GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 1 to 30 publications on 1243 in total

GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes

Florian Bénitière, Laurent Duret, Anamaria Necsulea

NAR Genomics and Bioinformatics . 6 ( 2 ) : lqae064

DOI: 10.1093/nargab/lqae064

Journal article

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Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections

Maxime Mahout, Ross Carlson, Laurent Simon, Sabine Peres

npj Systems Biology and Applications . 10 ( 1 ) : 34

DOI: 10.1038/s41540-024-00360-6

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Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids

Jesper Boman, Anna Qvarnström, Carina Mugal

BMC Biology . 22 ( 1 ) : 124

DOI: 10.1186/s12915-024-01920-2

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High prevalence of PRDM9-independent recombination hotspots in placental mammals

Julien Joseph, Djivan Prentout, Alexandre Laverré, Théo Tricou, Laurent Duret

Proceedings of the National Academy of Sciences of the United States of America . 121 ( 23 ) : e2401973121

DOI: 10.1073/pnas.2401973121

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LncRNA analyses reveal increased levels of non-coding centromeric transcripts in hepatocellular carcinoma

Anamaria Necsulea, Philippe Veber, Tuyana Boldanova, Charlotte K Y Ng, Stefan Wieland, Markus H Heim

DOI: 10.1101/2021.03.03.433778

Preprint

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Persistent homology reveals strong phylogenetic signal in 3D protein structures

Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet

PNAS Nexus . 3 ( 4 ) : 158

DOI: 10.1093/pnasnexus/pgae158

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The genetic legacy of the expansion of Bantu-speaking peoples in Africa

Cesar A Fortes-Lima, Concetta Burgarella, Rickard Hammarén, Anders Eriksson, Mário Vicente, Cecile Jolly...

Nature . 625 : 540–547

DOI: 10.1038/s41586-023-06770-6

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PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids

Marie Raynaud, Paola Sanna, Julien Joseph, Julie A. J. Clément, Yukiko Imai, Jean-Jacques Lareyre...

DOI: 10.1101/2024.03.06.583651

Preprint

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The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome †

Madeline Chase, Maurine Vilcot, Carina Mugal

Proceedings of the Royal Society B: Biological Sciences . 291 ( 2015 )

DOI: 10.1098/rspb.2023.2382

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Evidence that genetic drift not adaptation drives fast‐Z and large‐Z effects in Ficedula flycatchers

Madeline Chase, Maurine Vilcot, Carina Mugal

Molecular Ecology .

DOI: 10.1111/mec.17262

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Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov

N. Cotte-Pattat, Jean-Pierre Flandrois, Jérôme Briolay, Sylvie Reverchon, Céline Brochier-Armanet

Systematic and Applied Microbiology . 47 ( 2-3 ) : 126497

DOI: 10.1016/j.syapm.2024.126497

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MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation

Jérémy Tournayre, Valérie Polonais, Ivan Wawrzyniak, Reginald Florian Akossi, Nicolas Parisot, Emmanuelle Lerat...

International Journal of Molecular Sciences . 25 ( 2 ) : 880

DOI: 10.3390/ijms25020880

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Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans

Florian Bénitière, Anamaria Necsulea, Laurent Duret

eLife . 13 : RP93629

DOI: 10.7554/eLife.93629.3

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Mitigation of the diagenesis risk in biological apatite δ18O interpretation

Christophe Lécuyer, Jean-Pierre Flandrois

Palaeogeography, Palaeoclimatology, Palaeoecology . 630 : 111812

DOI: 10.1016/j.palaeo.2023.111812

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δ2H and δ18O of river water from a high-altitude humid plain of the southern Alps: Implications for the interpretation of the isotopic compositions of bioapatite from humans living close to mountain areas

Christophe Lécuyer, François Atrops, François Fourel, Thibault Clauzel, Jean-Pierre Flandrois

Journal of Archaeological Science: Reports . 49 : 104020

DOI: 10.1016/j.jasrep.2023.104020

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IFB/ELIXIR-FR, the french node of ELIXIR

Anne-Françoise Adam-Blondon, Jacques van Helden, Gildas Le Corguillé, Christophe Blanchet, Hélène Chiapello, Christine Gaspin...

ISMB ECCB 2023 .

Conference paper

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Genomic portrait and relatedness patterns of the Iron Age Log Coffin culture in northwestern Thailand

Selina Carlhoff, Wibhu Kutanan, Adam B Rohrlach, Cosimo Posth, Mark Stoneking, Kathrin Nägele...

Nature Communications . 14 ( 1 ) : 8527

DOI: 10.1038/s41467-023-44328-2

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Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry

Sandra Oliveira, Anne-Maria Fehn, Beatriz Amorim, Mark Stoneking, Jorge Rocha

Science Advances . 9 ( 38 )

DOI: 10.1126/sciadv.adh3822

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South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture

Wipada Woravatin, Mark Stoneking, Metawee Srikummool, Jatupol Kampuansai, Leonardo Arias, Wibhu Kutanan

PLoS ONE . 18 ( 9 ) : e0291547

DOI: 10.1371/journal.pone.0291547

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The genomic diversity of Taiwanese Austronesian groups: Implications for the “Into- and Out-of-Taiwan” models

Dang Liu, Albert Min-Shan Ko, Mark Stoneking

PNAS Nexus . 2 ( 5 )

DOI: 10.1093/pnasnexus/pgad122

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Genomic perspectives on human dispersals during the Holocene

Mark Stoneking, Leonardo Arias, Dang Liu, Sandra Oliveira, Irina Pugach, Jae Joseph Russell B Rodriguez

Proceedings of the National Academy of Sciences of the United States of America . 120 ( 4 )

DOI: 10.1073/pnas.2209475119

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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 .

Conference paper

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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

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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

Preprint

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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

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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

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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

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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

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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

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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

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