GECO Evolutionary and Computational Genomics

Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Takeshi Kawakami, Carina Mugal, Alexander Suh, Alexander Nater, Reto Burri, Linnéa Smeds...

Molecular Ecology . 26 ( 16 ) : 4158-4172

DOI: 10.1111/mec.14197

2017

Journal article

see the publication

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Ludovic Dutoit, Nagarjun Vijay, Carina Mugal, Christen Bossu, Reto Burri, Jochen Wolf...

Proceedings of the Royal Society B: Biological Sciences . 284 ( 1849 ) : 20162756

DOI: 10.1098/rspb.2016.2756

2017

Journal article

see the publication

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

Ludovic Dutoit, Reto Burri, Alexander Nater, Carina Mugal, Hans Ellegren

Molecular Ecology Resources . 17 ( 4 ) : 586-597

DOI: 10.1111/1755-0998.12602

2017

Journal article

see the publication

A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product

Xinhe Zhao, Mayssa Kasbi, Jingkui Chen, Sabine Pérès, Mario Jolicœur

Biotechnology and Bioengineering . 114 ( 12 ) : 2907 - 2919

DOI: 10.1002/bit.26393

2017

Journal article

see the publication

Computing EFMs consistent with equilibrium constants

Sabine Pérès, Philippe Dague, Mario Jolicœur, Stefan Schuster

Metabolic Pathway Analysis MPA 2017 .

2017

Conference paper

see the publication

HSM a reduced model of Central Carbon Metabolism: a dynamical approach

Bertrand Beauvoit, Sophie Colombie, Razanne Issa, Jean-Pierre Mazat, Christine Nazaret, Sabine Pérès

advances in Systems and Synthetic Biology .

2017

Conference paper

see the publication

How important is thermodynamics for identifying elementary flux modes?

Sabine Pérès, Mario Jolicœur, Cecile Moulin, Philippe Dague, Stefan Schuster

PLoS ONE . 12 ( 2 ) : e0171440

DOI: 10.1371/journal.pone.0171440

2017

Journal article

see the publication

Simulation-based estimation of branching models for LTR retrotransposons

Serge Moulin, Nicolas Seux, Stéphane Chrétien, Christophe Guyeux, Emmanuelle Lerat

Bioinformatics . 33 ( 3 ) : 320 - 326

DOI: 10.1093/bioinformatics/btw622

2017

Journal article

see the publication

Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

Magali Chabé, Ana Lokmer, Laure Ségurel

Trends in Parasitology . 33 ( 12 ) : 925-934

DOI: 10.1016/j.pt.2017.08.005

2017

Journal article

see the publication

Microbiome intestinal ancien et problématiques médicales contemporaines

Philippe Charlier, Anaïs Augias, Philippe Sansonetti, Céline Bon, Sean Kennedy, Laure Ségurel

Médecine/Sciences . 33 : 984-990

DOI: 10.1051/medsci/20173311016

2017

Other publication

see the publication

On the Evolution of Lactase Persistence in Humans

Laure Ségurel, Céline Bon

Annual Review of Genomics and Human Genetics . 18 ( 1 ) : 297-319

DOI: 10.1146/annurev-genom-091416-035340

2017

Journal article

see the publication

Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations

Nina Marchi, Tatyana Hegay, Philippe Mennecier, Myriam Georges, Romain Laurent, Mark Whitten...

American Journal of Physical Anthropology . 162 ( 4 ) : 627-640

DOI: 10.1002/ajpa.23151

2017

Journal article

see the publication

Latitude as a co-driver of human gut microbial diversity?

Emma Dikongué, Laure Ségurel

BioEssays . 39 ( 3 ) : 1600145

DOI: 10.1002/bies.201600145

2017

Journal article

see the publication

The global impact of Wolbachia on mitochondrial diversity and evolution

Marie Cariou, Laurent Duret, Sylvain Charlat

Journal of Evolutionary Biology . 30 ( 12 ) : 2204-2210

DOI: 10.1111/jeb.13186

2017

Journal article

see the publication

The Red Queen model of recombination hot-spot evolution: a theoretical investigation

Thibault Latrille, L. Duret, Nicolas Lartillot

Philosophical Transactions of the Royal Society B: Biological Sciences .

DOI: 10.1098/rstb.2016.0463

2017

Journal article

see the publication

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Alexey Dudnik, Filipa Almeida, Ricardo Andrade, Barbara Avila, Pilar Bañados, Barbay Diane...

Phytochemistry Reviews . : 1-36

DOI: 10.1007/s11101-017-9532-2

2017

Journal article

see the publication

Algorithms for k-meet-semidistributive lattices

Laurent Beaudou, Arnaud Mary, Lhouari Nourine

Theoretical Computer Science . 658 : 391 - 398

DOI: 10.1016/j.tcs.2015.10.029

2017

Journal article

see the publication

d18O-Derived incubation temperatures of oviraptorosaur eggs.

