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You are here: UNIL > Department of Ecology and Evolution > People > Group leaders > Prof. Marc Robinson-Rechavi

Marc Robinson-Rechavi - Professor

Presentation
Publications

My research has concerned rodent evolution, mammal phylogeny, evolutionary rates, gene and genome duplication, nuclear hormone receptors, and structural genomics. I am trained in experimental molecular biology, but have not touched a pipette since 1997. Your will find my present research interests on the webpage of my lab.

Teaching

UNIL:
Introduction to bioinformatics, Bachelor of Biology (semester 3)
Science and society, Bachelor of Biology (semester 3)
Bioinformatics for genomics, Bachelor of Biology (semester 6)
Transcriptome evolution, Bachelor of Biology (semester 6)
Programming for biologists, Bachelor of Biology (semester 4 or 6)
Orientation Bioinformatics, master Molecular Life Sciences (semesters 7-9)
Sequence a genome class, Master of Molecular Life Sciences (semesters 8-9); Blog: http://wp.unil.ch/sequenceagenome/
Seminars Bioinfo/Biostats, Master Biomedical (semesters 9-10)
Tutorial Genomes, Ecology, Evolution, etc, Doctoral school; Blog: http://wp.unil.ch/genomeeee
Course Blogging and using Twitter for scientific communication: http://www.cuso.ch/activity/?p=1128&id=2226

SIB:
Bioinformatics in the Chalet

Misc

Chair of the Educational Board of the SIB
ISI Researcher ID: E-9727-2011
Google scholar profile
Treasurer of the International Society for Biocuration
PLoS One Editorial board
Twitter ID: marc_rr
Blog in English: http://people.unil.ch/marcrobinsonrechavi/
Blog en français au Cafe des sciences : http://toutsepassecommesi.cafe-sciences.org/
Editorial board J Exp Zoology
ORCID record
Blog en français à L’Hebdo : http://www.hebdo.ch/les-blogs/robinson-rechavi-marc-soci%C3%A9t%C3%A9-le-sens-du-vivant

Curriculum Vitae

Born 1970, France
married, two children

2010
Associate Professor at Université de Lausanne
Department of Ecology and Evolution

2006
Group Leader at Swiss Institute of Bioinformatics

2005 - 2010
Assistant Professor at Université de Lausanne
Department of Ecology and Evolution

2003-2005
Visiting Assistant Research Scientist at University of California, San Diego
Joint Center for Structural Genomics

2003
Habilitation à Diriger des Recherches
"Importance of multigene families in functional evolutionary genomics: the example of nuclear receptors"

1998-2003
Maître de Conférences at the Ecole Normale Supérieure de Lyon
UMR CNRS 5665 - Biologie moléculaire et cellulaire
Lab of Prof. Vincent Laudet

1997-98
Post-doctorate at Tel Aviv University
Department of Zoology
Lab of Prof. Dan Graur

1994-97
Graduate studies at Université Lyon 1 Claude Bernard
UMR CNRS 5558 - Biométrie, Génétique et Biologie des Populations
Lab of Prof. Christian Gautier
PhD advisor: Dominique Mouchiroud.
Specialization: Biometrics
Title: "Diversity of evolutionary modes of rodent genomes"

Publications | Thesis

Publications

1 2 >

In press | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 |

In Press

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests

Komljenovic Andrea, Roux Julien, Robinson-Rechavi Marc, Bastian Frederic B. F1000Research, 5 p. 2748. Peer-reviewed.

[DOI] [serval:BIB_0AA1ED033ECE]

Selective constraints on coding sequences of nervous system genes are a major determinant of duplicate gene retention in vertebrates

Roux Julien, Liu Jialin, Robinson-Rechavi Marc bioRxiv.

[DOI] [serval:BIB_C757F185D6C7]

2017

preview resource BIB_8B3A5682EAF5.P001

Sex-specific changes in gene expression and delayed sex differentiation in response to estrogen pollution in grayling (Salmonidae)

Selmoni O. M., Maitre D., Roux J., Wilkins L. G. E., Marques da Cunha L., Vermeirssen E. L. M., Knörr S., Robinson-Rechavi M., Wedekind C., (SO & DM shared first authors; MRR & CW shared senior authors), 2017-05-09. bioRxiv.

