GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 1 to 30 publications on 1266 in total

Computing Thermodynamically Consistent Elementary Flux Modes with Answer Set Programming

Emma Crisci, Maxime Mahout, Sabine Peres

CMSB 2024 - 22nd International Conference Computational Methods in Systems Biology . LNCS-14971 : 80-88

DOI: 10.1007/978-3-031-71671-3_7

Conference paper

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A genome-wide study of ruminants reveals two endogenous retrovirus families still active in goats

Marie Verneret, Caroline Leroux, Thomas Faraut, Vincent Navratil, Emmanuelle Lerat, Jocelyn Turpin

DOI: 10.1101/2024.06.21.600049

Preprint

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Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats

Anthony B. Garza, Emmanuelle Lerat, Hani Z. Girgis

Mobile DNA . 15 ( 1 ) : 8

DOI: 10.1186/s13100-024-00317-w

Journal article

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Diversité et diversification des Pectobacteriaceae, une famille de bactéries phytopathogènes d’importance mondiale

Céline Brochier, Nicole Hugouvieux-Cotte-Pattat, Jean-Pierre Flandrois, Sylvie Reverchon, Jérôme Briolay

Cahiers Scientifiques de la Fondation Pierre Vérots . ( 10 ) : 19-29

Journal article

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ISMB/ECCB 2023 organization benefited from the strengths of the French bioinformatics community

Anna-Sophie Fiston-Lavier, Sandra Dérozier, Guy Perrière, Marie-France Sagot

Bioinformatics Advances . 4 ( 1 ) : vbae040

DOI: 10.1093/bioadv/vbae040

Journal article

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Bradyrhizobium hardenbergiae sp. nov., isolated from Hardenbergia violacea in Australia, represents a novel basal lineage of the B. elkanii supergroup

Bénédicte Lafay, Elina Coquery, Philippe M. Oger

Preprint

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A Wright–Fisher graph model and the impact of directional selection on genetic variation

Ingemar Kaj, Carina Mugal, Rebekka Müller-Widmann

Theoretical Population Biology . 159 : 13-24

DOI: 10.1016/j.tpb.2024.07.004

Journal article

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Investigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam

Dinh Huong Thao, Tran Huu Dinh, Shigeki Mitsunaga, La Duc Duy, Nguyen Thanh Phuong, Nguyen Phuong Anh...

PLoS ONE . 19 ( 6 ) : e0304964

DOI: 10.1371/journal.pone.0304964

Journal article

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Complete mitochondrial genomes of patients from Thailand with cardiovascular diseases

Wipada Woravatin, Rattanasak Wongkomonched, Wichittra Tassaneeyakul, Mark Stoneking, Pattarapong Makarawate, Wibhu Kutanan

PLoS ONE . 19 ( 7 ) : e0307036

DOI: 10.1371/journal.pone.0307036

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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 ( 7995 ) : 540–547

DOI: 10.1038/s41586-023-06770-6

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Rita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet...

Peer Community Journal . 4 ( e89 )

DOI: 10.24072/pcjournal.457

Journal article

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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

Journal article

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De novo analysis of splicing from RNA-seq data: models, algorithms and applications

Vincent Lacroix

HDR

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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