GECO Génomique Computationnelle et Evolutive

Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis

Caroline Monteil, Guy Perrière, Nicolas Menguy, Nicolas Ginet, Béatrice Alonso, Nicolas Waisbord...

Environmental Microbiology .

DOI: 10.1111/1462-2920.14364

2018

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Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Monique Aouad, Najwa Taïb, Anne Oudart, Michel Lecocq, Manolo Gouy, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 127 : 46-54

DOI: 10.1016/j.ympev.2018.04.011

2018

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Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

Andrej Benjak, Charlotte Avanzi, Yvonne Benito, Franck Breysse, Christophe Chartier, Maria-Laura Boschiroli...

MSphere . 3 ( 5 ) : e00405-18

DOI: 10.1128/mSphere.00405-18

2018

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Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron, Ghislaine Blasquez...

Scientific Reports . 8 ( 1 ) : 5855

DOI: 10.1038/s41598-018-24034-6

2018

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Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)

Christophe Lécuyer, François Atrops, Romain Amiot, Delphine Angst, Valérie Daux, Jean-Pierre Flandrois...

The Holocene .

DOI: 10.1177/0959683617752840

2018

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Multiple convergent supergene evolution events in mating-type chromosomes

Sara E Branco, Fantin E Carpentier, Ricardo Rodriguez de La Vega, Hélène Badouin, Alodie Snirc, Stéphanie Le Prieur...

Nature Communications . 9 ( 1 ) : 2000

DOI: 10.1038/s41467-018-04380-9

2018

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The sunflower genome provides insights into Asterid evolution and relationships between paleoploidization and the genetic architecture of a major breeding trait

Hélène E Badouin

Second Joint Congress on Evolutionary Biology .

2018

Acte de congrès

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The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond, Jerome Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, Arnaud Lemainque...

Nature Genetics . 50 ( 6 ) : 772-777

DOI: 10.1038/s41588-018-0110-3

2018

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Fast-SG: an alignment-free algorithm for hybrid assembly

Alex Di Genova, Gonzalo A Ruz, Marie-France Sagot, Alejandro Maass

GigaScience . 7 ( 5 ) : 1 - 15

DOI: 10.1093/gigascience/giy048

2018

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The palaeolatitudinal distribution of fossil wood genera as a proxy for European Jurassic terrestrial climate

Marc Philippe, Sara Puijalon, Guillaume C Suan, Sylvain Mousset, Frédéric Thévenard, Emanuela Mattioli

Palaeogeography, Palaeoclimatology, Palaeoecology . 466 ( 373–381 )

DOI: 10.1016/j.palaeo.2016.11.029

2017

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Genomic landscape of human diversity across Madagascar

Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Ignace Rakoto, Nelly Rabetokotany, Bodo Ravololomanga...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 32 ) : E6498-E6506

DOI: 10.1073/pnas.1704906114

2017

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Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Takeshi Kawakami, Carina Mugal, Alexander Suh, Alexander Nater, Reto Burri, Linnéa Smeds...

Molecular Ecology . 26 ( 16 ) : 4158-4172

DOI: 10.1111/mec.14197

2017

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Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Ludovic Dutoit, Nagarjun Vijay, Carina Mugal, Christen Bossu, Reto Burri, Jochen Wolf...

Proceedings of the Royal Society B: Biological Sciences . 284 ( 1849 ) : 20162756

DOI: 10.1098/rspb.2016.2756

2017

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Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Reto Burri, Alexander Nater, Carina Mugal, Hans Ellegren

Molecular Ecology Resources . 17 ( 4 ) : 586-597

DOI: 10.1111/1755-0998.12602

2017

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A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product

Xinhe Zhao, Mayssa Kasbi, Jingkui Chen, Sabine Pérès, Mario Jolicœur

Biotechnology and Bioengineering . 114 ( 12 ) : 2907 - 2919

DOI: 10.1002/bit.26393

2017

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Computing EFMs consistent with equilibrium constants

Sabine Pérès, Philippe Dague, Mario Jolicœur, Stefan Schuster

Metabolic Pathway Analysis MPA 2017 .

2017

Acte de congrès

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HSM a reduced model of Central Carbon Metabolism: a dynamical approach

Bertrand Beauvoit, Sophie Colombie, Razanne Issa, Jean-Pierre Mazat, Christine Nazaret, Sabine Pérès

advances in Systems and Synthetic Biology .