Romain Amiot, Xu Wang, Shuo Wang, Christophe Lécuyer, Jean-Michel Mazin, Jinyou Mo...

Palaeontology . : 1-15

DOI: 10.1111/pala.12311

2017

Journal article

see the publication

Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

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

DOI: 10.1101/074807

2017

Preprint

see the publication

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Panagiotis S Adam, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo

The International Society of Microbiologial Ecology Journal . 11 ( 11 ) : 2407-2425

DOI: 10.1038/ismej.2017.122

2017

Journal article

see the publication

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Roberto Feuda, Martin Dohrmann, Walker Pett, Herve Philippe, Omar Rota-Stabelli, Nicolas Lartillot...

Current Biology - CB . 27 ( 24 ) : 3864-3870.e4

DOI: 10.1016/j.cub.2017.11.008

2017

Journal article

see the publication

Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Sara E Branco, Hélène E Badouin, Ricardo E Rodríguez de La Vega, Jerome Gouzy, Fantin E Carpentier, Gabriela E Aguileta...

Proceedings of the National Academy of Sciences of the United States of America . 114 ( 27 ) : 7067-7072

DOI: 10.1073/pnas.1701658114

2017

Journal article

see the publication

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Helene Badouin, Pierre Gladieux, Jerome Gouzy, Sophie Siguenza, Gabriela Aguileta, Alodie Snirc...

Molecular Ecology . 26 ( 7 )

DOI: 10.1111/mec.13976

2017

Journal article

see the publication

Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

T. Boldanova, A. Suslov, M.H. Heim, A. Necsulea

EMBO Molecular Medicine . 9 : 816-834

DOI: 10.15252/emmm.201607006

2017

Journal article

see the publication

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

Emmanuelle Lerat, Marie Fablet, Laurent Modolo, Hélène Lopez-Maestre, Cristina Vieira

Nucleic Acids Research . 45 : 13

DOI: 10.1093/nar/gkw953

2017

Journal article

see the publication

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

C Grey, Julie a J Clément, J Buard, B Leblanc, I Gut, M Gut...

Genome Research . 27 ( 4 ) : 580-590

DOI: 10.1101/gr.217240.116

2017

Journal article

see the publication

Recombination, meiotic expression and human codon usage

F. Pouyet, Dominique Mouchiroud, L. Duret, M. Sémon

eLife . 6 : e27344

DOI: 10.7554/eLife.27344.001

2017

Journal article

see the publication

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Helene Lopez-Maestre, Camille Marchet, Vincent Miele...

Algorithms for Molecular Biology . 12 ( 1 ) : 2

DOI: 10.1186/s13015-017-0091-2

2017

Journal article

see the publication

OptPipe - a pipeline for optimizing metabolic engineering targets

András Hartmann, Ana Vila-Santa, Nicolai Kallscheuer, Michael Vogt, Alice Julien-Laferrière, Marie-France Sagot...

BMC Systems Biology . 11 : 1-9

DOI: 10.1186/s12918-017-0515-0

2017

Journal article

see the publication

On Bubble Generators in Directed Graphs

Vicente Acuna, Roberto Grossi, Giuseppe F Italiano, Leandro Lima, Romeo Rizzi, Gustavo Sacomoto...

WG 2017 - 43rd International Workshop on Graph-Theoretic Concepts in Computer Science . 10520 : 18-31

DOI: 10.1007/978-3-319-68705-6_2

2017

Conference paper

see the publication

GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Baobab Group

Publications

Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher ( Ficedula albicollis ) genome

A dynamic metabolic flux analysis of ABE (acetone-butanol-ethanol) fermentation by Clostridium acetobutylicum ATCC 824, with riboflavin as a by-product

Computing EFMs consistent with equilibrium constants

HSM a reduced model of Central Carbon Metabolism: a dynamical approach

How important is thermodynamics for identifying elementary flux modes?

Simulation-based estimation of branching models for LTR retrotransposons

Gut Protozoa: Friends or Foes of the Human Gut Microbiota?

Microbiome intestinal ancien et problématiques médicales contemporaines

On the Evolution of Lactase Persistence in Humans

Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations

Latitude as a co-driver of human gut microbial diversity?

The global impact of Wolbachia on mitochondrial diversity and evolution

The Red Queen model of recombination hot-spot evolution: a theoretical investigation

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Algorithms for k-meet-semidistributive lattices

d18O-Derived incubation temperatures of oviraptorosaur eggs.

Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

The growing tree of Archaea: new perspectives on their diversity, evolution and ecology

Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals

Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates

Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver

TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites

Recombination, meiotic expression and human codon usage

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

OptPipe - a pipeline for optimizing metabolic engineering targets

On Bubble Generators in Directed Graphs