Publications
Publications
In press |
2013 |
2012 |
2011 |
2010 |
2009 |
2008 |
2007 |
2006 |
Gharib W., Robinson-Rechavi M., In Press. The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC.
Molecular Biology and Evolution
.
Marta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson-Rechavi, Frederic B. Bastian, In Press. Uncovering hidden duplicated content in public transcriptomics data.
Database
. [url editor site]
[DOI]
Piasecka B., Lichocki P., Moretti S., Bergmann S., Robinson-Rechavi M., In Press. The hourglass and the early conservation models - co-existing evolutionary patterns in vertebrate development.
PLOS Genetics
. [Document]
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 Josephine T., Merks Roeland M.H., 2013. A Cell-Based Model of Extracellular-Matrix-Guided Endothelial Cell Migration During Angiogenesis.
Bulletin of Mathematical Biology
. [DOI]
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 (oxford, England)
29(6) pp. 815-816. [DOI]
[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., Grosdidier A., Hernandez C., Ioannidis V., Kuznetsov D., Liechti R., Moretti S., Mostaguir K., Redaschi N., Rossier G., Xenarios I., Stockinger H., 2012. ExPASy: SIB bioinformatics resource portal.
Nucleic Acids Research
40 pp. W597-W603. [DOI]
[Web of Science]
[Pubmed]
Gaudet Pascale, Arighi Cecilia, Bastian Frederic, Bateman Alex, Blake Judith A., Cherry Michael J., D'Eustachio Peter, Finn Robert, Giglio Michelle, Hirschman Lynette, Kania Renate, Klimke William, Martin Maria Jesus, Karsch-Mizrachi Ilene, Munoz-Torres Monica, Natale Darren, O'Donovan Claire, Ouellette Francis, Pruitt Kim D., Robinson-Rechavi Marc, Sansone Susanna-Assunta, Schofield Paul, Sutton Granger, Van Auken Kimberly, Vasudevan Sona, Wu Cathy, Young Jasmine, Mazumder Raja, 2012. Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.
Database
2012 pp. bas036. [url editor site]
[DOI]
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]
Piasecka B., Robinson-Rechavi M., Bergmann S., 2012. Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human.
Bioinformatics
28(14) pp. 1865-1872. [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. 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.
BMC Systems Biology
5(1) p. 138. [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]
Roux J., Robinson-Rechavi M., 2011. Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication.
Genome Research
21(3) pp. 357-363. [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., Mouchiroud D., Pontarotti P., Quintana-Murci L., Robinson-Rechavi M., Galtier N., 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., Vidal M., Goillot E., 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., 11-2009. Evolution of proteins after whole-genome duplication. 126 p., Université de Lausanne, Faculté de biologie et médecine, Robinson-Rechavi M. (dir.).
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]
[url editor site]
[DOI]
[Web of Science]
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., Caillaud M.C., Coutinho P.M., Dasilva C., De Luca F., Deau F., Esquibet M., Flutre T., Goldstone J.V., Hamamouch N., Hewezi T., Jaillon O., Jubin C., Leonetti P., Magliano M., Maier T.R., Markov G.V., McVeigh P., Pesole G., Poulain J., Robinson-Rechavi M., Sallet E., Ségurens B., Steinbach D., Tytgat T., Ugarte E., van Ghelder C., Veronico P., Baum T.J., Blaxter M., Bleve-Zacheo T., Davis E.L., Ewbank J.J., Favery B., Grenier E., Henrissat B., Jones J.T., Laudet V., Maule A.G., Quesneville H., Rosso M.N., Schiex T., Smant G., Weissenbach J., Wincker P., 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., Ferrier D.E., Garcia-Fernàndez J., Gibson-Brown J.J., Gissi C., Godzik A., Hallböök F., Hirose D., Hosomichi K., Ikuta T., Inoko H., Kasahara M., Kasamatsu J., Kawashima T., Kimura A., Kobayashi M., Kozmik Z., Kubokawa K., Laudet V., Litman G.W., McHardy A.C., Meulemans D., Nonaka M., Olinski R.P., Pancer Z., Pennacchio L.A., Pestarino M., Rast J.P., Rigoutsos I., Robinson-Rechavi M., Roch G., Saiga H., Sasakura Y., Satake M., Satou Y., Schubert M., Sherwood N., Shiina T., Takatori N., Tello J., Vopalensky P., Wada S., Xu A., Ye Y., Yoshida K., Yoshizaki F., Yu J.K., Zhang Q., Zmasek C.M., de Jong P.J., Osoegawa K., Putnam N.H., Rokhsar D.S., Satoh N., Holland P.W., 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., Benito-Gutiérrez E.L., Dubchak I., Garcia-Fernàndez J., Gibson-Brown J.J., Grigoriev I.V., Horton A.C., de Jong P.J., Jurka J., Kapitonov V.V., Kohara Y., Kuroki Y., Lindquist E., Lucas S., Osoegawa K., Pennacchio L.A., Salamov A.A., Satou Y., Sauka-Spengler T., Schmutz J., Shin-I T., Toyoda A., Bronner-Fraser M., Fujiyama A., Holland L.Z., Holland P.W., Satoh N., Rokhsar D.S., 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]
Robinson-Rechavi M., Alibés A., Godzik A., 2006. Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.
Journal of Molecular Biology
356(2) pp. 547-557. [Document]
[DOI]
[Web of Science]
[Pubmed]
