GECO Génomique Computationnelle et Evolutive

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

Article dans une revue

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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

Article dans une revue

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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

Article dans une revue

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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

Article dans une revue

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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

Article dans une revue

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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

Acte de congrès

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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent J. Henry, Arnaud Ferré, Christine Froidevaux, Anne Goelzer, Vincent V. Fromion, Sarah Cohen-Boulakia...

IC2016 - Ingénierie des Connaissances .

2016

Acte de congrès

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Représentation systémique multi-échelle des processus biologiques de la bactérie

Vincent Henry, Arnaud Ferré, Christine Froidevaux, Anne Goelzer, Vincent Fromion, Sarah Cohen-Boulakia...

IC201: 27es Journées francophones d'Ingénierie des Connaissances .

2016

Acte de congrès

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Human-Scale Metabolic Network of Central Carbon Metabolism: application to serine metabolism from glutamine in Cancer Cells

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

advances in Systems and Synthetic Biology .

2016

Acte de congrès

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Detection and interpretation of shared genetic influences on 42 human traits

Joseph Pickrell, Tomaz Berisa, Jimmy Liu, Laure Ségurel, Joyce Tung, David A Hinds

Nature Genetics . 48 ( 7 ) : 709-717

DOI: 10.1038/ng.3570

2016

Article dans une revue

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Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection

Elise Lucotte, Romain Laurent, Evelyne Heyer, Laure Ségurel, Bruno Toupance

Genome Biology and Evolution . 8 ( 5 ) : 1489-1500

DOI: 10.1093/gbe/evw090

2016

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How and how much does RAD-seq bias genetic diversity estimates?

M. Cariou, L. Duret, S. Charlat

BMC Evolutionary Biology . 16 : 240

DOI: 10.1186/s12862-016-0791-0

2016

Article dans une revue

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Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract

Mariana G Ferrarini, Franciele Maboni Siqueira, Scheila G Mucha, Tony L Palama, Elodie E Jobard, Bénédicte Elena-Herrmann...

JOBIM 2016 .

DOI: 10.1186/s12864-016-2644-z

2016

Poster

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A Combinatorial Algorithm for Microbial Consortia Synthetic Design

Alice Julien-Laferrière, Laurent Bulteau, Delphine Parrot, Alberto Marchetti-Spaccamela, Leen Stougie, Susana Vinga...

Scientific Reports .

DOI: 10.1038/srep29182

2016

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A Polynomial Delay Algorithm for Enumerating Minimal Dominating Sets in Chordal Graphs

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine, Takeaki Uno

WG 2015: Graph-Theoretic Concepts in Computer Science . : 138-153

DOI: 10.1007/978-3-662-53174-7_11

2016

Chapitre d'ouvrage

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Ancestral Reconstruction: Theory and Practice

Mathieu Groussin, Vincent Daubin, Eric Tannier, Manolo Gouy

Encyclopedia of Evolutionary Biology . : 70–77

DOI: 10.1016/B978-0-12-800049-6.00166-9

2016

Chapitre d'ouvrage

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Oxygen isotope fractionation between bird eggshell calcite and body water: application to fossil eggs from Lanzarote (Canary Islands)

Nicolas Lazzerini, Christophe Lécuyer, Romain Amiot, Delphine Angst, Eric Buffetaut, François Fourel...

The Science of Nature Naturwissenschaften . 103 ( 9-10 )

DOI: 10.1007/s00114-016-1404-x

2016

Article dans une revue

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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, Claire Lemaitre...

GigaScience . 5 ( 1 )

DOI: 10.1186/s13742-015-0105-2

2016

Article dans une revue

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Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

L Karaki, P da Silva, F Rizk, C Chouabe, N Chantret, V Eyraud...

BMC Plant Biology . 16 ( 1 ) : 63

DOI: 10.1186/s12870-016-0745-0

2016

Article dans une revue

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Novel genomic island modifies DNA with 7-deazaguanine derivatives

J.J. Thiaville, S.M. Kellner, Y. Yuan, G. Hutinet, P.C. Thiaville, W. Jumpathong...

