Marc Robinson‐Rechavi

University of Lausanne

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Vincent Laudet

Okinawa Institute of Science and Technology Graduate University

Frederic Bastian

SIB Swiss Institute of Bioinformatics

Julien Roux

University of Basel

Sébastien Moretti

University of Lausanne

Nicolas Salamin

University of Lausanne

Tanja Schwander

University of Lausanne

Darren J. Parker

University of Lausanne

Zoé Dumas

University of Lausanne

Héctor Escrivà

Sorbonne Université

Jens Bast

University of Cologne

Cooperative Institutions

University of Lausanne

227

Centre National de la Recherche Scientifique

198

SIB Swiss Institute of Bioinformatics

194

Inserm

University College London

European Bioinformatics Institute

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Université Claude Bernard Lyon 1

University of Geneva

Harvard University

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Inference of Evolutionary Forces Acting on Human Biological Pathways

Genome Biology and Evolution (2015)

Joséphine T. Daub Isabelle Dupanloup Marc Robinson‐Rechavi Laurent Excoffier

Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints than other genes and that their evolutionary response is correlated. We then introduce a new procedure to detect selection at the pathway level based on a decomposition of the classical McDonald–Kreitman test extended to multiple genes. This new test, called 2DNS, detects outlier gene sets and takes into account past demographic effects and evolutionary constraints specific to gene sets. Selective forces acting on gene sets can be easily identified by a mere visual inspection of the position of the gene sets relative to their two-dimensional null distribution. We thus find several outlier gene sets that show signals of positive, balancing, or purifying selection but also others showing an ancient relaxation of selective constraints. The principle of the 2DNS test can also be applied to other genomic contrasts. For instance, the comparison of patterns of polymorphisms private to African and non-African populations reveals that most pathways show a higher proportion of nonsynonymous mutations in non-Africans than in Africans, potentially due to different demographic histories and selective pressures.

Negative selection

Nonsynonymous substitution

Trait

10.1093/gbe/evv083

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Citations (15)

Evolution Moléculaire

L. Duret T. Bataillon N. Bierne Vincent Daubin J. Dutheil

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The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals

Nucleic Acids Research (2020)

Frederic Bastian Julien Roux Anne Niknejad Aurélie Comte Sara Simões Costa

Abstract Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as ‘healthy’ or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.

10.1093/nar/gkaa793

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Citations (153)

Evolution Moléculaire

HAL (Le Centre pour la Communication Scientifique Directe) (2010)

L. Duret T. Bataillon N. Bierne Vincent Daubin J. Dutheil

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The amphioxus genome illuminates vertebrate origins and cephalochordate biology (Genome Research (2008) 18, (1100-1111))

Genome Research (2008)

Linda Z. Holland Ricard Albalat Kaoru Azumi Èlia Benito‐Gutiérrez Matthew J. Blow

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Generation of expression calls for RNA-seq data

EMBnet journal (2013)

Marta Rosikiewicz Marc Robinson‐Rechavi

The Bgee database (database for Gene Expression Evolution) (Bastian et al., 2008) provides information about genes that are expressed in a different organs and tissues. In order to introduce and RNA-seq results into database we had to develop methodology for deriving expressed/unexpressed calls for genes. Such detection calls can be used for characterization of the tissue gene expression profile. Additionally detection calls are widely used in transcriptomic studies for filtering the genes used for differential expression analysis, clustering samples or building more reliable classifiers The goal of our work is to find automatic way for defining the cut-off value on transcription level that allows discrimination between expressed and non-expressed genomic features for each library individually.

RNA-Seq

Expression (computer science)

Transcription

10.14806/ej.19.a.670

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Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

Nature Biotechnology (2008)

Pierre Abad Jérôme Gouzy Jean‐Marc Aury Philippe Castagnone‐Sereno Étienne Danchin

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.

Root-knot nematode

10.1038/nbt.1482

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Citations (1,157)

<title>Discrimination of bottom underwater mine-like objects in different conditions using a wideband data set</title>

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE (2002)

Marc Robinson‐Rechavi M.R. Azimi-Sadjadi Arta A. Jamshidi

The problem of classification of underwater targets involves discrimination between mine-like and non-mine-like objects as well as the characterization of background clutter. In this work this problem is addressed using a newly collected wideband data set. The developed system consists of a pre- processing scheme, which includes removing multi-path effects and other artifacts from the acquired data. Features are then extracted and fed to a back-propagation neural network (BPNN). Test results will be given for the classification between various types of mine-like and non- mine-like objects and for different bottom conditions and depression/elevation angles of the sonar to test the robustness and generalization of the classification scheme.

Robustness

Wideband

Data set

10.1117/12.479118

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The Bgee database: gene expression data in animals

Valentine Rech de Laval Frederic Bastian Julien Roux Anne Niknejad Sébastien Moretti

Poster presenting the database Bgee presented at the JOBIM 2016 conference: http://jobim2016.sciencesconf.org/

10.6084/m9.figshare.3464582.v2

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