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 241 to 270 publications on 1399 in total

The ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus.

Charles Coluzzi, Julie Lao, Gérard Guédon, Marie-Dominique Devignes, Chloé Ambroset, Thomas Lacroix...

8th symposium on Antimicrobial Resistance in Animal and Environment .

Conference paper

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The ICE/IME Finder approach and its application to ICE/IME annotation in Streptococcus

Charles Coluzzi, Julie Lao, Gérard Guédon, Marie-Dominique Devignes, Chloé Ambroset, Thomas Lacroix...

4th International Workshop on Streptococcus suis .

Poster

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Naturally radioactive environments influence the rate and spectrum of mutation

Nathanaëlle Saclier, Patrick Chardon, Florian Malard, Lara Konecny-Dupré, D. Eme, Arnaud Bellec...

Annual conference of the Society for Molecular Biology and Evolution .

Poster

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Development of a dual RNA-seq strategy to unravel the molecular bases of host-symbiont interactions

Nicolas Parisot, Agnès Vallier, Justin Maire, Mariana G. Ferrarini, Benjamin Gillet, Sandrine Hughes...

Journée scientifique de la FR BioEnviS .

Poster

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High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids

Izabella L Tambones, Annabelle Haudry, Maryanna C Simão, Claudia M A Carareto

Mobile DNA . 10 ( 1 )

DOI: 10.1186/s13100-019-0184-1

Journal article

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Key role of chromosomal mobile genetic elements transferred by conjugation in the dissemination of antimicrobial resistance in S. suis

Virginie Libante, Yves Nombre, Charles Coluzzi, Johan Staub, Gérard Guédon, Marcelo Gottschalk...

4th International Workshop on Streptococcus suis .

Conference paper

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Development of a dual RNA-seq strategy to unravel the molecular bases of host-symbiont interactions

Nicolas Parisot, Agnès Vallier, Justin Maire, Mariana G. Ferrarini, Benjamin Gillet, Sandrine Hughes...

Auvergne Rhône-Alpes Regional Workshop on Microbiome .

Poster

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Archaic mitochondrial DNA inserts in modern day nuclear genomes

Robert Bücking, Murray Cox, Georgi Hudjashov, Lauri Saag, Herawati Sudoyo, Mark Stoneking

BMC Genomics . 20 ( 1 ) : 1017

DOI: 10.1186/s12864-019-6392-8

Journal article

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Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations

Wibhu Kutanan, Jatupol Kampuansai, Metawee Srikummool, Andrea Brunelli, Silvia Ghirotto, Leonardo Arias...

Molecular Biology and Evolution . 36 : 1490 - 1506

DOI: 10.1093/molbev/msz083

Journal article

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Sharing of heteroplasmies between human liver lobes varies across the mtDNA genome

Alexander Hübner, Manja Wachsmuth, Roland Schröder, Mingkun Li, Anna Maria Eis-Hübinger, Burkhard Madea...

Scientific Reports . 9 : 11219

DOI: 10.1038/s41598-019-47570-1

Journal article

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The Current Genomic Landscape of Western South America: Andes, Amazonia, and Pacific Coast

Chiara Barbieri, Rodrigo Barquera, Leonardo Arias, José R Sandoval, Oscar Acosta, Camilo Zurita...

Molecular Biology and Evolution . 36 ( 12 ) : 2698 - 2713

DOI: 10.1093/molbev/msz174

Journal article

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WGS-based telomere length analysis in Dutch family trios implicates stronger maternal inheritance and a role for RRM1 gene

Lilit Nersisyan, Maria Nikoghosyan, Laurent C Francioli, Androniki Menelaou, Sara L Pulit, Clara C Elbers...

Scientific Reports . 9 : 18758

DOI: 10.1038/s41598-019-55109-7

Journal article

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Multiple Deeply Divergent Denisovan Ancestries in Papuans

Guy Jacobs, Georgi Hudjashov, Lauri Saag, Pradiptajati Kusuma, Chelzie Darusallam, Daniel Lawson...

Cell .

DOI: 10.1016/j.cell.2019.02.035

Journal article

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Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia

Nicolas Brucato, Verónica Fernandes, Pradiptajati Kusuma, Viktor Černý, Connie Mulligan, Pedro Soares...

Genome Biology and Evolution . 11 ( 3 ) : 748-758

DOI: 10.1093/gbe/evz028

Journal article

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The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola

Sandra Oliveira, Alexander Hübner, Anne-Maria Fehn, Teresa Aço, Fernanda Lages, Brigitte Pakendorf...