[DOI] [serval:BIB_8B3A5682EAF5]

preview resource BIB_AA1BB60481BA.P001

Sex differentiation in grayling (Salmonidae) goes through an all-male stage and is delayed in genetic males who instead grow faster

Maitre D., Selmoni O. M., Uppal A., Marques da Cunha L., Wilkins L. G. E., Roux J., Mobley K. B., Knörr S., Robinson-Rechavi M., Wedekind C., 2017-05-08. bioRxiv.

[DOI] [serval:BIB_AA1BB60481BA]

A benchmark of gene expression tissue-specificity metrics.

Kryuchkova-Mostacci N., Robinson-Rechavi M., 2017. Briefings in Bioinformatics, 18 (2) pp. 205-214. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_87132E302513]

Detection of pathways affected by positive selection in primate lineages ancestral to humans

Daub Joséphine, Moretti Sébastien, Davydov Iakov I., Excoffier Laurent, Robinson-Rechavi Marc, 2017. Molecular Biology and Evolution. Peer-reviewed.

[DOI] [serval:BIB_00FD298E5C77]

Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans.

Daub J.T., Moretti S., Davydov I.I., Excoffier L., Robinson-Rechavi M., 2017. Molecular Biology and Evolution, 34 (6) pp. 1391-1402. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_E977192342AB]

preview resource BIB_6A5C276B250D.P001

No evidence for the radiation time lag model after whole genome duplications in Teleostei.

Laurent S., Salamin N., Robinson-Rechavi M., 2017. PLoS One, 12 (4) pp. e0176384. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_6A5C276B250D]

2016

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State aggregation for fast likelihood computations in molecular evolution.

Davydov I.I., Robinson-Rechavi M., Salamin N., 2016. Bioinformatics, 33 pp. 354-362. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_54224013033C]

preview resource BIB_71EF45D9A3D9.P001

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

SIB Swiss Institute of Bioinformatics Members, 2016. Nucleic Acids Research, 44 (D1) pp. D27-D37.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_71EF45D9A3D9]

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Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs.

Kryuchkova-Mostacci N., Robinson-Rechavi M., 2016. PLoS Computational Biology, 12 (12) pp. e1005274. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_F27D450F2B07]

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The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.

Morales M., Sentchilo V., Bertelli C., Komljenovic A., Kryuchkova-Mostacci N., Bourdilloud A., Linke B., Goesmann A., Harshman K., Segers F. et al., 2016. PloS one, 11 (11) pp. e0165850. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_14197457242A]

2015

Genomics is changing Evo-Devo.

Robinson-Rechavi M., 2015. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution, 324 (4) p. 315.

[DOI] [WoS] [Pmid] [serval:BIB_E8ACA475D130]

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Inference of Evolutionary Forces Acting on Human Biological Pathways.

Daub J.T., Dupanloup I., Robinson-Rechavi M., Excoffier L., 2015. Genome Biology and Evolution, 7 (6) pp. 1546-1558. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_F1C43009CD42]

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Detecting patterns of species diversification in the presence of both rate shifts and mass extinctions.

Laurent S., Robinson-Rechavi M., Salamin N., 2015. BMC Evolutionary Biology, 15 p. 157. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_01FF6A3D8DC9]

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Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse.

Kryuchkova-Mostacci N., Robinson-Rechavi M., 2015. Plos One, 10 (6) pp. e0131673. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_B6BE63795D1F]

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Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Miyazaki R., Bertelli C., Benaglio P., Canton J., De Coi N., Gharib W.H., Gjoksi B., Goesmann A., Greub G., Harshman K. et al., 2015. Environmental Microbiology, 17 (1) pp. 91-104.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_EBE76C19261B]

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The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Bastian F.B., Chibucos M.C., Gaudet P., Giglio M., Holliday G.L., Huang H., Lewis S.E., Niknejad A., Orchard S., Poux S. et al., 2015. Database, 2015 pp. bav043. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_60CACFAC405E]

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Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

Bertelli C., Aeby S., Chassot B., Clulow J., Hilfiker O., Rappo S., Ritzmann S., Schumacher P., Terrettaz C., Benaglio P. et al., 2015. Frontiers in Microbiology, 6 (101) p. 101. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_5BB2A564D83D]

What to compare and how: Comparative transcriptomics for Evo-Devo.

