GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Display of 511 to 540 publications on 1251 in total

Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26.

Jérémy Andres, Florence Arsène-Ploetze, Valérie Barbe, Céline Brochier-Armanet, Jessica Cleiss-Arnold, Jean-Yves Coppée...

Genome Biology and Evolution . 5 ( 5 ) : 934-53

DOI: 10.1093/gbe/evt061

Journal article

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Phylogenetic Patterns of GC-Biased Gene Conversion in Placental Mammals and the Evolutionary Dynamics of Recombination Landscapes

Nicolas Lartillot

Molecular Biology and Evolution . 30 ( 3 ) : 489-502

DOI: 10.1093/molbev/mss239

Journal article

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An Experimentally Tested Scenario for the Structural Evolution of Eukaryotic Cys2His2 Zinc Fingers from Eubacterial Ros Homologs

Fortuna Netti, Gaetano Malgieri, Sabrina Esposito, Maddalena Palmieri, Ilaria Baglivo, Carla Isernia...

Molecular Biology and Evolution . 30 ( 7 ) : 1504 - 1513

DOI: 10.1093/molbev/mst068

Journal article

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A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

M. Groussin, Bastien Boussau, Manolo Gouy

Systematic Biology . 62 ( 4 ) : 523-538

DOI: 10.1093/sysbio/syt016

Journal article

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Short and long-term genome stability analysis of prokaryotic genomes

Matteo Brilli, Pietro Liò, Vincent Lacroix, Marie-France Sagot

BMC Genomics . 14 ( 1 ) : 309

DOI: 10.1186/1471-2164-14-309

Journal article

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TPMS: a set of utilities for querying collections of gene trees.

Thomas Bigot, Vincent Daubin, Florent Lassalle, Guy Perrière

BMC Bioinformatics . 14 : 109

DOI: 10.1186/1471-2105-14-109

Journal article

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Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans

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

Conférence Jacques Monod .

Poster

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Geographical delimitation of a partial selective sweep in African \textitDrosophila melanogaster

L. Frezal, F. Meli, Sylvain Mousset, S. Mona, M. Veuille

Molecular ecology . 21 : 5702--14

DOI: 10.1111/mec.12004

Journal article

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The genetic prehistory of southern Africa

Joseph Pickrell, Nick Patterson, Chiara Barbieri, Falko Berthold, Linda Gerlach, Tom Güldemann...

Nature Communications . 3 : 1143

DOI: 10.1038/ncomms2140

Journal article

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Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands

F. Delfin, S. Myles, Y. Choi, D. Hughes, R. Illek, M. van Oven...

Molecular Biology and Evolution . 29 ( 2 ) : 545-564

DOI: 10.1093/molbev/msr186

Journal article

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Bringing together linguistic and genetic evidence to test the Bantu expansion

C. de Filippo, K. Bostoen, M. Stoneking, Brigitte Pakendorf

Proceedings of the Royal Society B: Biological Sciences . 279 ( 1741 ) : 3256-3263

DOI: 10.1098/rspb.2012.0318

Journal article

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The endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue

A. Mey, Hervé Acloque, Emmanuelle Lerat, S. Gounel, V. Tribollet, S. Blanc...

Retrovirology . 9 ( 1 ) : 21

DOI: 10.1186/1742-4690-9-21

Journal article

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Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

Ellen Miranda Leffler, Kevin Bullaughey, Daniel R Matute, Wynn Meyer, Laure Ségurel, Aarti A. Venkat...

PLoS Biology . 10 ( 9 ) : e1001388

DOI: 10.1371/journal.pbio.1001388

Journal article

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A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

A. Auton, A. Fledel-Alon, S. Pfeifer, O. Venn, L. Segurel, T. Street...

Science . 336 ( 6078 ) : 193-198

DOI: 10.1126/science.1216872

Journal article

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The ABO blood group is a trans-species polymorphism in primates

Laure L. Segurel, Emma E. E. E. Thompson, Timothée T. Flutre, Jessica J. Lovstad, Aarti A. Venkat, Susan W. S. W. Margulis...

