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 1415 in total

On the rarity of dioecy in flowering plants

Jos Käfer, Gabriel Marais, Jr. Pannell

Molecular Ecology . 26 : 1225-1241

DOI: 10.1111/mec.14020

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

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

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

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

Conference paper

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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

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

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

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

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

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

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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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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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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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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