Roux J., Rosikiewicz M., Robinson-Rechavi M., 2015. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution, 324 (4) pp. 372-382. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_E322E5E2A13A]

2014

Determinants of protein evolutionary rates in light of ENCODE functional genomics

Kryuchkova Nadezda, Robinson-Rechavi Marc, 2014. pp. A9 dans BMC Bioinformatics.

[DOI] [serval:BIB_603F1CF898E3]

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Patterns of positive selection in seven ant genomes.

Roux J., Privman E., Moretti S., Daub J.T., Robinson-Rechavi M., Keller L., 2014. Molecular Biology and Evolution, 31 (7) pp. 1661-1685. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_95722591AAD3]

preview resource BIB_0E5C20608CA6.P001

IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics.

Rosikiewicz M., Robinson-Rechavi M., 2014. Bioinformatics, 30 (10) pp. 1392-1399. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_0E5C20608CA6]

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Big data and other challenges in the quest for orthologs.

Sonnhammer E.L., Gabaldón T., Sousa da Silva A.W., Martin M., Robinson-Rechavi M., Boeckmann B., Thomas P.D., Dessimoz C., Quest for Orthologs consortium, 2014. Bioinformatics, 30 (21) pp. 2993-2998. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_172DE4708266]

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Optimization strategies for fast detection of positive selection on phylogenetic trees.

Valle M., Schabauer H., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Salamin N., 2014. Bioinformatics, 30 (8) pp. 1129-1137. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_EE03C80A1584]

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Selectome update: quality control and computational improvements to a database of positive selection.

Moretti S., Laurenczy B., Gharib W.H., Castella B., Kuzniar A., Schabauer H., Studer R.A., Valle M., Salamin N., Stockinger H. et al., 2014. Nucleic Acids Research, 42 (1) pp. D917-D921. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_BD16E97A0D18]

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Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Haendel M.A., Balhoff J.P., Bastian F.B., Blackburn D.C., Blake J.A., Bradford Y., Comte A., Dahdul W.M., Dececchi T.A., Druzinsky R.E. et al., 2014. Journal of Biomedical Semantics, 5 p. 21. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_F76940F670C4]

2013

Evidence for polygenic adaptation to pathogens in the human genome.

Daub J.T., Hofer T., Cutivet E., Dupanloup I., Quintana-Murci L., Robinson-Rechavi M., Excoffier L., 2013. Molecular Biology and Evolution, 30 (7) pp. 1544-1558. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_5B46808B83ED]

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Uncovering hidden duplicated content in public transcriptomics data.

Rosikiewicz M., Comte A., Niknejad A., Robinson-Rechavi M., Bastian F.B., 2013. Database, 2013 pp. bat010. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_230AE9FE1902]

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The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC.

Gharib W.H., Robinson-Rechavi M., 2013. Molecular Biology and Evolution, 30 (7) pp. 1675-1686. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_E31E37CD7B01]

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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. Plos Genetics, 9 (4) pp. e1003476. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_B03DCB0498A7]

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Community-wide plasmid gene mobilization and selection.

Sentchilo V., Mayer A.P., Guy L., Miyazaki R., Green Tringe S., Barry K., Malfatti S., Goessmann A., Robinson-Rechavi M., van der Meer J.R., 2013. ISME Journal, 7 (6) pp. 1173-1186.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_B5128FCC3FB5]

2012

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How much does the amphioxus genome represent the ancestor of chordates?

Louis A., Roest Crollius H., Robinson-Rechavi M., 2012. Briefings in Functional Genomics, 11 (2) pp. 89-95. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_093626E06B3F]

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Recent advances in biocuration: meeting report from the fifth International Biocuration Conference.

