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Bioinformatic study of molecular evolution in the context of animal development and anatomy

Titel Englisch Bioinformatic study of molecular evolution in the context of animal development and anatomy
Gesuchsteller/in Robinson-Rechavi Marc
Nummer 133011
Förderungsinstrument Projektförderung (Abt. I-III)
Forschungseinrichtung Département d'Ecologie et d'Evolution Faculté de Biologie et de Médecine Université de Lausanne
Hochschule Universität Lausanne - LA
Hauptdisziplin Genetik
Beginn/Ende 01.10.2011 - 30.09.2014
Bewilligter Betrag 331'000.00
Alle Daten anzeigen

Alle Disziplinen (2)

Disziplin
Genetik
Zoologie

Keywords (6)

bioinformatics; development; evolution; genomics; database; selection

Lay Summary (Englisch)

Lead
Lay summary

Results from flies, human, mouse and zebrafish, have shown that protein evolution and function is influenced by gene expression patterns and by the developmental role of genes. In other words, the anatomy and development of the animals in which genes are active influences their molecular evolution. In this project, we propose to study this influence systematically, taking advantage of new bioinformatic resources developed in our lab (http://bgee.unil.ch/; http://selectome.unil.ch/), and when necessary extending them. This project will allow us to contribute to two major aims: (i) a better explanatory model of molecular evolution in animals; and (ii) a better integration of genomics and molecular evolution with Evo-Devo. This project will also contribute new bioinformatic tools and resources, which will be of use to a wide community, in molecular evolution, Evo-Devo, and genomics, as well as in biomedical research.

Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics
Rosikiewicz Marta, Robinson-Rechavi Marc (2014), IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics, in Bioinformatics, 30(10), 1392-1399.
Patterns of Positive Selection in Seven Ant Genomes
Roux Julien, Privman Eyal, Moretti Sébastien, Daub Joséphine T., Robinson-Rechavi Marc, Keller Laurent (2014), Patterns of Positive Selection in Seven Ant Genomes, in Molecular Biology and Evolution, 31(7), 1661-1685.
Selectome update: quality control and computational improvements to a database of positive selection
Moretti Sébastien, Laurenczy Balazs, Gharib Walid H, Castella Briseis, Kuzniar Arnold, Schabauer Hannes, Studer Romain A, Valle Mario, Salamin Nicolas, Stockinger Heinz, Robinson-Rechavi Marc (2014), Selectome update: quality control and computational improvements to a database of positive selection, in Nucleic Acids Research, 42(D1), D917-D921.
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
Haendel Melissa A, Balhoff James P, Bastian Frédéric B, et al (18 authors) (2014), Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon, in Journal of Biomedical Semantics, 5, 21.
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC
Gharib W., Robinson-Rechavi M. (2013), The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC, in Molecular Biology and Evolution, 30, 1675-1686.
The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates
Piasecka B., Lichocki P., Moretti S., Bergmann S., Robinson-Rechavi M. (2013), The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates, in PLOS Genetics, 9, e1003476.
Uncovering hidden duplicated content in public transcriptomics data
Rosikiewicz M., Comte A., Niknejad A., Robinson-Rechavi M., Bastian F.B. (2013), Uncovering hidden duplicated content in public transcriptomics data, in Database, 2013, bat010.
Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs.
Roux Julien, Gonzàlez-Porta Mar, Robinson-Rechavi Marc (2012), Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs., in Nucleic acids research, 40(13), 5890-900.
How much does the amphioxus genome represent the ancestor of chordates?
Louis Alexandra, Roest Crollius Hugues, Robinson-Rechavi Marc (2012), How much does the amphioxus genome represent the ancestor of chordates?, in Briefings in functional genomics, 11(2), 89-95.
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.
Altenhoff Adrian M, Studer Romain A, Robinson-Rechavi Marc, Dessimoz Christophe (2012), Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs., in PLoS computational biology, 8(5), 1002514-1002514.
vHOG, a multispecies vertebrate ontology of homologous organs groups.
Niknejad Anne, Comte Aurélie, Parmentier Gilles, Roux Julien, Bastian Frederic B, Robinson-Rechavi Marc (2012), vHOG, a multispecies vertebrate ontology of homologous organs groups., in Bioinformatics (Oxford, England), 28(7), 1017-20.

Zusammenarbeit

Gruppe / Person Land
Formen der Zusammenarbeit
Sven Bergmann, UNIL Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Austausch von Mitarbeitern
Laurent Excoffier, UNIGE Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Ziheng Yang, UCL Grossbritannien und Nordirland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Alexis Stamatakis, Technical University of Munich Deutschland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
Berkeley Bioinformatics Open-source Projects Vereinigte Staaten von Amerika (Nordamerika)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Christophe Dessimoz, ETHZ Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
Nicolas Salamin, UNIL Schweiz (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Austausch von Mitarbeitern
Laurent Duret, CNRS Lyon Frankreich (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
ArrayExpress Grossbritannien und Nordirland (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Industrie/Wirtschaft/weitere anwendungs-orientierte Zusammenarbeit

