GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 541 to 570 publications on 1248 in total

Mod/Resc Parsimony Inference: Theory and application

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron...

Information and Computation . 213 : 23-32

DOI: 10.1016/j.ic.2011.03.008

Journal article

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Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

Vicente Acuña, Paulo Vieira Milreu, Ludovic Cottret, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot

Bioinformatics . 28 ( 19 ) : 2474-2483

DOI: 10.1093/bioinformatics/bts423

Journal article

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The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

Patrice Baa-Puyoulet, Augusto F. Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Toni Gabaldon, Marie-France Sagot...

13. Journées Ouvertes en Biologie, Informatique et Mathématiques . 978-2-7261-1301-1 : Pagination multiple

Conference paper

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Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

Vicente Acuña, Etienne Birmelé, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, Vincent Lacroix...

Theoretical Computer Science . 457 : 1--9

DOI: 10.1016/j.tcs.2012.07.023

Journal article

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Exploration of the core metabolism of symbiotic bacteria

Cecilia Coimbra Klein, Ludovic Cottret, Janice Kielbassa, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos...

BMC Genomics . 13 ( 1 ) : 438

DOI: 10.1186/1471-2164-13-438

Journal article

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ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark Rogers, Kristina Ibanez, Cesar Boullosa...

Nucleic Acids Research . 41 ( D1 ) : D142-D151

DOI: 10.1093/nar/gks1041

Journal article

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Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Milana Frenkel-Morgenstern, Vincent Lacroix, Iakes Ezkurdia, Yishai Levin, Alexandra Gabashvili, Jaime Prilusky...

Genome Research . 22 ( 7 ) : 1231-1242

DOI: 10.1101/gr.130062.111

Journal article

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Evidence for transcript networks composed of chimeric RNAs in human cells

Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge...

PLoS ONE . 7 ( 1 ) : Non paginé

DOI: 10.1371/journal.pone.0028213

Journal article

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Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix, Christelle Borel, Jonathan M. Mudge...

PLoS ONE . 7 : 1-22

Journal article

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Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archea

C. Petitjean, D. Moreira, P. Lopez-Garcia, Céline Brochier-Armanet

BMC Evolutionary Biology . 12 : 226

DOI: 10.1186/1471-2148-12-226

Journal article

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Primate evolutionary history contribution to the deciphering of SIV/HIV origin and diversification

Bénédicte Lafay

Evolution Ottawa - 1th Joint Congress on Evolutionary Biology .

Conference paper

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De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.

Priya Narasingarao, Sheila Podell, Juan A Ugalde, Céline Brochier-Armanet, Joanne B Emerson, Jochen J Brocks...

The International Society of Microbiologial Ecology Journal . 6 ( 1 ) : 81-93

DOI: 10.1038/ismej.2011.78

Journal article

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Interaction between Selection and Biased Gene Conversion in Mammalian Protein-Coding Sequence Evolution Revealed by a Phylogenetic Covariance Analysis

Nicolas Lartillot

Molecular Biology and Evolution . 30 : 356 - 368

DOI: 10.1093/molbev/mss231

Journal article

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Rapport du groupe de travail sur la gestion et le partage des données

Christine Gaspin, Dominique Pontier, Laurence Colinet, Frédéric Dardel, Alain Franc, Odile Hologne...

Report

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Rapid De Novo Evolution of X Chromosome Dosage Compensation in Silene latifolia a Plant with Young Sex Chromosomes

A. Muyle, N. Zemp, C. Deschamps, Sylvain Mousset, A. Wildmer, Gabriel Marais

PLoS Biology . 10 ( 4 ) : e1001308

DOI: 10.1371/journal.pbio.1001308

Journal article

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Structural and dynamical analysis of biological networks.

Cecilia C. Klein, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu, Matteo Brilli

Briefings in Functional Genomics and Proteomics . 14 : 309

DOI: 10.1093/bfgp/els030

Journal article

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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali, Cédric Saule, Cedric Chauve, Yves d'Aubenton-Carafa, Alain Denise, Christine Drevet...

Advances in Bioinformatics . 2012 : 1-5

DOI: 10.1155/2012/893048

Journal article

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Lateral gene transfer as a support for the tree of life.

Sophie S Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 13 ) : 4962-4967

DOI: 10.1073/pnas.1116871109

Journal article

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High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

Journal article

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High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.

Ivan Nasidze, Anna Schönberg, Christoph Theunert, Mingkun Li, Mark Stoneking

European Journal of Human Genetics .

DOI: 10.1038/ejhg.2011.62

Journal article

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Y-Chromosomal Variation in Sub-Saharan Africa: Insights Into the History of Niger-Congo Groups

C. de Filippo, C. Barbieri, M. Whitten, S. Mpoloka, E. Gunnarsdottir, K. Bostoen...

Molecular Biology and Evolution . 28 ( 3 ) : 1255-1269

DOI: 10.1093/molbev/msq312

Journal article

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Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra

Ellen Dröfn Gunnarsdóttir, Madhusudan Nandineni, Mingkun Li, Sean Myles, David Gil, Brigitte Pakendorf...

Nature Communications . 2 : 228

DOI: 10.1038/ncomms1235

Journal article

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Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content

Carina Mugal, Hans Ellegren

Genome Biology . 12 ( 6 ) : R58

DOI: 10.1186/gb-2011-12-6-r58

Journal article

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Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome

Laurence Molina, Nicolas Salvetat, Randa Ben Ameur, Sabine Pérès, Nicolas Sommerer, Faycal Jarraya...

Journal of Proteomics . 75 ( 1 ) : 70 - 80

DOI: 10.1016/j.jprot.2011.06.031

Journal article

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ACoM: A classification method for elementary flux modes based on motif finding

Sabine Pérès, Francois Vallee, Marie M. Beurton-Aimar, Jean-Pierre Mazat

BioSystems . 103 ( 3 ) : 410-419

Journal article

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Lactase persistence in central Asia: phenotype, genotype, and evolution.

Evelyne Heyer, Lionel Brazier, Laure Ségurel, Tatiana Hegay, Frédéric Austerlitz, Lluis Quintana-Murci...

Human Biology . 83 ( 3 ) : 379-92

DOI: 10.3378/027.083.0304

Journal article

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The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans

Laure Ségurel, Ellen Miranda Leffler, Molly M. Przeworski

PLoS Biology . 9 ( 12 ) : e1001211

DOI: 10.1371/journal.pbio.1001211

Journal article

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“ArthropodaCyc”: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Patrice Baa-Puyoulet, Augusto Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Toni Gabaldon, Marie-France Sagot...

5. Annual Arthropod Genomics Symposium “Arthropod Genomics 2011: Exploring Diversity, Relating Similarity” . : 33 p.

Poster

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