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Group Robinson-Rechavi - Evolutionary Bioinformatics.


Evolutionary Bioinformatics Group

Research in our group is mainly focused on linking the evolution of animal development to genome evolution. The group develops database for evolutionary biology, and studies genome evolution in vertebrates. The group is also involved in targeted projects in functional genomics.

Evo-Devo and Bgee

Bgee is a database to compare expression patterns between animal species. Bgee addresses difficulties such as complex anatomies and diverse sources of data by the use of ontologies and the explicit representation of homology. Homology relationships are defined both between genes and between anatomical features. The main efforts are the annotation of anatomical and developmental terms and their homology relationships, and the annotation and statistical treatment of transcriptome data. Such efforts provide an answer to the question "Where is this gene expressed?" from the analysis of data as diverse as ESTs, microarrays, and in situ hybridization. We have the aim of producing a database useful to disciplines such as comparative genomics, Evo-Devo, or transcriptome studies, whilst providing an improved integration of homology and related concepts into bioinformatics through ontologies and ontology tools.
Bgee is available at http://bgee.unil.ch/
A main use of Bgee in the lab is the integrated study of genome evolution and of Evo-Devo.

Genome duplication and positive selection

Gene and genome duplication are considered major mechanisms in the creation of new functions in genomes, or in the refinement of networks by the division of function among more genes. We are especially interested in the genome duplications which occurred in the Paleozoic, in the ancestor of vertebrates and in the ancestor of teleost fishes.
We are also interested in characterizing patterns of positive selection, especially ancient and rare events. For this we develop the database Selectome: http://selectome.unil.ch/

Comparative functional genomics: case studies

We collaborate with experimental biology laboratories, bringing expertise in comparative and functional genomics. We most notably have a long term interest in nuclear hormone receptors.

In press |  2015 |  2014 |  2013 |  2012 |  2011 |  2010 |  2009 |  2008 |  2007 |  2006 |  Thèses (doctorat) | 

In Press
Roux J., Rosikiewicz M., Robinson-Rechavi M., In Press. What to compare and how: comparative transcriptomics for Evo-Devo. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution . [url editor site] [DOI]
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. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database 2015 pp. bav043. [Document] [url editor site] [DOI]
Bertelli C., Aeby S., Chassot B., Clulow J., Hilfiker O., Rappo S., Ritzmann S., Schumacher P., Terrettaz C., Benaglio P. et al., 2015. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Frontiers in Microbiology 6(101) p. 101. [DOI] [Web of Science] [Pubmed]
Daub J.T., Dupanloup I., Robinson-Rechavi M., Excoffier L., 2015. Inference of evolutionary forces acting on human biological pathways. Genome Biology and Evolution . [url editor site] [DOI]
Daub J.T., Merks R.M., 2015. Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit. Methods in Molecular Biology 1214 pp. 67-127. [DOI] [Web of Science] [Pubmed]
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. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology 17(1) pp. 91-104. [Document] [DOI] [Web of Science] [Pubmed]
Bernard T., Bridge A., Morgat A., Moretti S., Xenarios I., Pagni M., 2014. Reconciliation of metabolites and biochemical reactions for metabolic networks. Briefings in Bioinformatics 15(1) pp. 123-135. [DOI] [Web of Science] [Pubmed]
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. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Journal of Biomedical Semantics 5 p. 21. [DOI] [Pubmed]
Kryuchkova Nadezda, Robinson-Rechavi Marc, 2014. Determinants of protein evolutionary rates in light of ENCODE functional genomics. pp. A9 in BMC Bioinformatics. [DOI]
Miyazaki Ryo, Bertelli Claire, Benaglio Paola, Canton Jonas, De Coi Nicoló, Gharib Walid H., Gjoksi Bebeka, Goesmann Alexander, Greub Gilbert, Harshman Keith et al., 2014. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology pp. n/a-n/a. [DOI]
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. Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Research 42(1) pp. D917-D921. [Document] [DOI] [Web of Science] [Pubmed]
Roux J., Privman E., Moretti S., Daub J.T., Robinson-Rechavi M., Keller L., 2014. Patterns of positive selection in seven ant genomes. Molecular Biology and Evolution 31(7) pp. 1661-1685. [Document] [DOI] [Web of Science] [Pubmed]
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. Big data and other challenges in the quest for orthologs. Bioinformatics 30(21) pp. 2993-2998. [DOI] [Web of Science] [Pubmed]
Stockinger H., Altenhoff A.M., Arnold K., Bairoch A., Bastian F., Bergmann S., Bougueleret L., Bucher P., Delorenzi M., Lane L. et al., 2014. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Research 42(Web Server issue) pp. W436-W441. [DOI] [Web of Science] [Pubmed]
Valle M., Schabauer H., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Salamin N., 2014. Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinformatics 30(8) pp. 1129-1137. [DOI] [Web of Science] [Pubmed]
Cohen D., Bogeat-Triboulot M.B., Vialet-Chabrand S., Merret R., Courty P.E., Moretti S., Bizet F., Guilliot A., Hummel I., 2013. Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy? PLoS One 8(2) pp. e55506. [DOI] [Web of Science] [Pubmed]
Daub J.T., Hofer T., Cutivet E., Dupanloup I., Quintana-Murci L., Robinson-Rechavi M., Excoffier L., 2013. Evidence for polygenic adaptation to pathogens in the human genome. Molecular Biology and Evolution 30(7) pp. 1544-1558. [DOI] [Web of Science] [Pubmed]
Daub J.T., Merks R.M., 2013. A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis. Bulletin of Mathematical Biology 75(8) pp. 1377-1399. [DOI] [Web of Science] [Pubmed]
Ganter M., Bernard T., Moretti S., Stelling J., Pagni M., 2013. MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. Bioinformatics 29(6) pp. 815-816. [DOI] [Web of Science] [Pubmed]
Muhammad N., Kryuchkova N., Dworeck T., Rodríguez-Ropero F., Fioroni M., 2013. Enhanced EGFP Fluorescence Emission in Presence of PEG Aqueous Solutions and PIB1000-PEG6000-PIB1000 Copolymer Vesicles. Biomed Research International 2013 p. 329087. [DOI] [Web of Science] [Pubmed]
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. PLoS Genetics 9(4) pp. e1003476. [Document] [DOI] [Web of Science] [Pubmed]
Rosikiewicz M., Comte A., Niknejad A., Robinson-Rechavi M., Bastian F.B., 2013. Uncovering hidden duplicated content in public transcriptomics data. Database 2013 pp. bat010. [DOI] [Web of Science] [Pubmed]
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. Community-wide plasmid gene mobilization and selection. ISME Journal 7(6) pp. 1173-1186. [DOI] [Web of Science] [Pubmed]
Altenhoff A.M., Studer R.A., Robinson-Rechavi M., Dessimoz C., 2012. Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Computational Biology 8(5) pp. e1002514. [DOI] [Web of Science] [Pubmed]
Artimo P., Jonnalagedda M., Arnold K., Baratin D., Csardi G., de Castro E., Duvaud S., Flegel V., Fortier A., Gasteiger E. et al., 2012. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research 40 pp. W597-W603. [DOI] [Web of Science] [Pubmed]
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. Recent advances in biocuration: meeting report from the fifth International Biocuration Conference. Database 2012 pp. bas036. [DOI] [Web of Science] [Pubmed]
Louis A., Roest Crollius H., Robinson-Rechavi M., 2012. How much does the amphioxus genome represent the ancestor of chordates? Briefings in Functional Genomics 11(2) pp. 89-95. [DOI] [Web of Science] [Pubmed]
Moretti S., Murri R., Maffioletti S., Kuzniar A., Castella B, Salamin N., Robinson-Rechavi M., Stockinger H., 2012. gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution. pp. 59-68 in Glatard T, Silverstein J (eds.) HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences. Studies in Health Technology and Informatics 175. IOS Press Books online. [Document] [url editor site] [DOI]
Niknejad A., Comte A., Parmentier G., Roux J., Bastian F.B., Robinson-Rechavi M., 2012. vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinformatics 28(7) pp. 1017-1020. [DOI] [Web of Science] [Pubmed]
Piasecka B., Kutalik Z., Roux J., Bergmann S., Robinson-Rechavi M., 2012. Comparative modular analysis of gene expression in vertebrate organs. Bmc Genomics 13 p. 124. [Document] [DOI] [Web of Science] [Pubmed]
Roux J., Gonzàlez-Porta M., Robinson-Rechavi M., 2012. Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Research 40(13) pp. 5890-5900. [DOI] [Web of Science] [Pubmed]
Schabauer H., Valle M., Pacher C., Stockinger H., Stamatakis A., Robinson-Rechavi M., Yang Z., Salamin N., 2012. SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model. pp. 700-708 in Aluru S., Bader D.A. (eds.) HiCOMB (11th IEEE International Workshop on High Performance Computational Biology). IEEE. [Document] [DOI]
Boeckmann B., Robinson-Rechavi M., Xenarios I., Dessimoz C., 2011. Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Briefings in Bioinformatics 12(5) pp. 423-435. [DOI] [Web of Science] [Pubmed]
Di Tommaso P., Moretti S., Xenarios I., Orobitg M., Montanyola A., Chang J.M., Taly J.F., Notredame C., 2011. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Research 39(Web Server issue) pp. W13-W17. [DOI] [Pubmed]
Gharib W.H., Robinson-Rechavi M., 2011. When orthologs diverge between human and mouse. Briefings in Bioinformatics 12(5) pp. 436-441. [DOI] [Web of Science] [Pubmed]
Jagannathan V., Robinson-Rechavi M., 2011. The challenge of modeling nuclear receptor regulatory networks in mammalian cells. Molecular and Cellular Endocrinology 334(1-2) pp. 91-97. [DOI] [Web of Science] [Pubmed]
Studer R.A., Person E., Robinson-Rechavi M., Rossier B.C., 2011. Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport. Physiological Genomics 43(13) pp. 844-854. [DOI] [Web of Science] [Pubmed]
Burri R., Salamin N., Studer R.A., Roulin A., Fumagalli L., 2010. Adaptive divergence of ancient gene duplicates in the avian MHC class II beta. Molecular Biology and Evolution 27(10) pp. 2360-2374. [DOI] [Web of Science] [Pubmed]
Comte A., Roux J., Robinson-Rechavi M., 2010. Molecular signaling in zebrafish development and the vertebrate phylotypic period. Evolution and Development 12(2) pp. 144-156. [Document] [url editor site] [DOI] [Web of Science]
Duret L., Bataillon T., Bierne N., Daubin V., Dutheil J., Gautier C., Glemin S., Gouy M., Heyer E., Marais G. et al., 2010. Evolution moléculaire. pp. 123-182 in Thomas F., Lefevre T., Raymond M. (eds.) Biologie évolutive. de Boeck. [url editor site]
Kraut A., Moretti S., Robinson-Rechavi M., Stockinger H., Flanders D., 2010. Phylogenetic Code in the Cloud - Can it Meet the Expectations? Studies in Health Technology and Informatics 159 pp. 55-63. [DOI] [Pubmed]
Parmentier G., Bastian F.B., Robinson-Rechavi M., 2010. Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics 26(14) pp. 1766-1771. [DOI] [Pubmed]
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. 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. Molecular and Cellular Proteomics 9(7) pp. 1578-1593. [DOI] [Pubmed]
Roux J., Robinson-Rechavi M., 2010. An ontology to clarify homology-related concepts. Trends in Genetics 26(3) pp. 99-102. [Document] [DOI] [Web of Science] [Pubmed]
Studer R.A., Robinson-Rechavi M., 2010. Large-scale analysis of orthologs and paralogs under covarion-like and constant-but-different models of amino acid evolution. Molecular Biology and Evolution 27(11) pp. 2618-2627. [DOI] [Pubmed]
Tzertzinis G., Egaña A.L., Palli S.R., Robinson-Rechavi M., Gissendanner C.R., Liu C., Unnasch T.R., Maina C.V., 2010. Molecular evidence for a functional ecdysone signaling system in Brugia malayi. PLoS Neglected Tropical Diseases 4(3) pp. e625. [DOI] [Web of Science] [Pubmed]
Cruz F., Roux J., Robinson-Rechavi M., 2009. The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes. BMC Genomics 10(1) p. 619. [Document] [DOI] [Web of Science] [Pubmed]
Iwema T., Chaumot A., Studer R.A., Robinson-Rechavi M., Billas I.M., Moras D., Laudet V., Bonneton F., 2009. Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects. Molecular Biology and Evolution 26(4) pp. 753-768. [DOI] [Web of Science] [Pubmed]
Proux E., Studer R.A., Moretti S., Robinson-Rechavi M., 2009. Selectome: a database of positive selection. Nucleic Acids Research 37(Database issue) pp. D404-D407. [DOI] [Web of Science] [Pubmed]
Robinson-Rechavi M., 2009. Bioinformatics for evolutionary developmental biology. pp. 355-378 in Appel R.D., Feytmans E. (eds.) Bioinformatics: A Swiss Perspective. World Scientific Publishing Company, Singapore. [Document] [url editor site]
Studer R.A., Robinson-Rechavi M., 2009. Evidence for an episodic model of protein sequence evolution. Biochemical Society transactions 37(Pt 4) pp. 783-786. [DOI] [Web of Science] [Pubmed]
Studer R.A., Robinson-Rechavi M., 2009. How confident can we be that orthologs are similar, but paralogs differ? Trends in Genetics 25(5) pp. 210-216. [Document] [DOI] [Web of Science]
Studer R.A., Robinson-Rechavi M., 2009. Large-Scale Analyses of Positive Selection Using Codon Models. pp. 217-236 in Pontarotti P. (eds.) Evolutionary Biology: Concept, Modeling, and Application. Springer‐Verlag, Berlin. [Document] [DOI]
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. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nature Biotechnology 26(8) pp. 909-915. [DOI] [Web of Science] [Pubmed]
Bastian F., Parmentier G., Roux J., Moretti S., Laudet V., Robinson-Rechavi M., 2008. Bgee: integrating and comparing heterogeneous transcriptome data among species. pp. 124-131 in Istrail S., Pevzner P., Waterman M. (eds.) Data Integration in Life Sciences. Lecture Notes in Computer Science 5109. Springer, Berlin. [Document] [url editor site] [DOI]
Crossgrove K., Maina C.V., Robinson-Rechavi M., Lochner M.C., 2008. Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis. Molecular and Biochemical Parasitology 157(1) pp. 92-97. [DOI] [Web of Science] [Pubmed]
Cruz F., Vilà C., Webster M.T., 2008. The legacy of domestication: accumulation of deleterious mutations in the dog genome. Molecular Biology and Evolution 25(11) pp. 2331-2336. [DOI] [Web of Science] [Pubmed]
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. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research 18(7) pp. 1100-1111. [DOI] [Web of Science] [Pubmed]
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. The amphioxus genome and the evolution of the chordate karyotype. Nature 453(7198) pp. 1064-1071. [DOI] [Web of Science] [Pubmed]
Robinson-Rechavi M., 2008. Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals. Molecular and Cellular Endocrinology 293(1-2) pp. 2-4. [Document] [DOI] [Web of Science] [Pubmed]
Roux J., Robinson-Rechavi M., 2008. Developmental constraints on vertebrate genome evolution. PLoS Genetics 4(12) pp. e1000311. [Document] [DOI] [Web of Science] [Pubmed]
Studer R.A., Penel S., Duret L., Robinson-Rechavi M., 2008. Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Research 18(9) pp. 1393-1402. [DOI] [Web of Science] [Pubmed]
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. A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Systems Biology 1 p. 34. [Document] [DOI] [Web of Science] [Pubmed]
Amoutzias G.D., Veron A.S., Weiner J., Robinson-Rechavi M., Bornberg-Bauer E., Oliver S.G., Robertson D.L., 2007. One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity. Molecular Biology and Evolution 24(3) pp. 827-835. [DOI] [Web of Science] [Pubmed]
Brunet F.G., Roest Crollius H., Paris M., Aury J.M., Gibert P., Jaillon O., Laudet V., Robinson-Rechavi M., 2006. Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Molecular Biology and Evolution 23(9) pp. 1808-1816. [DOI] [Web of Science] [Pubmed]
Escriva H., Bertrand S., Germain P., Robinson-Rechavi M., Umbhauer M., Cartry J., Duffraisse M., Holland L., Gronemeyer H., Laudet V., 2006. Neofunctionalization in vertebrates: the example of retinoic acid receptors. PLoS Genetics 2(7) pp. e102. [Document] [DOI] [Web of Science] [Pubmed]
Phd thesis
Studer R.A., 11-2009. Evolution of proteins after whole-genome duplication. 126 p., Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).


Félix Imhof © UNIL

Marc Robinson-Rechavi
Office room: 3219
Phone: +41(0)21 692 42 20
Fax: +41(0)21 692 41 65

Administrative assistant
Office room: 3106
Phone: +4121 692 4200
Fax: +4121 692 4265

Biophore - CH-1015 Lausanne  - Switzerland  -  Tel. +41 21 692 41 60  -  Fax +41 21 692 41 65
Swiss University