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 601 to 630 publications on 1415 in total

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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Mesotoga infera sp. nov., a mesophilic member of the order Thermotogales, isolated from an underground gas storage aquifer.

Wajdi Ben Hania, Anne Postec, Thomas Aüllo, Anthony Ranchou-Peyruse, Gaël Erauso, Céline Brochier-Armanet...

International Journal of Systematic and Evolutionary Microbiology . 63 ( Pt 8 ) : 3003-8

DOI: 10.1099/ijs.0.047993-0

Journal article

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Metagenomics of Kamchatkan hot spring filaments reveal two new major (hyper)thermophilic lineages related to Thaumarchaeota

L. Eme, Lj. Reigstad, A. Spang, A. Lanzen, T. Weinmaier, T. Rattei...

Research in Microbiology . 164 : 425--38

DOI: 10.1016/j.resmic.2013.02.006

Journal article

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Utilization of Machine-Learning Methodologies in Order to Understand Complex Evolutionary and Functional Links among Bacterial Genomes

Olivier Poirion, Bénédicte Lafay

IFCS2013 Book of abstracts . : p. 203

Conference paper

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Tracing the origin of megaplasmids and secondary chromosomes in bacterial genomes

Olivier Poirion, Laurent Krähenbühl, Bénédicte Lafay

SBME . : A049 363

Conference paper

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Visualization and analysis of an interconnected network of genomic elements

Olivier Poirion, Bénédicte Lafay

AdO'13: Apprentissage et données Omiques - Atelier de la conférence d'apprentissage Francophone CAp'13 - PFIA 2013 8ème Plate-Forme Intelligence Artificielle . : AdO-13_paper_6

Conference paper

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Lateral Gene Transfer from the Dead.

Gergely J Szöllosi, Eric Tannier, Nicolas Lartillot, Vincent Daubin

Systematic Biology . 62 ( 3 ) : 386-397

DOI: 10.1093/sysbio/syt003

Journal article

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Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

Benoit Nabholz, Nicole Uwimana, Nicolas Lartillot

Genome Biology and Evolution . 5 ( 7 ) : 1273 - 1290

DOI: 10.1093/gbe/evt083

Journal article

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Transcriptome Characterisation of the Ant Formica exsecta with New Insights into the Evolution of Desaturase Genes in Social Hymenoptera

Hélène E Badouin, Khalid Belkhir, Emma Gregson, Juan Galindo, Liselotte Sundström, Stephen Martin...

PLoS ONE . 8 ( 7 ) : e68200

DOI: 10.1371/journal.pone.0068200

Journal article

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Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

Journal article

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« ArthropodaCyc » : une collection de bases de données enrichies à l’aide de CycADS pour étudier et comparer le métabolisme des arthropodes.

Patrice Baa-Puyoulet, Stefano Colella, Augusto Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Federica Calevro...

17. Colloque de Biologie de l’Insecte - CBI-2013 .

Poster

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Nickel import in bacteria, structural study of extracytoplasmic nickel-binding proteins

Hugo Lebrette, Christine Cavazza, Céline Brochier-Armanet, Elise Borezée-Durant

16. International Conference on Biological Inorganic Chemistry (ICBIC) . 19 : 1

Conference paper

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Procédé de fabrication de Gaz Naturel de Synthèse par couplage d'une méthanation avec une électrolyse de vapeur d'eau à haute température

Myriam de Saint Jean, Vincent Lacroix, Pierre Baurens, Chakib Bouallou

XIVeme congrès SFGP . 104 : 2012214

Conference paper

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XACT, a long non-coding transcript coating the active X chromosome in human pluripotent cells

Céline Vallot, Christophe Huret, Yann Lesecque, Alissa Resch, Noufϊssa Oudrhiri, Annelise Bennaceur...

Epigenetics and Chromatin: Interactions and processes . 6 ( Suppl 1 ) : O33

DOI: 10.1186/1756-8935-6-S1-O33

Conference paper

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New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data

Alice Julien-Laferriere, Gustavo Sacomoto, Rayan Chikhi, Erwan Scaon, David P. Parsons, Marie-France Sagot...

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) .

Conference paper

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Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

João Alves, Cecilia Klein, Flávia Maia da Silva, André Costa-Martins, Myrna Serrano, Gregory Buck...

BMC Evolutionary Biology . 13 ( 1 ) : 190

DOI: 10.1186/1471-2148-13-190

Journal article

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Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses

Cecilia C Klein, João M P Alves, Myrna G Serrano, Gregory A Buck, Ana Tereza R Vasconcelos, Marie-France Sagot...

PLoS ONE . 8 ( 11 ) : e79786

DOI: 10.1371/journal.pone.0079786

Journal article

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Bio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution

Laurent Gueguen, Sylvain Gaillard, Bastien Boussau, Manolo Gouy, Mathieu Groussin, Nicolas C. Rochette...

Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750

DOI: 10.1093/molbev/mst097

Journal article

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Experimental assessment of the accuracy of genomic selection in sugarcane

M. Gouy, Y. Rousselle, Denis Bastianelli, Philippe Lecomte, Laurent Bonnal, D. Roques...

TAG Theoretical and Applied Genetics . 126 ( 10 ) : 2575-2586

DOI: 10.1007/s00122-013-2156-z

Journal article

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Egyptian mummies record increasing aridity in the Nile valley from 5500 to 1500yr before present

Alexandra Touzeau, Janne Blichert-Toft, Romain Amiot, François Fourel, François Martineau, Jenefer Cockitt...

Earth and Planetary Science Letters . 375 : 92-100

DOI: 10.1016/j.epsl.2013.05.014

Journal article

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Phylogenies of Central Element Proteins Reveal the Dynamic Evolutionary History of the Mammalian Synaptonemal Complex: Ancient and Recent Components

J. Fraune, Céline Brochier-Armanet, M. Alsheimer, R. Benavente

GENETICS . 195 : 781--793

DOI: 10.1534/genetics.113.156679

Journal article

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LUCA, ancêtre de tous les êtres vivants

Simonetta Gribaldo, Céline Brochier-Armanet

Les Dossiers de la Recherche . 2 : 29--31

Journal article

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An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

Annabelle A. Haudry, Adrian Platts, Emilio Vello, Douglas Hoen, Mickael Leclercq, Robert Williamson...

Nature Genetics . 45 ( 8 ) : 891 - 898

DOI: 10.1038/ng.2684

Journal article

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