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
Biocuration 2014 Vortrag im Rahmen einer Tagung Mapping All Animal Species Anatomies 06.04.2014 Toronto, Kanada Robinson-Rechavi Marc; Bastian Frédéric;
ESEB Vortrag im Rahmen einer Tagung Determinants of protein evolutionary rates in light of ENCODE functional genomics 23.08.2013 Lisbon, Portugal Kryuchkova Nadezda; Robinson-Rechavi Marc;
Quest for Orthologs Vortrag im Rahmen einer Tagung Ongoing exploration of functional differences between human and mouse orthologs 26.07.2013 Lausanne, Schweiz Robinson-Rechavi Marc;
seminar Uni Fribourg Einzelvortrag Does gene duplication affect evolution? 28.05.2013 Fribourg, Schweiz Robinson-Rechavi Marc;
The Next NGS Challenge Poster Generation of expression calls for RNA-seq data 15.05.2013 Valencia, Spanien Rosikiewicz Marta;
Biocuration 2013 Poster IQRray – an efficient method for Affymetrix microarray quality control for meta-analysis and database curation 07.04.2013 http://www.ebi.ac.uk/biocuration2013/, Grossbritannien und Nordirland Robinson-Rechavi Marc; Niknejad Anne; Rosikiewicz Marta; Bastian Frédéric;
Student retreat Population genomics doctoral school Vortrag im Rahmen einer Tagung Transcriptomic study of Evo-Devo 23.03.2013 Charmey, Schweiz Robinson-Rechavi Marc;
symposium Upsalla University Einzelvortrag Computational challenges in testing the obvious:do paralogs really diverge? 28.02.2013 Upsalla, Schweden Robinson-Rechavi Marc;
Swiss-Israel Bioinformatics symposium Vortrag im Rahmen einer Tagung Bgee: advances in integrating and comparing expression data from animals 30.01.2013 Biel, Schweiz Robinson-Rechavi Marc;
seminar at European Bioinformatics Institute Einzelvortrag Evolution and gene expression in vertebrates 06.11.2012 Cambridge, Grossbritannien und Nordirland Robinson-Rechavi Marc;
ECCB 2012 Poster Average rank IQR – a new improved method for Affymetrix microarray quality control for metaanalysis and database curation 09.09.2012 Basel, Schweiz Robinson-Rechavi Marc; Rosikiewicz Marta;
SMBE 2012 Poster Bgee, a database for the study of gene expression evolution 23.06.2012 Dublin, Irland Rosikiewicz Marta; Bastian Frédéric; Niknejad Anne; Comte Aurélie; Robinson-Rechavi Marc;
Biocuration 2012 Poster Curation of homology relations between anatomical structures in Bgee 02.04.2012 Washington, Vereinigte Staaten von Amerika Robinson-Rechavi Marc; Niknejad Anne; Bastian Frédéric; Comte Aurélie; Rosikiewicz Marta;
Lausanne Genomics Days Vortrag im Rahmen einer Tagung Evolution and gene expression in vertebrates 16.02.2012 Lausanne, Schweiz Robinson-Rechavi Marc;


Selber organisiert

Titel Datum Ort
OntoSIB 26.08.2013 Geneve, Schweiz
ESEB symposium 22.08.2013 Lisbon, Portugal
Quest for Orthologs 24.07.2013 Lausanne, Schweiz
workshop Quality information in support of annotations at Biocuration 2012 03.04.2012 Washington, Vereinigte Staaten von Amerika

Kommunikation mit der Öffentlichkeit

Kommunikation Titel Medien Ort Jahr
Referate/Veranstaltungen/Ausstellungen Pint of Science Westschweiz 2014
Neue Medien (Web, Blogs, Podcasts, NewsFeed, usw.) Tout se passe comme si blog Westschweiz International 2012

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
116798 The evolutionary significance of whole genome duplication in teleost fishes 01.12.2007 Projektförderung (Abt. I-III)
120624 Comparative modular analysis of gene expression in vertebrate development 01.10.2008 ProDoc
130309 Detection of adaptive genomic interactions at different evolutionary time scales 01.09.2010 ProDoc
153341 Bioinformatics search for adaptive evolution in vertebrate development 01.10.2014 Projektförderung (Abt. I-III)

Abstract

A few years ago, we seemed on the verge of determining "universals of protein evolution", i.e. features of proteins which would explain most of the variance in their evolutionary rates and patterns, across the tree of life. Some level of optimism was justified by consistent results from yeast and bacteria. But more recently, the rules have been shown not to apply in a straightforward manner in animals. Results from flies, human, mouse and zebrafish, have shown that many relations between features of protein evolution and function are influenced either by gene expression patterns, or by the developmental role of genes. In other words, the anatomy and development of the animals in which genes are active influences their molecular evolution in a fundamental way.In this project, I propose to study this influence systematically, taking advantage of new bioinformatic resources developed in my lab, and when necessary extending them. This project is organized in two subprojects, which are strongly integrated. The first will focus on data analysis in mouse and zebrafish, organisms in which my lab already has experience, and for which the bioinformatic framework is well established. This will also allow us to take into account the role of whole genome duplications. The second subproject will integrate fly into our bioinformatic resources, and allow a systematic comparison of the evolutionary patterns between model vertebrates, and an arthropod.This project aims to shed light on fundamental features of molecular evolution in animals. In addition, we hope to contribute both to linking genome evolution and evolutionary developmental biology (Evo-Devo), and to new bioinformatic resources which will be of wide use to the community.
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