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 331 to 360 publications on 1377 in total

Amphioxus functional genomics and the origins of vertebrate gene regulation

Ferdinand Marletaz, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, Malcolm Perry...

Nature . 564 ( 7734 ) : 64-70

DOI: 10.1038/s41586-018-0734-6

Journal article

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Fast-SG: an alignment-free algorithm for hybrid assembly

Alex Di Genova, Gonzalo A Ruz, Marie-France Sagot, Alejandro Maass

GigaScience . 7 ( 5 ) : 1 - 15

DOI: 10.1093/gigascience/giy048

Journal article

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Genomic imprinting mediates dosage compensation in a young plant XY system

Aline Muyle, Niklaus Zemp, Cécile Fruchard, Radim Cegan, Jan Vrána, Clothilde Deschamps...

Nature Plants . 4 ( 9 ) : 677-680

DOI: 10.1038/s41477-018-0221-y

Journal article

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Integrative Mobilizable Element (IMEs): a reservoir of antibiotic resistance genes in the zoonotic pathogen Streptococcus suis

Virginie Libante, Nombre Yves, Charles Coluzzi, Gérard Guédon, Marcelo Gottschalk, Nahuel Fittipaldi...

GDR 3546 - Les elements mobiles du mécanisme aux populations, une approche intégrative .

Conference paper

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L'exploration des génomes par l'outil ICEFinder révèle la forte prévalence et l'extrême diversité des ICE et des IME de streptocoques

Charles Coluzzi

Thesis

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A Glimpse into the World of Integrative and Mobilizable Elements in Streptococci Reveals an Unexpected Diversity and Novel Families of Mobilization Proteins

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

Frontiers in Microbiology . 8 : 16

DOI: 10.3389/fmicb.2017.00443

Journal article

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The obscure world of integrative and mobilizable elements

Gérard Guédon, Virginie Libante, Charles Coluzzi, Sophie Payot, Nathalie N. Leblond-Bourget

Genes . 8 ( 11 ) : 337

DOI: 10.3390/genes8110337

Journal article

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The palaeolatitudinal distribution of fossil wood genera as a proxy for European Jurassic terrestrial climate

Marc Philippe, Sara Puijalon, Guillaume C Suan, Sylvain Mousset, Frédéric Thévenard, Emanuela Mattioli

Palaeogeography, Palaeoclimatology, Palaeoecology . 466 ( 373–381 )

DOI: 10.1016/j.palaeo.2016.11.029

Journal article

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Genomic landscape of human diversity across Madagascar

Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Ignace Rakoto, Nelly Rabetokotany, Bodo Ravololomanga...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 32 ) : E6498-E6506

DOI: 10.1073/pnas.1704906114

Journal article

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Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Takeshi Kawakami, Carina Mugal, Alexander Suh, Alexander Nater, Reto Burri, Linnéa Smeds...

Molecular Ecology . 26 ( 16 ) : 4158-4172

DOI: 10.1111/mec.14197

Journal article

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Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Ludovic Dutoit, Nagarjun Vijay, Carina Mugal, Christen Bossu, Reto Burri, Jochen Wolf...

Proceedings of the Royal Society B: Biological Sciences . 284 ( 1849 ) : 20162756

DOI: 10.1098/rspb.2016.2756

Journal article

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Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Reto Burri, Alexander Nater, Carina Mugal, Hans Ellegren

Molecular Ecology Resources . 17 ( 4 ) : 586-597

DOI: 10.1111/1755-0998.12602

Journal article

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A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product

Xinhe Zhao, Mayssa Kasbi, Jingkui Chen, Sabine Pérès, Mario Jolicœur

Biotechnology and Bioengineering . 114 ( 12 ) : 2907 - 2919

DOI: 10.1002/bit.26393

Journal article

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Computing EFMs consistent with equilibrium constants

Sabine Pérès, Philippe Dague, Mario Jolicœur, Stefan Schuster

Metabolic Pathway Analysis MPA 2017 .

Conference paper

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HSM a reduced model of Central Carbon Metabolism: a dynamical approach

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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How important is thermodynamics for identifying elementary flux modes?

Sabine Pérès, Mario Jolicœur, Cecile Moulin, Philippe Dague, Stefan Schuster

PLoS ONE . 12 ( 2 ) : e0171440

DOI: 10.1371/journal.pone.0171440

Journal article

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Simulation-based estimation of branching models for LTR retrotransposons

Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat

Bioinformatics . 33 ( 3 ) : 320 - 326

DOI: 10.1093/bioinformatics/btw622

Journal article

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Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

Magali Chabé, Ana Lokmer, Laure Ségurel

Trends in Parasitology . 33 ( 12 ) : 925-934

DOI: 10.1016/j.pt.2017.08.005

Journal article

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Microbiome intestinal ancien et problématiques médicales contemporaines

Philippe Charlier, Anaïs Augias, Philippe Sansonetti, Céline Bon, Sean Kennedy, Laure Ségurel

Médecine/Sciences . 33 : 984-990

DOI: 10.1051/medsci/20173311016

Other publication

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Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations

Nina Marchi, Tatyana Hegay, Philippe Mennecier, Myriam Georges, Romain Laurent, Mark Whitten...

American Journal of Physical Anthropology . 162 ( 4 ) : 627-640

DOI: 10.1002/ajpa.23151

Journal article

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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

Journal article

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The global impact of Wolbachia on mitochondrial diversity and evolution

Marie Cariou, Laurent Duret, Sylvain Charlat

Journal of Evolutionary Biology . 30 ( 12 ) : 2204-2210

DOI: 10.1111/jeb.13186

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

DOI: 10.1101/074807

Preprint

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The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Panagiotis S Adam, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

The International Society of Microbiologial Ecology Journal . 11 ( 11 ) : 2407-2425

DOI: 10.1038/ismej.2017.122

Journal article

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