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 571 to 600 publications on 1407 in total

Sex uncovered: the evolutionary biology of reproductive systems

T. Schwander, Gabriel Marais, D. Roze

Journal of Evolutionary Biology . 27 : 1287-91

Journal article

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Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

Rui Ferreira, Roberto Grossi, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot

22th Annual European Symposium on Algorithms . 8737 : 418-429

DOI: 10.1007/978-3-662-44777-2_35

Conference paper

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Specific Activation of an I-Like Element in Drosophila Interspecific Hybrids

Elias a G Carnelossi, Emmanuelle Lerat, Hélène Henri, Sonia Martinez, Claudia M A Carareto, Cristina Vieira

Genome Biology and Evolution . 6 : 1806 - 1817

DOI: 10.1093/gbe/evu141

Journal article

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GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance

Y. Lesecque, D. Mouchiroud, L. Duret

Molecular Biology and Evolution . 30 : 1409--19

DOI: 10.1093/molbev/mst056

Journal article

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XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

C. Vallot, C. Huret, Yann Lesecque, A. Resch, N. Oudrhiri, A. Bennaceur-Griscelli...

Nature Genetics . 45 : 239--41

DOI: 10.1038/ng.2530

Journal article

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The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

S. B. Montgomery, D. L. Goode, E. Kvikstad, C. A. Albers, Z. D. Zhang, X. J. Mu...

Genome Research . 23 : 749--61

DOI: 10.1101/gr.148718.112

Journal article

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PCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla

K. Gerard, E. Guilloton, S. Arnaud-Haond, Didier Aurelle, R. Bastrop, Pierre Chevaldonné...

Marine Genomics . 12 : 1-8

DOI: 10.1016/j.margen.2013.10.001

Journal article

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The short-term impact of wetland restoration on the genetic diversity of a predominantly clonal plant species

Jehanne Oudot-Canaff, Gudrun Bornette, Marie-Rose Viricel, Florence Piola, Sylvain Mousset, Evelyne Martel

Aquatic Botany . 110 : 16-23

DOI: 10.1016/j.aquabot.2013.04.006

Journal article

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Ancient Substructure in Early mtDNA Lineages of Southern Africa

Chiara Barbieri, Mário Vicente, Jorge Rocha, Sununguko w. Mpoloka, Mark Stoneking, Brigitte Pakendorf

American Journal of Human Genetics . 92 ( 2 ) : 285-292

DOI: 10.1016/j.ajhg.2012.12.010

Journal article

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Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination

Carina Mugal, Benoit Nabholz, Hans Ellegren

BMC Genomics . 14 ( 1 ) : 86

DOI: 10.1186/1471-2164-14-86

Journal article

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Twisted Signatures of GC-Biased Gene Conversion Embedded in an Evolutionary Stable Karyotype

Carina Mugal, Peter Arndt, Hans Ellegren

Molecular Biology and Evolution . 30 ( 7 ) : 1700-1712

DOI: 10.1093/molbev/mst067

Journal article

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Elementary Flux Modes Analysis of Functional Domain Networks Allows a Better Metabolic Pathway Interpretation

Sabine Pérès, Liza L. Felicori, Franck Molina

PLoS ONE . 8 ( 10 )

DOI: 10.1371/journal.pone.0076143

Journal article

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Analysis of metabolic networks using elementary flux modes

Sabine Pérès

Advances in systems and synthetic biology . : 165--170

Conference paper

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Human Genetic Data Reveal Contrasting Demographic Patterns between Sedentary and Nomadic Populations That Predate the Emergence of Farming

Carla Aimé, Guillaume Laval, Etienne Patin, Paul Verdu, Laure L. Segurel, Raphaëlle Chaix...

Molecular Biology and Evolution . 30 ( 12 ) : 2629 - 2644

DOI: 10.1093/molbev/mst156

Journal article

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Ancestry runs deeper than blood: The evolutionary history of ABO points to cryptic variation of functional importance

Laure L. Segurel, Ziyue Gao, Molly Przeworski

BioEssays . : n/a-n/a

DOI: 10.1002/bies.201300030

Journal article

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Multiple Instances of Ancient Balancing Selection Shared Between Humans and Chimpanzees

E. Leffler, Z. Gao, S. Pfeifer, L. Segurel, A. Auton, O. Venn...

Science . 339 ( 6127 ) : 1578-1582

DOI: 10.1126/science.1234070

Journal article

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Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia

Laure Ségurel, Frédéric Austerlitz, Bruno Toupance, Mathieu M. Gautier, Joanna L Kelley, Patrick Pasquet...

European Journal of Human Genetics . 21 ( 10 ) : 1146-1151

DOI: 10.1038/ejhg.2012.295

Journal article

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Eloge de l'ADN poubelle

Laurent Duret, Sylvain Charlat

Pour la science . 81 : 10--17

Journal article

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Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

Marie Cariou, Laurent Duret, Sylvain Charlat

Ecology and Evolution . 3 ( 4 ) : 846-852

DOI: 10.1002/ece3.512

Journal article

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On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data

Igor Nor, Jan Engelstädter, Olivier Duron, Max Reuter, Marie-France Sagot, Sylvain Charlat

The American Naturalist . 182 ( 1 ) : 15-24

DOI: 10.1086/670612

Journal article

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A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

Gustavo Akio Tominaga Sacomoto, Vincent Lacroix, Marie-France Sagot

Workshop on Algorithms in Bioinformatics (WABI) .

Conference paper

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Telling Stories Fast

Michele Borassi, Pierluigi Crescenzi, Vincent Lacroix, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu

12th International Symposium Experimental Algorithms (SEA) . 7933 : 200-211

Conference paper

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Predicting the proteins of Angomonas deanei, Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family

Maria Cristina Machado Motta, Allan Cezar de Azevedo Martins, Silvana Sant'Anna de Souza, Carolina Moura Costa Catta-Preta, Rosane Silva, Cecilia Coimbra Klein...

PLoS ONE . 8 ( 4 ) : e60209

DOI: 10.1371/journal.pone.0060209

Journal article

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Génomes, protéomes et transcriptomes à foison

G. Perrière

Pour la science . 433 : 38--39

Journal article

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The molecular signal for the adaptation to cold temperature during early life on Earth

Mathieu Groussin, Bastien Boussau, Sandrine Charles, Samuel Blanquart, Manolo Gouy

Biology Letters . 9 ( 5 ) : 20130608

DOI: 10.1098/rsbl.2013.0608

Journal article

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Bioinformatique : cours et cas pratique

Gilbert Deléage, Manolo Gouy

978-2-10-058751-3

Book

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Mycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle.

Véronique Guérin-Faublée, Jean-Pierre Flandrois, Catherine Pichat, Maria Laura Boschiroli, Brigitte Lamy

International Journal of Systematic and Evolutionary Microbiology . 63 ( Pt 12 ) : 4669-74

DOI: 10.1099/ijs.0.051979-0

Journal article

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Candida albicans and non- Candida albicans fungemia in an institutional hospital during a decade

Jean-Pierre Flandrois, Laurence Parmeland, Mathieu Gazon, Claude Guérin, Laurent Argaud, Jean-Jacques Lehot...

Medical Mycology . 51 ( 1 ) : 33-37

DOI: 10.3109/13693786.2012.686673

Journal article

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Diminution of 2,3,5-triphenyltetrazolium chloride toxicity on Listeria monocytogenes growth by iron source addition to the culture medium

T. Junillon, Jp. Flandrois

Food Microbiology . 38 : 1--5

DOI: 10.1016/j.fm.2013.07.005

Journal article

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