European Journal of Human Genetics . 27 ( 3 ) : 475-483

DOI: 10.1038/s41431-018-0304-2

Journal article

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A kinetic metabolic study of lipid production in Chlorella protothecoides under heterotrophic condition

Xiaojie Ren, Jean-Sébastien Deschênes, Réjean Tremblay, Sabine Pérès, Mario Jolicœur

Microbial Cell Factories . 18 ( 1 ) : 113

DOI: 10.1186/s12934-019-1163-4

Journal article

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Metabolic therapies inhibit tumor growth in vivo and in silico

Jorgelindo da Veiga Moreira, Minoo Hamraz, Mohammad Abolhassani, Laurent H Schwartz, Mario Jolicœur, Sabine Pérès

Scientific Reports . 9 ( 1 ) : 3153

DOI: 10.1038/s41598-019-39109-1

Journal article

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Modulating mitochondria horsepower for biotechnological applications

Jorgelindo da Veiga Moreira, Laurent Schwartz, Sabine S. Peres

Metabolic Pathway Analysis 2019 .

Conference paper

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Using a hybrid approach to model central carbon metabolism across the cell cycle

Cecile Moulin, Laurent Tournier, Sabine Pérès

International Workshop on Hybrid Systems Biology . 11705

DOI: 10.1007/978-3-030-28042-0_9

Conference paper

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Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels

Ana Lokmer, Amandine Cian, Alain Froment, Nausicaa Gantois, Eric Viscogliosi, Magali Chabé...

PLoS ONE . 14 ( 2 ) : e0211139

DOI: 10.1371/journal.pone.0211139

Journal article

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Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny

Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot

IEEE/ACM Transactions on Computational Biology and Bioinformatics . : 1-11

DOI: 10.1109/TCBB.2018.2838667

Journal article

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Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss, Gladys Mialdea, Vincent Miele, Damien M. de Vienne, Jean Peccoud, Clément Gilbert...

PLoS Genetics . 15 ( 2 ) : e1007965

DOI: 10.1371/journal.pgen.1007965

Journal article

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A Distance-based block searching algorithm

M-F. Sagot, Alain Viari, H. Soldano

Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95) . 3 : 322-331

Conference paper

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The Perfect Matching Reconfiguration Problem

Marthe Bonamy, Nicolas Bousquet, Marc Heinrich, Takehiro Ito, Yusuke Kobayashi, Arnaud Mary...

MFCS 2019 - 44th International Symposium on Mathematical Foundations of Computer Science . : 1-14

DOI: 10.4230/LIPIcs.MFCS.2019.80

Conference paper

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Article 22. Crise du stockage: conserver les molécules d'ADN ou les données informatiques de l'ADN ?

Dominique D. Joly, Guy Perriere

101 Secrets de l'ADN. CNRS Editions, Paris, pp 90-91 . : 90-91

Book chapter

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Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

Jean-Pierre Flandrois, Céline Brochier-Armanet, Jérôme Briolay, Danis Abrouk, Guillaume P Schwob, Philippe Normand...

Research in Microbiology . 170 ( 6-7 ) : 280-287

DOI: 10.1016/j.resmic.2019.06.005

Journal article

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Structure, Function, and Evolution of the Pseudomonas aeruginosa Lysine Decarboxylase LdcA

Eaazhisai Kandiah, Diego Carriel, Pierre Simon Garcia, Jan Felix, Manuel Banzhaf, George Kritikos...

Structure .

DOI: 10.1016/j.str.2019.10.003

Journal article

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The bacterial MrpORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis

Romain Pardoux, Anouchka Fiévet, Cíntia Carreira, Céline Brochier-Armanet, Odile Valette, Zorah Dermoun...

Scientific Reports . 9 ( 1 ) : 360-373

DOI: 10.1038/s41598-018-37021-8

Journal article

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Description Osteo-Oto-Hepato-Enteric (O2HE) syndrome, a new recessive autosomal syndrome secondary to loss of function mutations in the UNC45A gene

L. Faivre, Clothilde Esteve, L. Francescatto, P. L. Tan, A. Bourchany, C. Delafoulhouze...

European Journal of Human Genetics . 27 ( 1 ) : 795-796

Journal article

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On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Emmanuelle Lerat, Josep Casacuberta, Cristian Chaparro, Cristina Vieira

Genes . 10 ( 4 ) : 258

DOI: 10.3390/genes10040258

Journal article

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