2017

Acte de congrès

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How important is thermodynamics for identifying elementary flux modes?

Sabine Pérès, Mario Jolicœur, Cecile Moulin, Philippe Dague, Stefan Schuster

PLoS ONE . 12 ( 2 )

DOI: 10.1371/journal.pone.0171440

2017

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Simulation-based estimation of branching models for LTR retrotransposons

Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat

Bioinformatics . 33 ( 3 ) : 320 - 326

DOI: 10.1093/bioinformatics/btw622

2017

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Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

Magali Chabé, Ana Lokmer, Laure Ségurel

Trends in Parasitology . 33 ( 12 ) : 925-934

DOI: 10.1016/j.pt.2017.08.005

2017

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Microbiome intestinal ancien et problématiques médicales contemporaines

Philippe Charlier, Anaïs Augias, Philippe Sansonetti, Céline Bon, Sean Kennedy, Laure Ségurel

Médecine/Sciences . 33 : 984-990

DOI: 10.1051/medsci/20173311016

2017

Autre publication

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On the Evolution of Lactase Persistence in Humans

Laure Ségurel, Céline Bon

Annual Review of Genomics and Human Genetics . 18 ( 1 ) : 297-319

DOI: 10.1146/annurev-genom-091416-035340

2017

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Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations

Nina Marchi, Tatyana Hegay, Philippe Mennecier, Myriam Georges, Romain Laurent, Mark Whitten...

American Journal of Physical Anthropology . 162 ( 4 ) : 627-640

DOI: 10.1002/ajpa.23151

2017

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Latitude as a co-driver of human gut microbial diversity?

Emma Dikongué, Laure Ségurel

BioEssays . 39 ( 3 ) : 1600145

DOI: 10.1002/bies.201600145

2017

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The global impact of Wolbachia on mitochondrial diversity and evolution

Marie Cariou, Laurent Duret, Sylvain Charlat

Journal of Evolutionary Biology . 30 ( 12 ) : 2204-2210

DOI: 10.1111/jeb.13186

2017

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The Red Queen model of recombination hot-spot evolution: a theoretical investigation

Thibault Latrille, L. Duret, Nicolas Lartillot

Philosophical Transactions of the Royal Society B: Biological Sciences .

DOI: 10.1098/rstb.2016.0463

2017

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BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Alexey Dudnik, Filipa Almeida, Ricardo Andrade, Barbara Avila, Pilar Bañados, Barbay Diane...

Phytochemistry Reviews . : 1-36

DOI: 10.1007/s11101-017-9532-2

2017

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Algorithms for k-meet-semidistributive lattices

Laurent Beaudou, Arnaud Mary, Lhouari Nourine

Theoretical Computer Science . 658 : 391 - 398

DOI: 10.1016/j.tcs.2015.10.029

2017

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d18O-Derived incubation temperatures of oviraptorosaur eggs.

Romain Amiot, Xu Wang, Shuo Wang, Christophe Lécuyer, Jean-Michel Mazin, Jinyou Mo...

Palaeontology . : 1-15

DOI: 10.1111/pala.12311

2017

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Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

DOI: 10.1101/074807

2017

Pré-publication

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis

Extreme halophilic archaea derive from two distinct methanogen Class II lineages

Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli

Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)

Multiple convergent supergene evolution events in mating-type chromosomes

The sunflower genome provides insights into Asterid evolution and relationships between paleoploidization and the genetic architecture of a major breeding trait

The Rosa genome provides new insights into the domestication of modern roses

Fast-SG: an alignment-free algorithm for hybrid assembly

The palaeolatitudinal distribution of fossil wood genera as a proxy for European Jurassic terrestrial climate

Genomic landscape of human diversity across Madagascar

Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product

Computing EFMs consistent with equilibrium constants

HSM a reduced model of Central Carbon Metabolism: a dynamical approach

How important is thermodynamics for identifying elementary flux modes?

Simulation-based estimation of branching models for LTR retrotransposons

Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

Microbiome intestinal ancien et problématiques médicales contemporaines

On the Evolution of Lactase Persistence in Humans

Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations

Latitude as a co-driver of human gut microbial diversity?

The global impact of Wolbachia on mitochondrial diversity and evolution

The Red Queen model of recombination hot-spot evolution: a theoretical investigation

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Algorithms for k-meet-semidistributive lattices

d18O-Derived incubation temperatures of oviraptorosaur eggs.

Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data