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 511 to 540 publications on 1415 in total

The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

Abdel Belkorchia, Cyrielle Gasc, Valérie Polonais, Nicolas Parisot, Nicolas Gallois, Céline Ribière...

PLoS ONE . 10 ( 9 ) : 1-12

DOI: 10.1371/journal.pone.0139075

Journal article

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Probabilistic models of eukaryotic evolution: time for integration

Nicolas Lartillot

Philosophical Transactions of the Royal Society B: Biological Sciences . 370 ( 1678 ) : 20140338

DOI: 10.1098/rstb.2014.0338

Journal article

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Genomic data do not support comb jellies as the sister group to all other animals

Davide Pisani, Walker Pett, Martin Dohrmann, Roberto Feuda, Omar Rota Stabelli, Herve Philippe...

Proceedings of the National Academy of Sciences of the United States of America . 112 ( 50 ) : 15402-15407

DOI: 10.1073/pnas.1518127112

Journal article

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Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees

M. Groussin, J. K. Hobbs, G. J. Szollosi, S. Gribaldo, V. L. Arcus, Manolo Gouy

Molecular Biology and Evolution . 32 : 13-22

DOI: 10.1093/molbev/msu305

Journal article

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Occurrence of a non deleterious gene conversion event in the BRCA1 gene

C. Tessereau, M. Leone, M. Buisson, L. Duret, O. M. Sinilnikova, S. Mazoyer

Genes, Chromosomes & Cancer . 54 : 646-52

DOI: 10.1002/gcc.22278

Journal article

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Prévalence et diversité des éléments intégratifs conjugatifs et mobilisables chez les streptocoques

Charles Coluzzi

: 70

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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 Ségurel, Raphaëlle Chaix...

European Journal of Human Genetics . 22 ( 10 ) : 1201-1207

DOI: 10.1093/molbev/mst156

Journal article

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Estimation of the RNU2 macrosatellite mutation rate by BRCA1 mutation tracing

C. Tessereau, Yann Lesecque, N. Monnet, M. Buisson, L. Barjhoux, M. Leone...

Nucleic Acids Research . 42 ( 14 ) : 9121-30

DOI: 10.1093/nar/gku639

Journal article

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Tracing Pastoralist Migrations to Southern Africa with Lactase Persistence Alleles

Enrico Macholdt, Vera Lede, Chiara Barbieri, Sununguko Mpoloka, Hua Chen, Montgomery Slatkin...

Current Biology . 24 ( 8 ) : 875-879

DOI: 10.1016/j.cub.2014.03.027

Journal article

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Ancient west Eurasian ancestry in southern and eastern Africa

Joseph Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking...

Proceedings of the National Academy of Sciences of the United States of America . 111 ( 7 ) : 2632-2637

DOI: 10.1073/pnas.1313787111

Journal article

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Unraveling the complex maternal history of southern African Khoisan populations

Chiara Barbieri, Tom Güldemann, Linda Gerlach, Falko Berthold, Hirosi Nakagawa, Sununguko Mpoloka...

American Journal of Physical Anthropology . 153 ( 3 ) : 435-448

DOI: 10.1002/ajpa.22441

Journal article

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New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa

Enrico Macholdt, Montgomery Slatkin, Brigitte Pakendorf, Mark Stoneking

American Journal of Physical Anthropology . 156 ( 4 ) : 661-664

DOI: 10.1002/ajpa.22675

Journal article

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Migration and Interaction in a Contact Zone: mtDNA Variation among Bantu-Speakers in Southern Africa

Chiara Barbieri, Mário Vicente, Sandra Oliveira, Koen Bostoen, Jorge Rocha, Mark Stoneking...

PLoS ONE . 9 ( 6 ) : e99117

DOI: 10.1371/journal.pone.0099117

Journal article

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A high‐density linkage map enables a second‐generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

Takeshi Kawakami, Linnéa Smeds, Niclas Backström, Arild Husby, Anna Qvarnström, Carina Mugal...

