GECO Génomique Computationnelle et Evolutive

Efficient enumeration of solutions produced by closure operations

Arnaud Mary, Yann Strozecki

Discrete Mathematics and Theoretical Computer Science . : 1-30

DOI: 10.23638/DMTCS-21-3-22

2019

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The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Alexandre Duprey, Najwa Taïb, Simon Leonard, Tiffany Garin, Jean-Pierre Flandrois, William Nasser...

Environmental Microbiology . 21 ( 8 ) : 2809-2835

DOI: 10.1111/1462-2920.14627

2019

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New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients

Audric Cologne, Clara Benoit-Pilven, Alicia Besson, Audrey Putoux, Amandine Campan-Fournier, Michael B Bober...

RNA . : 1-21

DOI: 10.1261/rna.071423.119

2019

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Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Usama Ashraf, Clara Benoit-Pilven, Vincent Lacroix, Vincent Navratil, Nadia Naffakh

Trends in Microbiology . 27 ( 3 ) : 268-281

DOI: 10.1016/j.tim.2018.11.004

2019

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Francisella tularensis: FupA mutation contributes tofluoroquinolone resistance by increasing vesicle secretion and biofilm formation

Claire Siebert, Helena Lindgren, Sabrina Ferré, Corinne Villers, Sandrine Boisset, Julien Pérard...

Emerging microbes & infections . 8 ( 1 ) : 808-822

DOI: 10.1080/22221751.2019.1615848

2019

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Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation

Lorine Bethencourt, Hasna Boubakri, Najwa Taïb, Philippe Normand, J. Armengaud, Pascale P Fournier...

Research in Microbiology . 170 ( 4-5 ) : 202-213

DOI: 10.1016/j.resmic.2019.04.002

2019

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Evolutionary placement of Methanonatronarchaeia

Monique Aouad, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

Nature Microbiology .

DOI: 10.1038/s41564-019-0359-z

2019

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GeneSpy, a user-friendly and flexible genomic context visualizer

Pierre Simon Garcia, Frédéric Jauffrit, Christophe Grangeasse, Céline Brochier-Armanet

Bioinformatics . 35 ( 2 ) : 329-331

DOI: 10.1093/bioinformatics/bty459

2019

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Article 5. L’émergence des eucaryotes : une mosaïque d’ADN

Dominique D. Joly, Celine Brochier-Armanet

101 secrets de l’ADN. CNRS Éditions, Paris, pp 39-41 . : 39-41

2019

Chapitre d'ouvrage

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Neo-formation of chromosomes in bacteria.

Olivier Poirion, Bénédicte Lafay

DOI: 10.1101/264945

2019

Pré-publication

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Repeat in genomes: how and why you should consider them in genome analyses

Emmanuelle Lerat

Encyclopedia of Bioinformatics and Computational Biology . 2 : 210-220

DOI: 10.1016/B978-0-12-809633-8.20227-6

2019

Chapitre d'ouvrage

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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

DOI: 10.1002/ajpa.23378

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

DOI: 10.1002/ajpa.23345

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

Acte de congrès

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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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GECO Génomique Computationnelle et Evolutive

Equipe Bioinformatique, Phylogénie et Génomique Évolutive

Equipe Baobab

Publications

Efficient enumeration of solutions produced by closure operations

The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients

Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing

Francisella tularensis: FupA mutation contributes tofluoroquinolone resistance by increasing vesicle secretion and biofilm formation

Comparative genomics and proteogenomics highlight key molecular players involved in Frankia sporulation

Evolutionary placement of Methanonatronarchaeia

GeneSpy, a user-friendly and flexible genomic context visualizer

Article 5. L’émergence des eucaryotes : une mosaïque d’ADN

Neo-formation of chromosomes in bacteria.

Repeat in genomes: how and why you should consider them in genome analyses

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