Proceedings of the National Academy of Sciences of the United States of America . 113 : e1452-e1459

DOI: 10.1073/pnas.1518570113

2016

Article dans une revue

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Evolutionary history of the mammalian synaptonemal complex

J. Fraune, Céline Brochier-Armanet, M. Alsheimer, J. N. Volff, K. Schucker, R. Benavente

Chromosoma . 125 : 355-60

DOI: 10.1007/s00412-016-0583-8

2016

Article dans une revue

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Closing the gap between rocks and clocks using total-evidence dating

F. Ronquist, Nicolas Lartillot, M.J. Phillips

Philosophical Transactions of the Royal Society B: Biological Sciences . 371 : 20150136

DOI: 10.1098/rstb.2015.0136

2016

Article dans une revue

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Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl

Gabriela G. Aguileta, Helene Badouin, Michael E Hood, Anders Pape Møller, Stephanie Le Prieur, Alodie Snirc...

Molecular Ecology . 25 ( 14 ) : 3370-83

DOI: 10.1111/mec.13675

2016

Article dans une revue

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The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together

J. B. Dacks, M. C. Field, R. Buick, L. Eme, Simonetta Gribaldo, A. J. Roger...

Journal of Cell Science . 129 ( 20 ) : 3695-3703

DOI: 10.1242/jcs.178566

2016

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A mixed relaxed clock model

Nicolas Lartillot, M. J. Phillips, F. Ronquist

Philosophical Transactions of the Royal Society B: Biological Sciences . 371 : 20150132

DOI: 10.1098/rstb.2015.0132

2016

Article dans une revue

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Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing

Taiadjana M. Fortuna, Alodie Snirc, Hélène Badouin, Jerome Gouzy, Sophie Siguenza, Diane Esquerre...

PLoS ONE . 11 ( 11 ) : e0165656

DOI: 10.1371/journal.pone.0165656

2016

Article dans une revue

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny...

Nucleic Acids Research .

DOI: 10.1093/nar/gkw655

2016

Article dans une revue

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Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

Mariana G. Ferrarini, Franciele M. Siqueira, Scheila G. Mucha, Tony Lionel Palama, Elodie Jobard, Bénédicte Elena-Herrmann...

BMC Genomics . 17 ( 1 ) : 353

DOI: 10.1186/s12864-016-2644-z

2016

Article dans une revue

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DegreeCox – a network-based regularization method for survival analysis

André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga

BMC Bioinformatics . 17 ( Suppl 16 ) : 109-121

DOI: 10.1186/s12859-016-1310-4

2016

Article dans une revue

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Enumeration of minimal stoichiometric precursor sets in metabolic networks

Ricardo Andrade, Martin Wannagat, Cecilia C. Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V. Milreu...

Algorithms for Molecular Biology . 11 ( 1 ) : 25

DOI: 10.1186/s13015-016-0087-3

2016

Article dans une revue

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

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

Représentation systémique multi-échelle des processus biologiques de la bactérie

Représentation systémique multi-échelle des processus biologiques de la bactérie

Human-Scale Metabolic Network of Central Carbon Metabolism: application to serine metabolism from glutamine in Cancer Cells

Detection and interpretation of shared genetic influences on 42 human traits

Detection of Allelic Frequency Differences between the Sexes in Humans: A Signature of Sexually Antagonistic Selection

How and how much does RAD-seq bias genetic diversity estimates?

Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract

A Combinatorial Algorithm for Microbial Consortia Synthetic Design

A Polynomial Delay Algorithm for Enumerating Minimal Dominating Sets in Chordal Graphs

Ancestral Reconstruction: Theory and Practice

Oxygen isotope fractionation between bird eggshell calcite and body water: application to fossil eggs from Lanzarote (Canary Islands)

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

Novel genomic island modifies DNA with 7-deazaguanine derivatives

Evolutionary history of the mammalian synaptonemal complex

Closing the gap between rocks and clocks using total-evidence dating

Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl

The changing view of eukaryogenesis - fossils, cells, lineages and how they all come together

A mixed relaxed clock model

Polymorphic Microsatellite Markers for the Tetrapolar Anther-Smut Fungus Microbotryum saponariae Based on Genome Sequencing

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

DegreeCox – a network-based regularization method for survival analysis

Enumeration of minimal stoichiometric precursor sets in metabolic networks