Gaudet P., Arighi C., Bastian F., Bateman A., Blake J.A., Cherry M.J., D'Eustachio P., Finn R., Giglio M., Hirschman L. et al., 2012. Database, 2012 pp. bas036. Peer-reviewed.

[URN] [DOI] [Pmid] [serval:BIB_C16E4B98CEB3]

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Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs.

Roux J., Gonzàlez-Porta M., Robinson-Rechavi M., 2012. Nucleic Acids Research, 40 (13) pp. 5890-5900. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_062426040422]

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Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human.

Piasecka B., Robinson-Rechavi M., Bergmann S., 2012. Bioinformatics, 28 (14) pp. 1865-1872. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_FFE8D8F98971]

preview resource BIB_542C5BE6E2B7.P001

gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

Moretti S., Murri R., Maffioletti S., Kuzniar A., Castella B, Salamin N., Robinson-Rechavi M., Stockinger H., 2012. pp. 59-68 dans Glatard T, Silverstein J (eds.) HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences, IOS Press Books online.

[URN] [DOI] [serval:BIB_542C5BE6E2B7]

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SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model

Schabauer H., Valle M., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Yang Z., Salamin N., 2012. pp. 700-708 dans Aluru S., Bader D.A. (eds.) HiCOMB (11th IEEE International Workshop on High Performance Computational Biology). Peer-reviewed, IEEE.

[URN] [DOI] [serval:BIB_5F7B13551FF8]

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Comparative modular analysis of gene expression in vertebrate organs.

Piasecka B., Kutalik Z., Roux J., Bergmann S., Robinson-Rechavi M., 2012. Bmc Genomics, 13 p. 124. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_94FEE072331D]

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vHOG, a multispecies vertebrate ontology of homologous organs groups.

Niknejad A., Comte A., Parmentier G., Roux J., Bastian F.B., Robinson-Rechavi M., 2012. Bioinformatics, 28 (7) pp. 1017-1020. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_5605BDB61FC5]

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Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs.

Altenhoff A.M., Studer R.A., Robinson-Rechavi M., Dessimoz C., 2012. PLoS Computational Biology, 8 (5) pp. e1002514. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_89CB0AF6A1E2]

2011

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Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair.

Jagannathan V., Robinson-Rechavi M., 2011. BMC Systems Biology, 5 (1) p. 138. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_8CDBA887EAAA]

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Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication.

Roux J., Robinson-Rechavi M., 2011. Genome Research, 21 (3) pp. 357-363. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_21E4AE52DF8C]

The challenge of modeling nuclear receptor regulatory networks in mammalian cells.

Jagannathan V., Robinson-Rechavi M., 2011. Molecular and Cellular Endocrinology, 334 (1-2) pp. 91-97. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_64B60EC69445]

Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport.

Studer R.A., Person E., Robinson-Rechavi M., Rossier B.C., 2011. Physiological Genomics, 43 (13) pp. 844-854. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_FAC3750250F9]

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Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees.

Boeckmann B., Robinson-Rechavi M., Xenarios I., Dessimoz C., 2011. Briefings in Bioinformatics, 12 (5) pp. 423-435. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_3EF9A7BDC38C]

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When orthologs diverge between human and mouse.

Gharib W.H., Robinson-Rechavi M., 2011. Briefings in Bioinformatics, 12 (5) pp. 436-441. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_006579177FCC]

2010

Evolution moléculaire

Duret L., Bataillon T., Bierne N., Daubin V., Dutheil J., Gautier C., Glemin S., Gouy M., Heyer E., Marais G. et al., 2010. pp. 123-182 dans Thomas F., Lefevre T., Raymond M. (eds.) Biologie évolutive chap. 5, de Boeck.

[serval:BIB_F2FDBFECBF3D]

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Molecular evidence for a functional ecdysone signaling system in Brugia malayi.

Tzertzinis G., Egaña A.L., Palli S.R., Robinson-Rechavi M., Gissendanner C.R., Liu C., Unnasch T.R., Maina C.V., 2010. PLoS Neglected Tropical Diseases, 4 (3) pp. e625. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_3EC23B792936]

Phylogenetic Code in the Cloud - Can it Meet the Expectations?