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 45 ) : 18493 - 18498

DOI: 10.1073/pnas.1210603109

Journal article

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Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

Eugénie Pessia, Alexandra Popa, Sylvain Mousset, Clément Rezvoy, Laurent Duret, G. Marais

Genome Biology and Evolution . 4 : 787-794

DOI: 10.1093/gbe/evs052

Journal article

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Efficient Bubble Enumeration in Directed Graphs

Etienne E. Birmelé, Pierluigi Crescenzi, Rui Ferreira, Roberto Grossi, Vincent Lacroix, Andrea Marino...

String Processing and Information Retrieval (SPIRE) . 7608 : 118-129

DOI: 10.1007/978-3-642-34109-0_13

Conference paper

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Minimum ratio cover of matrix columns by extreme rays of its induced cone

Alexandre da Silva Freire, Vicente Acuña, Pierluigi Crescenzi, Carlos Eduardo Ferreira, Vincent Lacroix, Paulo Vieira Milreu...

Proceedings of the Second international Symposium on Combinatorial Optimization (ISCO) . 7422 : 165--177

DOI: 10.1007/978-3-642-32147-4_16

Conference paper

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Sampling solution traces for the problem of sorting permutations by signed reversals

Christian Baudet, Zanoni Dias, Marie-France Sagot

Algorithms for Molecular Biology . 7 ( 1 ) : 18

DOI: 10.1186/1748-7188-7-18

Journal article

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KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

Gustavo Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot...

BMC Bioinformatics . 13 ( Suppl 6 ) : S5

DOI: 10.1186/1471-2105-13-S6-S5

Journal article

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Toward community standards in the quest for orthologs

Christophe Dessimoz, Toni Gabaldon, David Roos, Erik L L Sonnhammer, Javier Herrero, Alfonso Valencia...

Bioinformatics . 28 ( 6 ) : 900-904

DOI: 10.1093/bioinformatics/bts050

Journal article

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Simplified detection of food-borne pathogens: An in situ high affinity capture and staining concept

T. Junillon, A. Vimont, D. Mosticone, B. Mallen, F. Baril, C. Rozand...

Journal of Microbiological Methods . 91 : 501--505

DOI: 10.1016/j.mimet.2012.09.015

Journal article

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Modelling and simulating generic RNA-Seq experiments with the flux simulator.

Thasso Griebel, Benedikt Zacher, Paolo Ribeca, Emanuele Raineri, Vincent Lacroix, Roderic Guigó...

Nucleic Acids Research . 40 ( 20 ) : 10073-10083

DOI: 10.1093/nar/gks666

Journal article

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Les défis de la systématique face au monde microbien

Céline Brochier-Armanet, Simonetta Gribaldo

incollection . 328 : 49-52

Journal article

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Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage

V. de Crécy-Lagard, F. Forouhar, Céline Brochier-Armanet, L. Tong, Jf. Hunt

Biology Direct . 7 : 1--13

DOI: 10.1186/1745-6150-7-32

Journal article

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A comparative analysis of the amounts and dynamics of transposable elements in natural populations of Drosophila melanogaster and Drosophila simulans.

Cristina Vieira, Marie Fablet, Emmanuelle Lerat, Matthieu Boulesteix, Rita Rebollo, Nelly Burlet...

Journal of Environmental Radioactivity . 113 : 83-86

DOI: 10.1016/j.jenvrad.2012.04.001

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 Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Toni Gabaldon, Marie-France Sagot...

5. Réunion Réseau BAPOA .

Poster

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Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.

Nuno D Mendes, Steffen Heyne, Ana T Freitas, Marie-France Sagot, Rolf Backofen

Bioinformatics . 28 ( 23 ) : 3034-3041

DOI: 10.1093/bioinformatics/bts574

Journal article

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Analysis of RNA Transcripts by High-Throughput RNA Sequencing

Paolo Ribeca, Vincent Lacroix, Michael Sammeth, Roderic Guigó

Alternative pre-mRNA Splicing: Theory and Protocols . 9783527636778

DOI: 10.1002/9783527636778.ch50

Book chapter

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