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 421 to 450 publications on 1415 in total

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

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

see the publication

Evolutionary history of the mammalian synaptonemal complex

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

Chromosoma Biology of the Nucleus . 125 : 355-60

DOI: 10.1007/s00412-016-0583-8

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

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

Journal article

see the publication

Robustness of the Parsimonious Reconciliation Method in Cophylogeny

Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot

Lecture Notes in Computer Science . 9702 : 12

DOI: 10.1007/978-3-319-38827-4_10

Journal article

see the publication

Computing and Listing st-Paths in Subway Networks

Kateřina Böhmová, Matúš Mihalák, Tobias Pröger, Gustavo Sacomoto, Marie-France Sagot, Peter Widmayer

CSR 2016 - 11th International Computer Science Symposium in Russia . 9691 : 102-116

DOI: 10.1007/978-3-319-34171-2_8

Conference paper

see the publication

Introduction to the Special Theme - Tackling Big Data in the Life Sciences

Roeland M.H. Merks, Marie-France Sagot

Other publication

see the publication

Qualité des données NGS : de la séquence aux bases de données

Pierre Peyret, Julie Aubert, Vincent Breton, François Enault, Line Le Gall, Denis Le Paslier...

La génomique environnementale . 978-1-78405-151-8 : 180 p.

Book chapter

see the publication

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

Mathieu Groussin, Bastien Boussau, Gergely J Szollosi, Laura Eme, Manolo Gouy, Céline Brochier-Armanet...

Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310

DOI: 10.1093/molbev/msv249

Journal article

see the publication

RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien M de Vienne, Manolo Gouy...

Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172

DOI: 10.1093/molbev/msw088

Journal article

see the publication