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Items: 1 to 50 of 100

1.

Sex-specific changes in gene expression in response to estrogen pollution around the onset of sex differentiation in grayling (Salmonidae).

Selmoni OM, Maitre D, Roux J, Wilkins LGE, Marques da Cunha L, Vermeirssen ELM, Knörr S, Robinson-Rechavi M, Wedekind C.

BMC Genomics. 2019 Jul 15;20(1):583. doi: 10.1186/s12864-019-5955-z.

2.

Cross-species functional modules link proteostasis to human normal aging.

Komljenovic A, Li H, Sorrentino V, Kutalik Z, Auwerx J, Robinson-Rechavi M.

PLoS Comput Biol. 2019 Jul 3;15(7):e1007162. doi: 10.1371/journal.pcbi.1007162. eCollection 2019 Jul.

3.

Genomic signatures accompanying the dietary shift to phytophagy in polyphagan beetles.

Seppey M, Ioannidis P, Emerson BC, Pitteloud C, Robinson-Rechavi M, Roux J, Escalona HE, McKenna DD, Misof B, Shin S, Zhou X, Waterhouse RM, Alvarez N.

Genome Biol. 2019 May 17;20(1):98. doi: 10.1186/s13059-019-1704-5.

4.

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5.

Ellegaard KM, Brochet S, Bonilla-Rosso G, Emery O, Glover N, Hadadi N, Jaron KS, van der Meer JR, Robinson-Rechavi M, Sentchilo V, Tagini F; SAGE class 2016-17, Engel P.

Mol Ecol. 2019 May;28(9):2224-2237. doi: 10.1111/mec.15075. Epub 2019 May 29.

PMID:
30864192
5.

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.

Davydov II, Salamin N, Robinson-Rechavi M.

Mol Biol Evol. 2019 Jun 1;36(6):1316-1332. doi: 10.1093/molbev/msz048.

6.

Repeated Evolution of Asexuality Involves Convergent Gene Expression Changes.

Parker DJ, Bast J, Jalvingh K, Dumas Z, Robinson-Rechavi M, Schwander T.

Mol Biol Evol. 2019 Feb 1;36(2):350-364. doi: 10.1093/molbev/msy217.

7.

Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo.

Liu J, Robinson-Rechavi M.

Mol Biol Evol. 2018 Dec 1;35(12):2862-2872. doi: 10.1093/molbev/msy175.

8.

Developmental Constraints on Genome Evolution in Four Bilaterian Model Species.

Liu J, Robinson-Rechavi M.

Genome Biol Evol. 2018 Sep 1;10(9):2266-2277. doi: 10.1093/gbe/evy177.

9.

Low number of fixed somatic mutations in a long-lived oak tree.

Schmid-Siegert E, Sarkar N, Iseli C, Calderon S, Gouhier-Darimont C, Chrast J, Cattaneo P, Schütz F, Farinelli L, Pagni M, Schneider M, Voumard J, Jaboyedoff M, Fankhauser C, Hardtke CS, Keller L, Pannell JR, Reymond A, Robinson-Rechavi M, Xenarios I, Reymond P.

Nat Plants. 2017 Dec;3(12):926-929. doi: 10.1038/s41477-017-0066-9. Epub 2017 Dec 4.

PMID:
29209081
10.

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

Maitre D, Selmoni OM, Uppal A, Marques da Cunha L, Wilkins LGE, Roux J, Mobley KB, Castro I, Knörr S, Robinson-Rechavi M, Wedekind C.

Sci Rep. 2017 Nov 3;7(1):15024. doi: 10.1038/s41598-017-14905-9.

11.

Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates.

Roux J, Liu J, Robinson-Rechavi M.

Mol Biol Evol. 2017 Nov 1;34(11):2773-2791. doi: 10.1093/molbev/msx199.

12.

Bayesian association scan reveals loci associated with human lifespan and linked biomarkers.

McDaid AF, Joshi PK, Porcu E, Komljenovic A, Li H, Sorrentino V, Litovchenko M, Bevers RPJ, Rüeger S, Reymond A, Bochud M, Deplancke B, Williams RW, Robinson-Rechavi M, Paccaud F, Rousson V, Auwerx J, Wilson JF, Kutalik Z.

