GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 151 to 180 publications on 1308 in total

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 ) : 244

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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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

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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

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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

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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

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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

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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

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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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