GECO Evolutionary and Computational Genomics

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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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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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

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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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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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

Conference paper

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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 : 208

DOI: 10.1186/s13059-017-1344-6

2017

Journal article

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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

Journal article

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How Long Does Wolbachia Remain on Board?

Marc Bailly-Bechet, Patricia Martins-Simões, Gergely Szöllősi, Gladys Mialdea, Marie-France Sagot, Sylvain Charlat

Molecular Biology and Evolution . 34 ( 5 ) : 1183 - 1193

DOI: 10.1093/molbev/msx073

2017

Journal article

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A genomic history of Aboriginal Australia

Anna-Sapfo Malaspinas, Michael Westaway, Craig Muller, Vitor Hugo Sousa, Oscar Lao, Isabel Alves...

Nature . 538 ( 7624 ) : 207-214

DOI: 10.1038/nature18299

2016

Journal article

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The Complex Admixture History and Recent Southern Origins of Siberian Populations

Irina Pugach, Rostislav Matveev, Viktor Spitsyn, Sergey Makarov, Innokentiy Novgorodov, Vladimir Osakovsky...

Molecular Biology and Evolution . 33 ( 7 ) : 1777-1795

DOI: 10.1093/molbev/msw055

2016

Journal article

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Refining the Y chromosome phylogeny with southern African sequences

Chiara Barbieri, Alexander Hübner, Enrico Macholdt, Shengyu Ni, Sebastian Lippold, Roland Schröder...

Human Genetics . 135 ( 5 ) : 541 - 553

DOI: 10.1007/s00439-016-1651-0

2016

Journal article

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High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

Linnéa Smeds, Carina Mugal, Anna Qvarnström, Hans Ellegren

PLoS Genetics . 12 ( 5 ) : e1006044

DOI: 10.1371/journal.pgen.1006044

2016

Journal article

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Divergence in gene expression within and between two closely related flycatcher species

Severin Uebbing, Axel Künstner, Hannu Mäkinen, Niclas Backström, Paulina Bolivar, Reto Burri...

Molecular Ecology . 25 ( 9 ) : 2015-2028

DOI: 10.1111/mec.13596

2016

Journal article

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The non-equilibrium allele frequency spectrum in a Poisson random field framework

Ingemar Kaj, Carina Mugal

Theoretical Population Biology . 111 : 51-64

DOI: 10.1016/j.tpb.2016.06.003

2016

Journal article

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The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect

Jorgelindo da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Erwan Bigan, Sabine Pérès, Loïc Paulevé...

Metabolites . 6 ( 4 ) : 12 p.

DOI: 10.3390/metabo6040033

2016

Journal article

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Minimality of Metabolic Flux Modes under Boolean Regulation Constraints

Morterol Martin, Philippe Dague, Sabine Pérès, Laurent Simon

12th International Workshop on Constraint-Based Methods for Bioinformatics WCB’16 .

2016

Conference paper

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GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

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

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

δ 18 O-derived incubation temperatures of oviraptorosaur eggs

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

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

Token Jumping in minor-closed classes

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

Less effective selection leads to larger genomes

How Long Does Wolbachia Remain on Board?

A genomic history of Aboriginal Australia

The Complex Admixture History and Recent Southern Origins of Siberian Populations

Refining the Y chromosome phylogeny with southern African sequences

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

Divergence in gene expression within and between two closely related flycatcher species

The non-equilibrium allele frequency spectrum in a Poisson random field framework

The Redox Status of Cancer Cells Supports Mechanisms behind the Warburg Effect

Minimality of Metabolic Flux Modes under Boolean Regulation Constraints