Nat Commun. 2017 Jul 27;8:15842. doi: 10.1038/ncomms15842.

13.

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

Laurent S, Salamin N, Robinson-Rechavi M.

PLoS One. 2017 Apr 20;12(4):e0176384. doi: 10.1371/journal.pone.0176384. eCollection 2017.

14.

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

Daub JT, Moretti S, Davydov II, Excoffier L, Robinson-Rechavi M.

Mol Biol Evol. 2017 Jun 1;34(6):1391-1402. doi: 10.1093/molbev/msx083. Erratum in: Mol Biol Evol. 2017 Jun 1;34(6):1549.

15.

State aggregation for fast likelihood computations in molecular evolution.

Davydov II, Robinson-Rechavi M, Salamin N.

Bioinformatics. 2017 Feb 1;33(3):354-362. doi: 10.1093/bioinformatics/btw632.

16.

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

Kryuchkova-Mostacci N, Robinson-Rechavi M.

PLoS Comput Biol. 2016 Dec 28;12(12):e1005274. doi: 10.1371/journal.pcbi.1005274. eCollection 2016 Dec.

17.

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

Komljenovic A, Roux J, Wollbrett J, Robinson-Rechavi M, Bastian FB.

Version 2. F1000Res. 2016 Nov 23 [revised 2018 Jan 1];5:2748. doi: 10.12688/f1000research.9973.2. eCollection 2016.

18.

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, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Ruiz Buendia G, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Ben Jeddou F, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, van der Meer JR.

PLoS One. 2016 Nov 3;11(11):e0165850. doi: 10.1371/journal.pone.0165850. eCollection 2016.

19.

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.

Bioinformatics. 2016 Aug 15;32(16):2565. doi: 10.1093/bioinformatics/btw374. Epub 2016 Jul 3. No abstract available.

PMID:
27373894
20.

A benchmark of gene expression tissue-specificity metrics.

Kryuchkova-Mostacci N, Robinson-Rechavi M.

Brief Bioinform. 2017 Mar 1;18(2):205-214. doi: 10.1093/bib/bbw008.

21.

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

Laurent S, Robinson-Rechavi M, Salamin N.

BMC Evol Biol. 2015 Aug 11;15:157. doi: 10.1186/s12862-015-0432-z.

22.

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

Kryuchkova-Mostacci N, Robinson-Rechavi M.

PLoS One. 2015 Jun 29;10(6):e0131673. doi: 10.1371/journal.pone.0131673. eCollection 2015.

23.

Genomics is changing Evo-Devo.

Robinson-Rechavi M.

J Exp Zool B Mol Dev Evol. 2015 Jun;324(4):315. doi: 10.1002/jez.b.22633. No abstract available.

PMID:
26010365
24.

Inference of Evolutionary Forces Acting on Human Biological Pathways.

Daub JT, Dupanloup I, Robinson-Rechavi M, Excoffier L.

Genome Biol Evol. 2015 May 13;7(6):1546-58. doi: 10.1093/gbe/evv083.

25.

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

Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M.

Database (Oxford). 2015 May 9;2015:bav043. doi: 10.1093/database/bav043. Print 2015.

26.

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

Roux J, Rosikiewicz M, Robinson-Rechavi M.

J Exp Zool B Mol Dev Evol. 2015 Jun;324(4):372-82. doi: 10.1002/jez.b.22618. Epub 2015 Apr 10. Review.

27.

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, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G.

Front Microbiol. 2015 Feb 19;6:101. doi: 10.3389/fmicb.2015.00101. eCollection 2015.

28.

Big data and other challenges in the quest for orthologs.

Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C; Quest for Orthologs consortium.

Bioinformatics. 2014 Nov 1;30(21):2993-8. doi: 10.1093/bioinformatics/btu492. Epub 2014 Jul 26.

29.

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

Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ.

J Biomed Semantics. 2014 May 19;5:21. doi: 10.1186/2041-1480-5-21. eCollection 2014.

30.

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 WH, Gjoksi B, Goesmann A, Greub G, Harshman K, Linke B, Mikulic J, Mueller L, Nicolas D, Robinson-Rechavi M, Rivolta C, Roggo C, Roy S, Sentchilo V, Siebenthal AV, Falquet L, van der Meer JR.

