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 271 to 300 publications on 1377 in total

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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Book chapter

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Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua

Paris Veltsos, Kate Ridout, Melissa Toups, Santiago González-Martínez, Aline Muyle, Olivier Emery...

Genetics . 212 ( 3 ) : 815-835

DOI: 10.1534/genetics.119.302045

Journal article

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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

Journal article

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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

Journal article

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Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems

Hélène Martin, Fantin E Carpentier, Sophie Gallina, Cécile Godé, Eric Schmitt, Aline Muyle...

Genome Biology and Evolution . 11 ( 2 ) : 350-361

DOI: 10.1093/gbe/evz001

Journal article

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Genomic imprinting mediates dosage compensation in a young plant XY system.

Aline Muyle, Niklaus Zemp, Cécile Fruchard, Radim Cegan, Jan Vrána, Clothilde Deschamps...

DOI: 10.1101/179044

Preprint

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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

Sabine Pérès

Computational systems biology for cancer .

Conference paper

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