Molecular Ecology . 23 ( 16 ) : 4035-4058

DOI: 10.1111/mec.12810

Journal article

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Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

Carina Mugal, Jochen B.W. Wolf, Ingemar Kaj

Molecular Biology and Evolution . 31 ( 1 ) : 212-231

DOI: 10.1093/molbev/mst192

Journal article

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SAT-Based Metabolics Pathways Analysis without Compilation

Sabine Pérès, Morterol Martin, Laurent Simon

CMSB 2014 .

Conference paper

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Systematic study of a metabolic network

Bertrand P Beauvoit, Sophie Colombié, Jean-Pierre Mazat, Christine Nazaret, Sabine Pérès

advances in Systems and Synthetic Biology . 978-2-7598-1201-1 : 173 p.

Conference paper

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Preserving immune diversity through ancient inheritance and admixture

Laure L. Segurel, Lluis Quintana-Murci

Current Opinion in Immunology . 30 : 79-84

DOI: 10.1016/j.coi.2014.08.002

Journal article

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TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception

Amir Kermany, Laure L. Segurel, Tiffany Oliver, Molly Przeworski

Bioinformatics . 30 ( 14 ) : 2035-2042

DOI: 10.1093/bioinformatics/btu159

Journal article

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Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia

Carla Aimé, Paul Verdu, Laure L. Segurel, Begoña Martinez-Cruz, Tatyana Hegay, Evelyne Heyer...

European Journal of Human Genetics . 22 ( 10 ) : 1201-1207

DOI: 10.1038/ejhg.2014.2

Journal article

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A call for benchmarking transposable element annotation methods.

Douglas R Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte...

Mobile DNA . 6 : 13

DOI: 10.1186/s13100-015-0044-6

Journal article

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Subcellular Localization of ENS-1/ERNI in Chick Embryonic Stem Cells

Sophie Blanc, Florence Ruggiero, Anne-Marie Birot, Hervé Acloque, Didier Decimo, Emmanuelle Lerat...

PLoS ONE . 9 ( 3 ) : e92039

DOI: 10.1371/journal.pone.0092039

Journal article

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The spatiotemporal program of DNA replication is associated with specific combinations of chromatin marks in human cells.

Franck Picard, Jean-Charles Cadoret, Benjamin Audit, Alain Arneodo, Adriana A. Alberti, Christophe Battail...

PLoS Genetics . 10 ( 5 ) : e1004282

DOI: 10.1371/journal.pgen.1004282

Journal article

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The Red Queen Model of Recombination Hotspots Evolution in the Light of Archaic and Modern Human Genomes

Y Lesecque, S. S. Glemin, N. Lartillot, D. Mouchiroud, L. Duret

PLoS Genetics . 10 : e1004790

DOI: 10.1371/journal.pgen.1004790

Journal article

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Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome

E. M. Kvikstad, L. Duret

Molecular Biology and Evolution . 31 : 23-36

DOI: 10.1093/molbev/mst185

Journal article

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Annotating arthropods genome to study and compare their metabolism: the ArthropodaCyc collection of Cyc databases powered by CycADS

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

13. European Conference on Computational Biology (ECCB) . : 1 p.

Poster

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Amortized Õ(\textbarV)-Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

R. Ferreira, R. Grossi, R. Rizzi, Gustavo Sacomoto, Marie-France Sagot

Lecture Notes in Computer Science . 8737 : 418-429

Journal article

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On the Enumeration of Minimal Dominating Sets and Related Notions

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine

SIAM Journal on Discrete Mathematics . 28 ( 4 ) : 1916 - 1929

DOI: 10.1137/120862612

Journal article

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Diet of ancient Egyptians inferred from stable isotope systematics

Alexandra Touzeau, Romain Amiot, Janne Blichert-Toft, Jean-Pierre Flandrois, François Fourel, Vincent Grossi...

Journal of Archaeological Science . 46 : 114-124

DOI: 10.1016/j.jas.2014.03.005

Journal article

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