Kraut A., Moretti S., Robinson-Rechavi M., Stockinger H., Flanders D., 2010. Studies in Health Technology and Informatics, 159 pp. 55-63. Peer-reviewed.

[DOI] [Pmid] [serval:BIB_1F5A96C03D27]

Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor.

Pilot-Storck F., Chopin E., Rual J.F., Baudot A., Dobrokhotov P., Robinson-Rechavi M., Brun C., Cusick M.E., Hill D.E., Schaeffer L. et al., 2010. Molecular and Cellular Proteomics, 9 (7) pp. 1578-1593. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_99B5C8832AB6]

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An ontology to clarify homology-related concepts.

Roux J., Robinson-Rechavi M., 2010. Trends in Genetics, 26 (3) pp. 99-102. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_611EAEEC4DD5]

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Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution.

Studer R.A., Robinson-Rechavi M., 2010. Molecular Biology and Evolution, 27 (11) pp. 2618-2627. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_47EE94487936]

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Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy.

Parmentier G., Bastian F.B., Robinson-Rechavi M., 2010. Bioinformatics, 26 (14) pp. 1766-1771. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_1DA8753017CD]

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Molecular signaling in zebrafish development and the vertebrate phylotypic period

Comte A., Roux J., Robinson-Rechavi M., 2010. Evolution and Development, 12 (2) pp. 144-156. Peer-reviewed.

[URN] [DOI] [WoS] [serval:BIB_AD3A9D7540C9]

2009

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Bioinformatics for evolutionary developmental biology

Robinson-Rechavi M., 2009. pp. 355-378 dans Appel R.D., Feytmans E. (eds.) Bioinformatics: A Swiss Perspective chap. 13, World Scientific Publishing Company.

[URN] [serval:BIB_55CE3435659A]

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Selectome: a database of positive selection.

Proux E., Studer R.A., Moretti S., Robinson-Rechavi M., 2009. Nucleic Acids Research, 37 (Database issue) pp. D404-D407. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_92B1AFBBA077]

Evidence for an episodic model of protein sequence evolution.

Studer R.A., Robinson-Rechavi M., 2009. Biochemical Society transactions, 37 (Pt 4) pp. 783-786. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_43CBA0DC9689]

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The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes.

Cruz F., Roux J., Robinson-Rechavi M., 2009. BMC Genomics, 10 (1) p. 619. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_AE3C1C5E6707]

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Large-Scale Analyses of Positive Selection Using Codon Models

Studer R.A., Robinson-Rechavi M., 2009. pp. 217-236 dans Pontarotti P. (eds.) Evolutionary Biology: Concept, Modeling, and Application chap. 13, Springer‐Verlag.

[URN] [DOI] [serval:BIB_69764375A158]

Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects.

Iwema T., Chaumot A., Studer R.A., Robinson-Rechavi M., Billas I.M., Moras D., Laudet V., Bonneton F., 2009. Molecular Biology and Evolution, 26 (4) pp. 753-768. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_6C84793F923C]

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How confident can we be that orthologs are similar, but paralogs differ?

Studer R.A., Robinson-Rechavi M., 2009. Trends in Genetics, 25 (5) pp. 210-216. Peer-reviewed.

[URN] [DOI] [WoS] [serval:BIB_39F8106EE698]

2008

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.

Abad P., Gouzy J., Aury J.M., Castagnone-Sereno P., Danchin E.G., Deleury E., Perfus-Barbeoch L., Anthouard V., Artiguenave F., Blok V.C. et al., 2008. Nature Biotechnology, 26 (8) pp. 909-915. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_0FED258C5533]

The amphioxus genome and the evolution of the chordate karyotype.

Putnam N.H., Butts T., Ferrier D.E., Furlong R.F., Hellsten U., Kawashima T., Robinson-Rechavi M., Shoguchi E., Terry A., Yu J.K. et al., 2008. Nature, 453 (7198) pp. 1064-1071. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_335B81A678B3]

Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis.

Crossgrove K., Maina C.V., Robinson-Rechavi M., Lochner M.C., 2008. Molecular and Biochemical Parasitology, 157 (1) pp. 92-97. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_3BBFB417BF02]

preview resource BIB_C469EC983655.P001

Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals.

Robinson-Rechavi M., 2008. Molecular and Cellular Endocrinology, 293 (1-2) pp. 2-4.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_C469EC983655]

preview resource BIB_5A6F9D63F92D.P001

Bgee: integrating and comparing heterogeneous transcriptome data among species

Bastian F., Parmentier G., Roux J., Moretti S., Laudet V., Robinson-Rechavi M., 2008. pp. 124-131 dans Istrail S., Pevzner P., Waterman M. (eds.) Data Integration in Life Sciences, Lecture Notes in Computer Science. Peer-reviewed, Springer.

[URN] [DOI] [serval:BIB_5A6F9D63F92D]

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes.

Studer R.A., Penel S., Duret L., Robinson-Rechavi M., 2008. Genome Research, 18 (9) pp. 1393-1402. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_08713507D4D6]

The amphioxus genome illuminates vertebrate origins and cephalochordate biology.

Holland L.Z., Albalat R., Azumi K., Benito-Gutiérrez E., Blow M.J., Bronner-Fraser M., Brunet F., Butts T., Candiani S., Dishaw L.J. et al., 2008. Genome Research, 18 (7) pp. 1100-1111. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_987DB6FE8B4B]

preview resource BIB_F11302BD61EC.P001

Developmental constraints on vertebrate genome evolution.

Roux J., Robinson-Rechavi M., 2008. PLoS Genetics, 4 (12) pp. e1000311. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_F11302BD61EC]

2007

preview resource BIB_8C6B61D79078.P001

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.

Amoutzias G.D., Pichler E.E., Mian N., De Graaf D., Imsiridou A., Robinson-Rechavi M., Bornberg-Bauer E., Robertson D.L., Oliver S.G., 2007. BMC Systems Biology, 1 p. 34. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_8C6B61D79078]

One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity.

Amoutzias G.D., Veron A.S., Weiner J., Robinson-Rechavi M., Bornberg-Bauer E., Oliver S.G., Robertson D.L., 2007. Molecular Biology and Evolution, 24 (3) pp. 827-835.

[DOI] [WoS] [Pmid] [serval:BIB_A168E290C027]

2006

preview resource BIB_DE7A148B9A94.P001

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Robinson-Rechavi M., Alibés A., Godzik A., 2006. Journal of Molecular Biology, 356 (2) pp. 547-557. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_DE7A148B9A94]

preview resource BIB_9B994D87AC3D.P001

Neofunctionalization in vertebrates: the example of retinoic acid receptors.

Escriva H., Bertrand S., Germain P., Robinson-Rechavi M., Umbhauer M., Cartry J., Duffraisse M., Holland L., Gronemeyer H., Laudet V., 2006. PLoS Genetics, 2 (7) pp. e102. Peer-reviewed.

[URN] [DOI] [WoS] [Pmid] [serval:BIB_9B994D87AC3D]

Gene loss and evolutionary rates following whole-genome duplication in teleost fishes.

Brunet F.G., Roest Crollius H., Paris M., Aury J.M., Gibert P., Jaillon O., Laudet V., Robinson-Rechavi M., 2006. Molecular Biology and Evolution, 23 (9) pp. 1808-1816. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_90789EA4F9CB]

2005

Les poissons : une duplication génomique réussie

Robinson-Rechavi M., 2005. Biofutur, 254 pp. 29-33. Peer-reviewed.

[WoS] [serval:BIB_BFFE216B8EB5]

Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes.

Robinson-Rechavi M., Maina C.V., Gissendanner C.R., Laudet V., Sluder A., 2005. Journal of Molecular Evolution, 60 (5) pp. 577-586.

[DOI] [WoS] [Pmid] [serval:BIB_9196CB34590C]

Structural genomics of thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability.

Robinson-Rechavi M., Godzik A., 2005. Structure, 13 (6) pp. 857-860.

[DOI] [WoS] [Pmid] [serval:BIB_88A740162689]

A conserved retinoid X receptor (RXR) from the mollusk Biomphalaria glabrata transactivates transcription in the presence of retinoids.

Bouton D., Escriva H., de Mendonça R.L., Glineur C., Bertin B., Noël C., Robinson-Rechavi M., de Groot A., Cornette J., Laudet V. et al., 2005. Journal of Molecular Endocrinology, 34 (2) pp. 567-582. Peer-reviewed.

[DOI] [WoS] [Pmid] [serval:BIB_41B0E841AA18]

2004

Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems.

Bertrand S., Brunet F.G., Escriva H., Parmentier G., Laudet V., Robinson-Rechavi M., 2004. Molecular Biology and Evolution, 21 (10) pp. 1923-1937.

[DOI] [WoS] [Pmid] [serval:BIB_C4066A213A2D]

Update of NUREBASE: nuclear hormone receptor functional genomics.

Ruau D., Duarte J., Ourjdal T., Perrière G., Laudet V., Robinson-Rechavi M., 2004. Nucleic Acids Research, 32 (Database issue) pp. D165-D167.

[DOI] [WoS] [Pmid] [serval:BIB_9DA05444ED38]

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Jaillon O., Aury J.M., Brunet F., Petit J.L., Stange-Thomann N., Mauceli E., Bouneau L., Fischer C., Ozouf-Costaz C., Bernot A. et al., 2004. Nature, 431 (7011) pp. 946-957.

[DOI] [WoS] [Pmid] [serval:BIB_402583637C48]

Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish reference.

Robinson-Rechavi M., Boussau B., Laudet V., 2004. Molecular Biology and Evolution, 21 (3) pp. 580-586.

[DOI] [WoS] [Pmid] [serval:BIB_94C2A0759739]

2003

Nuclear receptors are markers of animal genome evolution.

Escrivá García H., Laudet V., Robinson-Rechavi M., 2003. Journal of Structural and Functional Genomics, 3 (1-4) pp. 177-184.

[DOI] [Pmid] [serval:BIB_7719A0CB03D7]

Molecular evolution of angrogen receptors in fish

Douard V., Robinson-Rechavi M., Laudet V., Guiguen Y., 2003. Fish Physiology and Biochemistry, 28 (1-4) pp. 207-208. Peer-reviewed.

[DOI] [WoS] [serval:BIB_84AA70FE06E5]

Bioinformatics of nuclear receptors.

Robinson-Rechavi M., Laudet V., 2003. Methods in Enzymology, 364 pp. 95-118.

[DOI] [WoS] [Pmid] [serval:BIB_F41EDCF97163]

The nuclear receptor superfamily.

Robinson-Rechavi M., Escriva Garcia H., Laudet V., 2003. Journal of Cell Science, 116 (Pt 4) pp. 585-586.

[DOI] [WoS] [Pmid] [serval:BIB_64E2AC8ABD82]

Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMY.

Lutfalla G., Roest Crollius H., Brunet F.G., Laudet V., Robinson-Rechavi M., 2003. Journal of Molecular Evolution, 57 (Suppl 1) pp. S148-S153.

[DOI] [WoS] [Pmid] [serval:BIB_FECDD6DFB606]

Evidence for two distinct functional glucocorticoid receptors in teleost fish.

Bury N.R., Sturm A., Le Rouzic P., Lethimonier C., Ducouret B., Guiguen Y., Robinson-Rechavi M., Laudet V., Rafestin-Oblin M.E., Prunet P., 2003. Journal of Molecular Endocrinology, 31 (1) pp. 141-156.

[DOI] [WoS] [Pmid] [serval:BIB_5B32425BB5FE]

Rapid divergence of the ecdysone receptor in Diptera and Lepidoptera suggests coevolution between ECR and USP-RXR.

Bonneton F., Zelus D., Iwema T., Robinson-Rechavi M., Laudet V., 2003. Molecular Biology and Evolution, 20 (4) pp. 541-553.

[DOI] [WoS] [Pmid] [serval:BIB_2D3C67757A81]

2002

NUREBASE: database of nuclear hormone receptors.

Duarte J., Perrière G., Laudet V., Robinson-Rechavi M., 2002. Nucleic Acids Research, 30 (1) pp. 364-368.

[DOI] [WoS] [Pmid] [serval:BIB_A44CB893F4DD]

Characterization of oestrogen receptors in zebrafish (Danio rerio).

Bardet P.L., Horard B., Robinson-Rechavi M., Laudet V., Vanacker J.M., 2002. Journal of Molecular Endocrinology, 28 (3) pp. 153-163.

[DOI] [WoS] [Pmid] [serval:BIB_8DE3ED904289]

2001

Euteleost fish genomes are characterized by expansion of gene families.

Robinson-Rechavi M., Marchand O., Escriva H., Bardet P.L., Zelus D., Hughes S., Laudet V., 2001. Genome Research, 11 (5) pp. 781-788.

[DOI] [WoS] [Pmid] [serval:BIB_28AB4513BA82]

Evolutionary rates of duplicate genes in fish and mammals.

Robinson-Rechavi M., Laudet V., 2001. Molecular Biology and Evolution, 18 (4) pp. 681-683.

[WoS] [Pmid] [serval:BIB_84ABEF83C5A3]

How many nuclear hormone receptors are there in the human genome?

Robinson-Rechavi M., Carpentier A.S., Duffraisse M., Laudet V., 2001. Trends in Genetics, 17 (10) pp. 554-556.

[DOI] [WoS] [Pmid] [serval:BIB_99E03031CB99]

Re: Revisiting recent challenges to the ancient fish-specific genome duplication hypothesis

Robinson-Rechavi M., Marchand O., Escriva H., Laudet V., 2001. Current Biology, 11 (24) pp. R1007-R1008.

[DOI] [WoS] [serval:BIB_6CFF2C43B0E6]

Usage optimization of unevenly sampled data through the combination of quartet trees: A eutherian draft phylogeny based on 640 nuclear and mitochondrial proteins

Robinson-Rechavi M., Graur D., 2001. Israel Journal of Zoology, 47 (3) pp. 259-270. Peer-reviewed.

[DOI] [WoS] [serval:BIB_6388C496A90B]

An ancestral whole-genome duplication may not have been responsible for the abundance of duplicated fish genes.

Robinson-Rechavi M., Marchand O., Escriva H., Laudet V., 2001. Current Biology, 11 (12) pp. R458-R459.

[DOI] [WoS] [Pmid] [serval:BIB_DF6FCFC481A1]

2000

Fast evolution of interleukin-2 in mammals and positive selection in ruminants.

Zelus D., Robinson-Rechavi M., Delacre M., Auriault C., Laudet V., 2000. Journal of Molecular Evolution, 51 (3) pp. 234-244.

[WoS] [Pmid] [serval:BIB_DB61D6AA834B]

Regulation of heat-shock response in bacteria

Ron E. Z., Segal G., Sirkis R., Robinson M., Graur D., 2000. pp. 649-655 dans Bell C. R., Brylinsky M., Johnson-Green P. (eds.) Microbial biosystems : new frontiers, Atlantic Canada Society for Microbial Ecology.

[serval:BIB_1670E9C6C08F]

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Thesis

2016 | 2013 | 2012 | 2011 | 2009 |

2016

preview resource BIB_8E5536BAC604.P001

Long term evolutionary responses to whole genome duplication

Laurent S., 2016-08. 134, Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).

[URN] [serval:BIB_8E5536BAC604]

2013

Bioinformatic study of selection in animal genomes

Gharib W., 2013. 115, Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).

[serval:BIB_A722A8DEB7F9]

2012

preview resource BIB_CB3081439982.P001

Comparative modular analysis of gene expression in vertebrate development

Piasecka B., 2012-11., Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).

[URN] [serval:BIB_CB3081439982]

2011

preview resource BIB_B0AA59BBE0A7.P001

Analysis of gene expression patterns in animals

Bastian F.B., 2011-09. 302, Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).

[URN] [serval:BIB_B0AA59BBE0A7]

2009

Evolution of proteins after whole-genome duplication

Studer R.A., 2009-11. 126, Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).

[serval:BIB_A8059F103686]

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