GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

The main goal of the GECO department is to foster integration and synergies between theoretical and methodological research relevant for the analysis of genomes (computational genomics) and empirical analysis of genomic and multi-omic data (evolutionary and functional genomics). The department is structured in two teams, BAOBAB and BPGE:

BAOBAB is deeply rooted in computer science. Its strengths are in algorithms, models, and mathematical analysis of graphs and networks, with applications to transcriptomics and metabolic networks.

BPGE is oriented towards bioinformatics, phylogenetics and evolutionary genomics. Its research projects cover a broad range of subjects, such as methodological developments for phylogenetic inference, their applications to the reconstruction of the evolutionary history of bacteria and archaea, the role of mobile genetic elements in the evolution of bacteria and of antibioresistance, or the role of recombination, of genomic rearrangements and of transposable elements in the evolution of eukaryotic genomes.

As detailed on their pages, the research conducted in both teams integrates deep and long-ranging theoretical and methodological (algorithmic and computational) developments with data analysis driven by empirical questions. This integration is bi-directional: methodological developments are guided by empirical questions and then used in empirical applications, while theoretical modeling helps clarify the conceptual basis of subsequent empirical analyses.

Publications

Display of 391 to 420 publications on 1402 in total

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

Journal article

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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

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

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

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

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

Journal article

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New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration

Chloé C. Ambroset, Charles Coluzzi, Gérard Guédon, Marie-Dominique Devignes, Valentin Loux, Thomas Lacroix...

Frontiers in Microbiology . 6 ( 6 ) : 1483

DOI: 10.3389/fmicb.2015.01483

Journal article

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A glimpse into an unexplored world: very high diversity of integrative and mobilizable elements in Streptococci

Charles Coluzzi, Gérard Guédon, Chloé Ambroset, Marie-Dominique Devignes, Sophie Payot, Nathalie N. Leblond-Bourget

8th ASM conference on Streptococcal Genetics .

Poster

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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

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

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

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

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

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

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

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 .

Conference paper

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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 .

Conference paper

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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 .

Conference paper

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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 .

Conference paper

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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

Journal article

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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

Journal article

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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

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

Journal article

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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

Book chapter

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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