Marie-France Sagot, Nuno P Mira, Susana Vinga

BMC Bioinformatics . 21 ( 1 ) : 1-13

DOI: 10.1186/s12859-020-3377-1

2020

Article dans une revue

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A Family of Tree-Based Generators for Bubbles in Directed Graphs

Vicente Acuña, Leandro Ishi Soares de Lima, Giuseppe F Italiano, Luca Pepè Sciarria, Marie-France Sagot, Blerina Sinaimeri

IWOCA 2020 - 31st International Workshop on Combinatorial Algorithms . 12126 : 17-29

DOI: 10.1007/978-3-030-48966-3_2

2020

Acte de congrès

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MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network

Taneli Pusa, Mariana G. Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela, Leen Stougie...

Bioinformatics . 36 ( 2 ) : 514-523

DOI: 10.1093/bioinformatics/btz584

2020

Article dans une revue

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Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells

Scheila Gabriele Mucha, Mariana G. Ferrarini, Carol Moraga, Alex Di Genova, Laurent Guyon, Florence Tardy...

Scientific Reports . 10 ( 13707 )

DOI: 10.1038/s41598-020-70040-y

2020

Article dans une revue

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Transposable element activity in the transcriptomic analysis of mouse pancreatic tumors

A new tool to cross and analyze TE and gene annotations

A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

Universal probabilistic programming offers a powerful approach to statistical phylogenetics

Reconstructing the History of Variation in Effective Population Size along Phylogenies

Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

Climatic change and diet of the pre-Hispanic population of Gran Canaria (Canary Archipelago, Spain) during the Medieval Warm Period and Little Ice Age

Chromosomal Conjugative and Mobilizable Elements in Streptococcus suis: Major Actors in the Spreading of Antimicrobial Resistance and Bacteriocin Synthesis Genes

Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism

Ancient DNA from Guam and the peopling of the Pacific

Expanding the Geographic Characterisation of Epstein–Barr Virus Variation through Gene-Based Approaches

Ancient DNA indicates human population shifts and admixture in northern and southern China

Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand

Papuan mitochondrial genomes and the settlement of Sahul

The paternal and maternal genetic history of Vietnamese populations

Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity

Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F 1 hybrids

Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species

Cancer and Alzheimer’s disease: intracellular pH scales the metabolic disorders

Thermodynamic Approaches in Flux Analysis

Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity

Why and when was lactase persistence selected for? Insights from Central Asian herders and ancient DNA

Response of the human gut and saliva microbiome to urbanization in cameroon

How consistent is RAD‐seq divergence with DNA‐barcode based clustering in insects?

Evolutionary plasticity of mating-type determination mechanisms in Paramecium aurelia sibling species

Efficient hybrid de novo assembly of human genomes with WENGAN

MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

A Family of Tree-Based Generators for Bubbles in Directed Graphs

MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network

Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells