GECO Evolutionary and Computational Genomics

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

Journal article

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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

Journal article

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MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps

Aurélie Siberchicot, Adrien Bessy, Laurent Gueguen, Gabriel A. B. Marais

Genome Biology and Evolution . 9 ( 10 ) : 2506-2509

DOI: 10.1093/gbe/evx178

2017

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Preprint

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The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Panagiotis S Adam, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

The International Society of Microbiologial Ecology Journal . 11 ( 11 ) : 2407-2425

DOI: 10.1038/ismej.2017.122

2017

Journal article

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Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Roberto Feuda, Martin Dohrmann, Walker Pett, Herve Philippe, Omar Rota-Stabelli, Nicolas Lartillot...

Current Biology . 27 ( 24 ) : 3864-3870.e4

DOI: 10.1016/j.cub.2017.11.008

2017

Journal article

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Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Sara E Branco, Hélène E Badouin, Ricardo E Rodríguez de La Vega, Jerome Gouzy, Fantin E Carpentier, Gabriela E Aguileta...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 27 ) : 7067-7072

DOI: 10.1073/pnas.1701658114

2017

Journal article

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Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Helene Badouin, Pierre Gladieux, Jerome Gouzy, Sophie Siguenza, Gabriela Aguileta, Alodie Snirc...

Molecular Ecology . 26 ( 7 )

DOI: 10.1111/mec.13976

2017

Journal article

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Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

T. Boldanova, A. Suslov, M.H. Heim, A. Necsulea

EMBO Molecular Medicine . 9 : 816-834

DOI: 10.15252/emmm.201607006

2017

Journal article

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TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira

Nucleic Acids Research . 45 : 13

DOI: 10.1093/nar/gkw953

2017

Journal article

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On the rarity of dioecy in flowering plants

Jos Käfer, Gabriel Marais, Jr. Pannell

Molecular Ecology . 26 : 1225-1241

DOI: 10.1111/mec.14020

2017

Journal article

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In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

C Grey, Julie a J Clément, J Buard, B Leblanc, I Gut, M Gut...

Genome Research . 27 ( 4 ) : 580-590

DOI: 10.1101/gr.217240.116

2017

Journal article

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Recombination, meiotic expression and human codon usage

F. Pouyet, Dominique Mouchiroud, L. Duret, M. Sémon

eLife . 6 : e27344

DOI: 10.7554/eLife.27344.001

2017

Journal article

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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele...

Algorithms for Molecular Biology . 12 ( 1 ) : 2

DOI: 10.1186/s13015-017-0091-2

2017

Journal article

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OptPipe - a pipeline for optimizing metabolic engineering targets

András Hartmann, Ana Vila-Santa, Nicolai Kallscheuer, Michael Vogt, Alice Julien-Laferrière, Marie-France Sagot...

BMC Systems Biology . 11 : 1-9

DOI: 10.1186/s12918-017-0515-0

2017

Journal article

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On Bubble Generators in Directed Graphs

Vicente Acuna, Roberto Grossi, Giuseppe F Italiano, Leandro Lima, Romeo Rizzi, Gustavo Sacomoto...

WG 2017 - 43rd International Workshop on Graph-Theoretic Concepts in Computer Science . 10520 : 18-31

DOI: 10.1007/978-3-319-68705-6_2

2017

Conference paper

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IsoSel: Protein Isoform Selector for phylogenetic reconstructions

H. Philippon, A. Souvane, Céline Brochier-Armanet, G. Perriere

PLoS ONE . 12 : e0174250

DOI: 10.1371/journal.pone.0174250

2017

Journal article

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Record of Nile seasonality in Nubian neonates.

Céline Martin, Bruno Maureille, Romain Amiot, Alexandra Touzeau, Aurélien Royer, François Fourel...

Isotopes in Environmental and Health Studies . 53 ( 3 ) : 223-242

DOI: 10.1080/10256016.2016.1229667

2017

Journal article

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Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

Jean-Philippe Rasigade, Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron...

Scientific Reports . 7 : 45326

DOI: 10.1038/srep45326

2017

Journal article

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The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein.

J. Timm, C. Brochier-Armanet, J. Pérard, B. Zambelli, S. Ollagnier de Choudens, S. Ciurli...

Metallomics . 9 ( 5 ) : 575-583

DOI: 10.1039/c7mt00063d

2017

Journal article

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Evolutionary history of LTR-retrotransposons among 20 Drosophila species

N. Bargues, Emmanuelle Lerat

Mobile DNA . 8 : 7

DOI: 10.1186/s13100-017-0090-3

2017

Journal article

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A newly evolved W(olbachia) sex chromosome in pillbug!

Gabriel Marais, Sylvain Charlat

Peer Community In Evolutionary Biology .

DOI: 10.24072/pci.evolbiol.100016

2017

Journal article

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Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

Sara Branco, Ke Bi, Hui-Ling Liao, Pierre Gladieux, Helene Badouin, Christopher E Ellison...

Molecular Ecology . 26 ( 7 ) : 2063-2076

DOI: 10.1111/mec.13892

2017

Journal article

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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Hélène Badouin, Jerome Gouzy, Christopher Grassa, Florent Murat, S Evan Staton, Ludovic Cottret...

Nature . 546 ( 7656 ) : 148-152

DOI: 10.1038/nature22380

2017

Journal article

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Identification of misexpressed genetic elements in hybrids between Drosophila-related species

Hélène Lopez-Maestre, Elias Alberto Gutierrez Carnelossi, Vincent Lacroix, Nelly Burlet, Bruno Mugat, Séverine Chambeyron...

Scientific Reports . 7 : 40618

DOI: 10.1038/srep40618

2017

Journal article

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GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

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

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

MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps

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

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

On the rarity of dioecy in flowering plants

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

Recombination, meiotic expression and human codon usage

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

OptPipe - a pipeline for optimizing metabolic engineering targets

On Bubble Generators in Directed Graphs

IsoSel: Protein Isoform Selector for phylogenetic reconstructions

Record of Nile seasonality in Nubian neonates.

Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

The CO dehydrogenase accessory protein CooT is a novel nickel-binding protein.

Evolutionary history of LTR-retrotransposons among 20 Drosophila species

A newly evolved W(olbachia) sex chromosome in pillbug!

Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Identification of misexpressed genetic elements in hybrids between Drosophila-related species