GECO Génomique Computationnelle et Evolutive

Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon...

Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11

DOI: 10.1098/rstb.2018.0234

2019

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Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Camille Sessegolo, Corinne Cruaud, Corinne da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien...

Scientific Reports . 9 ( 1 ) : 14908

DOI: 10.1038/s41598-019-51470-9

2019

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Metabolic Games

Taneli Pusa, Martin Wannagat, Marie-France Sagot

Frontiers in Applied Mathematics and Statistics . 5 : 1-13

DOI: 10.3389/fams.2019.00018

2019

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Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia

Nguyen Thuy Duong, Enrico Macholdt, Nguyen Dang Ton, Leonardo Arias, Roland Schröder, Nguyen van Phong...

Scientific Reports . 8 ( 1 )

DOI: 10.1038/s41598-018-29989-0

2018

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Genetic structure and sex-biased gene flow in the history of southern African populations

Vladimir Bajić, Chiara Barbieri, Alexander Hübner, Tom Tom Güldemann, Christfried Naumann, Linda Gerlach...

American Journal of Physical Anthropology . 167 ( 3 ) : 656-671

DOI: 10.1002/ajpa.23694

2018

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Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa

Sandra Oliveira, Anne-Maria Fehn, Teresa Aço, Fernanda Lages, Magdalena Gayà-Vidal, Brigitte Pakendorf...

American Journal of Physical Anthropology . 165 ( 3 ) : 518-535

2018

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High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia

Leonardo Arias, Chiara Barbieri, Guillermo Barreto, Mark Stoneking, Brigitte Pakendorf

American Journal of Physical Anthropology . 165 ( 2 ) : 238-255

2018

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Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

Denis Pierron, Margit Heiske, Harilanto Razafindrazaka, Veronica Pereda-Loth, Jazmin Sanchez, Omar Alva...

Nature Communications . 9 ( 1 ) : 932

DOI: 10.1038/s41467-018-03342-5

2018

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The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor

Nicolas Brucato, Verónica Fernandes, Stéphane Mazières, Pradiptajati Kusuma, Murray Cox, Joseph Wainaina Ng'Ang'A...

American Journal of Human Genetics . 102 ( 1 ) : 58-68

DOI: 10.1016/j.ajhg.2017.11.011

2018

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Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

Leonardo Arias, Roland Schröder, Alexander Hübner, Guillermo Barreto, Mark Stoneking, Brigitte Pakendorf

Molecular Biology and Evolution . 35 ( 11 ) : 2719-2735

DOI: 10.1093/molbev/msy169

2018

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Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Paulina Bolívar, Carina Mugal, Matteo Rossi, Alexander Nater, Mi Wang, Ludovic Dutoit...

Molecular Biology and Evolution . 35 ( 10 ) : 2475-2486

DOI: 10.1093/molbev/msy149

2018

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Sex‐biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Carina Mugal, Paulina Bolívar, Mi Wang, Krystyna Nadachowska-Brzyska, Linnéa Smeds...

Molecular Ecology . 27 ( 18 ) : 3572-3581

DOI: 10.1111/mec.14789

2018

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Positive selection on human gamete-recognition genes

Michael Hart, Daryn Stover, Vanessa Guerra, Sahar Mozaffari, Carole Ober, Carina Mugal...

PeerJ . 6 : e4259

DOI: 10.7717/peerj.4259

2018

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Thermodynamic constraints for identifying elementary flux modes

Sabine Pérès, Stefan Schuster, Philippe Dague

Biochemical Society Transactions . 46 ( 3 ) : 641-647

DOI: 10.1042/BST20170260

2018

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Identifying Biomarkers of Wharton’s Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect

Benoît Laflaquière, Gabrielle Leclercq, Chandarong Choey, Jingkui Chen, Sabine Pérès, Caryn Ito...

Metabolites . 8 ( 1 ) : 18

DOI: 10.3390/metabo8010018

2018

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Metabolic view of tumor growth: a kinetic model to screen potential therapeutic targets

Sabine Pérès

Computational systems biology for cancer .

2018

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Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

Nina Marchi, Philippe Mennecier, Myriam Georges, Sophie Lafosse, Tatyana Hegay, Choduraa Dorzhu...

Scientific Reports . 8 : 9397

DOI: 10.1038/s41598-018-27047-3

2018

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Bounding the Order of a Graph Using Its Diameter and Metric Dimension: A Study Through Tree Decompositions and VC Dimension

Laurent Beaudou, Peter Dankelmann, Florent Foucaud, Michael Antony Henning, Arnaud Mary, Aline Parreau

SIAM Journal on Discrete Mathematics . 32 ( 2 ) : 902 - 918

DOI: 10.1137/16M1097833

2018

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A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Diego Carriel, Pierre Simon Garcia, Florence Castelli, Patricia Lamourette, François Fenaille, Céline Brochier-Armanet...

