GECO Génomique Computationnelle et Evolutive

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix...

PLoS Genetics . : 1-28

DOI: 10.1371/journal.pgen.1007758

2018

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Sex gap in aging and longevity: can sex chromosomes play a role?

Gabriel A.B. Marais, Jean-Michel Gaillard, Cristina Vieira, Ingrid Plotton, Damien Sanlaville, François Gueyffier...

Biology of Sex Differences . 9 ( 1 ) : 1-14

DOI: 10.1186/s13293-018-0181-y

2018

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δ 18 O-derived incubation temperatures of oviraptorosaur eggs

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

Palaeontology . 60 ( 5 ) : 633-647

DOI: 10.1111/pala.12311

2017

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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 - CB . 27 ( 24 ) : 3864-3870.e4

DOI: 10.1016/j.cub.2017.11.008

2017

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Simulation-based estimation of branching models for LTR retrotransposons

Serge Moulin, Nicolas Seux, Stephane Chretien, Christophe Guyeux, Emmanuelle Lerat

Bioinformatics . 33 ( 3 )

DOI: 10.1093/bioinformatics/btw622

2017

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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

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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

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

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

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

DOI: 10.1073/pnas.1701658114

2017

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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

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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

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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

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Environmental assessment of urban mobility: Combining life cycle assessment with land-use and transport interaction modelling—Application to Lyon (France)

Cyrille François, Natacha Gondran, Jean-Pierre Nicolas, David Parsons

Ecological Indicators . 72 : Pages 597–604

DOI: 10.1016/j.ecolind.2016.07.014

2017

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

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

Scientific Reports . 7 : 40618

DOI: 10.1038/srep40618

2017

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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

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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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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

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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

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The Evolution of Sex Chromosomes and Dosage Compensation in Plants

A. Muyle, R. Shearn, Gabriel Marais

Genome Biology and Evolution . 9 : 627-645

DOI: 10.1093/gbe/evw282

2017

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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

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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

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Token Jumping in minor-closed classes

Nicolas Bousquet, Arnaud Mary, Aline Parreau

International symposium on fundamentals of computer theory (FCT 2017) . 10472 : 136-149

DOI: 10.1007/978-3-662-55751-8_12

2017

Actes de congrès

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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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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

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On Bubble Generators in Directed Graphs

Vicente Acuna, Roberto Grossi, Giuseppe 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

Actes de congrès

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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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The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Baptiste Saudemont, Alexandra Popa, Joanna Parmley, Vincent Rocher, Corinne Blugeon, Anamaria Necsulea...

Genome Biology . 18 ( 1 )

DOI: 10.1186/s13059-017-1344-6

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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In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

C Grey, Ja Clement, J Buard, B Leblanc, I Gut, M Gut...

Genome Research . 27 ( 4 ) : 580-590

DOI: 10.1101/gr.217240.116

2017

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Less effective selection leads to larger genomes

Tristan Lefébure, Claire Morvan, Florian Malard, Clémentine François, Lara Konecny-Dupré, Laurent Guéguen...

Genome Research . 27 : 1016-1028

DOI: 10.1101/gr.212589.116

2017

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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

Articles

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Equipe Sexe et Evolution

Publications

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Sex gap in aging and longevity: can sex chromosomes play a role?

δ 18 O-derived incubation temperatures of oviraptorosaur eggs

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

Simulation-based estimation of branching models for LTR retrotransposons

Evolutionary history of LTR-retrotransposons among 20 Drosophila species

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

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

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

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

Environmental assessment of urban mobility: Combining life cycle assessment with land-use and transport interaction modelling—Application to Lyon (France)

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

Record of Nile seasonality in Nubian neonates.

d18O-Derived incubation temperatures of oviraptorosaur eggs.

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

IsoSel: Protein Isoform Selector for phylogenetic reconstructions

The Evolution of Sex Chromosomes and Dosage Compensation in Plants

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

On the rarity of dioecy in flowering plants

Token Jumping in minor-closed classes

Algorithms for k-meet-semidistributive lattices

OptPipe - a pipeline for optimizing metabolic engineering targets

On Bubble Generators in Directed Graphs

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

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

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

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

Less effective selection leads to larger genomes

Recombination, meiotic expression and human codon usage