GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 91 to 120 publications on 1198 in total

Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data.

Emeric Figuet, Marion Ballenghien, Nicolas Lartillot, Nicolas Galtier

Peer Community Journal . 1 : e42

DOI: 10.24072/pcjournal.42

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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

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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 )

DOI: 10.1038/s42003-021-01753-7

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Exploring protein space: From hydrolase to ligase by substitution

Nir Hecht, Caroline Monteil, Guy Perriere, Marina Vishkautzan, Eyal Gur

Molecular Biology and Evolution .

DOI: 10.1093/molbev/msaa215

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Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria

Caroline Monteil, Denis Grouzdev, Guy Perriere, Béatrice Alonso, Zoé Rouy, Stéphane Cruveiller...

The International Society of Microbiologial Ecology Journal .

DOI: 10.1038/s41396-020-0647-x

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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

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Influenza virus infection induces widespread alterations of host cell splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Navratil, Cécile Ligneau, Guillaume Fournier, Sandie Munier...

NAR Genomics and Bioinformatics . 2 ( 4 )

DOI: 10.1093/nargab/lqaa095

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The TERB1-TERB2-MAJIN complex of mouse meiotic telomeres dates back to the common ancestor of metazoans

Irene da Cruz, Celine Brochier-Armanet, Ricardo Benavente

BMC Evolutionary Biology . 20 ( 1 )

DOI: 10.1186/s12862-020-01612-9

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