Genome Biology and Evolution . 10 ( 11 ) : 3058-3075

DOI: 10.1093/gbe/evy228

2018

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Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Laurent Guéguen, Laurent Duret

Molecular Biology and Evolution . 35 ( 3 ) : 734-742

DOI: 10.1093/molbev/msx308

2018

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Exploring and Visualising Spaces of Tree Reconciliations

Katharina Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri

Systematic Biology . : 1-36

DOI: 10.1093/sysbio/syy075

2018

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Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Ifigeneia Kyrkou, Taneli Pusa, Lea Ellegaard-Jensen, Marie-France Sagot, Lars Hestbjerg Hansen

Frontiers in Microbiology . 9 : 1-23

DOI: 10.3389/fmicb.2018.02141

2018

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Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae

Mariana G. Ferrarini, Scheila Gabriele Mucha, Delphine Parrot, Guillaume Meiffren, José Fernando Ruggiero Bachega, Gilles Comte...

Molecular Microbiology . : 1-45

DOI: 10.1111/mmi.13957

2018

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A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix...

PLoS Genetics . 14 ( 11 ) : 1-28

DOI: 10.1371/journal.pgen.1007758

2018

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Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

Clara Benoit-Pilven, Camille Marchet, Emilie Chautard, Leandro Lima, Marie-Pierre Lambert, Gustavo Sacomoto...

Scientific Reports . 8 ( 1 )

DOI: 10.1038/s41598-018-21770-7

2018

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Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility

Clothilde Esteve, Ludmila Francescatto, Perciliz Tan, Aurélie Bourchany, Cécile de Leusse, Evelyne Marinier...

American Journal of Human Genetics . 102 ( 3 ) : 364 - 374

DOI: 10.1016/j.ajhg.2018.01.009

2018

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PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae

L. Zucchini, C. Mercy, Ps. Garcia, C. Cluzel, V. Gueguen-Chaignon, F. Galisson...

Nature Microbiology . 3 ( 2 ) : 197-209

DOI: 10.1038/s41564-017-0069-3

2018

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Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae , in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor

Khaled Fadhlaoui, Wagdi Ben Hania, Fabrice Armougom, Manon Joseph, Marie-Laure Fardeau, Gaël Erauso...

Environmental Microbiology . 20 ( 1 ) : 281-292

DOI: 10.1111/1462-2920.13995

2018

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Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Simon Laurin-Lemay, Nicolas Rodrigue, Nicolas Lartillot, Herve Philippe

Molecular Biology and Evolution . 35 ( 11 ) : 2819-2834

DOI: 10.1093/molbev/msy173

2018

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Population specific dynamics and selection patterns of transposable element insertions in European natural populations

Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira...

Molecular Ecology . : 1-17

DOI: 10.1111/mec.14963

2018

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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Detecting adaptive convergent amino acid evolution

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules

Metabolic Games

Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia

Genetic structure and sex-biased gene flow in the history of southern African populations

Matriclans shape populations: Insights from the Angolan Namib Desert into the maternal genetic history of southern Africa

High-resolution mitochondrial DNA analysis sheds light on human diversity, cultural interactions, and population mobility in Northwestern Amazonia

Strong selection during the last millennium for African ancestry in the admixed population of Madagascar

The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor

Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia

Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Sex‐biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher ( Ficedula albicollis ) genome

Positive selection on human gamete-recognition genes

Thermodynamic constraints for identifying elementary flux modes

Identifying Biomarkers of Wharton’s Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect

Metabolic view of tumor growth: a kinetic model to screen potential therapeutic targets

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy

Bounding the Order of a Graph Using Its Diameter and Metric Dimension: A Study Through Tree Decompositions and VC Dimension

A novel subfamily of bacterial AAT-fold basic amino acid decarboxylases and functional characterization of its first representative: Pseudomonas aeruginosa LdcA

Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition

Exploring and Visualising Spaces of Tree Reconciliations

Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae

A fast and agnostic method for bacterial genome-wide association studies: bridging the gap between k-mers and genetic events

Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

Loss-of-Function Mutations in UNC45A Cause a Syndrome Associating Cholestasis, Diarrhea, Impaired Hearing, and Bone Fragility

PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae

Obligate sugar oxidation in Mesotoga spp., phylum Thermotogae , in the presence of either elemental sulfur or hydrogenotrophic sulfate-reducers as electron acceptor

Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation–Selection Models

Population specific dynamics and selection patterns of transposable element insertions in European natural populations