Environ Microbiol. 2015 Jan;17(1):91-104. doi: 10.1111/1462-2920.12498. Epub 2014 May 28.

31.

Patterns of positive selection in seven ant genomes.

Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L.

Mol Biol Evol. 2014 Jul;31(7):1661-85. doi: 10.1093/molbev/msu141. Epub 2014 Apr 29.

32.

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.

Bioinformatics. 2014 Apr 15;30(8):1129-1137. Epub 2014 Jan 2.

33.

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.

Bioinformatics. 2014 May 15;30(10):1392-9. doi: 10.1093/bioinformatics/btu027. Epub 2014 Jan 21. Erratum in: Bioinformatics. 2016 Aug 15;32(16):2565.

34.

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

Gaudet P, Munoz-Torres M, Robinson-Rechavi M, Attwood T, Bateman A, Cherry JM, Kania R, O'Donovan C, Yamasaki C.

Database (Oxford). 2013 Dec 6;2013:bat077. doi: 10.1093/database/bat077. Print 2013. No abstract available.

35.

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

Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M.

Nucleic Acids Res. 2014 Jan;42(Database issue):D917-21. doi: 10.1093/nar/gkt1065. Epub 2013 Nov 12.

36.

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.

PLoS Genet. 2013 Apr;9(4):e1003476. doi: 10.1371/journal.pgen.1003476. Epub 2013 Apr 25.

37.

Evidence for polygenic adaptation to pathogens in the human genome.

Daub JT, Hofer T, Cutivet E, Dupanloup I, Quintana-Murci L, Robinson-Rechavi M, Excoffier L.

Mol Biol Evol. 2013 Jul;30(7):1544-58. doi: 10.1093/molbev/mst080. Epub 2013 Apr 26.

PMID:
23625889
38.

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

Gharib WH, Robinson-Rechavi M.

Mol Biol Evol. 2013 Jul;30(7):1675-86. doi: 10.1093/molbev/mst062. Epub 2013 Apr 4.

39.

Uncovering hidden duplicated content in public transcriptomics data.

Rosikiewicz M, Comte A, Niknejad A, Robinson-Rechavi M, Bastian FB.

Database (Oxford). 2013 Mar 13;2013:bat010. doi: 10.1093/database/bat010. Print 2013.

40.

Community-wide plasmid gene mobilization and selection.

Sentchilo V, Mayer AP, Guy L, Miyazaki R, Green Tringe S, Barry K, Malfatti S, Goessmann A, Robinson-Rechavi M, van der Meer JR.

ISME J. 2013 Jun;7(6):1173-86. doi: 10.1038/ismej.2013.13. Epub 2013 Feb 14.

41.

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

Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Cherry MJ, D'Eustachio P, Finn R, Giglio M, Hirschman L, Kania R, Klimke W, Martin MJ, Karsch-Mizrachi I, Munoz-Torres M, Natale D, O'Donovan C, Ouellette F, Pruitt KD, Robinson-Rechavi M, Sansone SA, Schofield P, Sutton G, Van Auken K, Vasudevan S, Wu C, Young J, Mazumder R.

Database (Oxford). 2012 Oct 29;2012:bas036. doi: 10.1093/database/bas036. Print 2012.

42.

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.

Stud Health Technol Inform. 2012;175:59-68.

PMID:
22941988
43.

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

Altenhoff AM, Studer RA, Robinson-Rechavi M, Dessimoz C.

PLoS Comput Biol. 2012;8(5):e1002514. doi: 10.1371/journal.pcbi.1002514. Epub 2012 May 17.

44.

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.

Bioinformatics. 2012 Jul 15;28(14):1865-72. doi: 10.1093/bioinformatics/bts266. Epub 2012 May 9.

45.

Comparative modular analysis of gene expression in vertebrate organs.

Piasecka B, Kutalik Z, Roux J, Bergmann S, Robinson-Rechavi M.

BMC Genomics. 2012 Mar 29;13:124. doi: 10.1186/1471-2164-13-124.

46.

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

Roux J, Gonzàlez-Porta M, Robinson-Rechavi M.

Nucleic Acids Res. 2012 Jul;40(13):5890-900. doi: 10.1093/nar/gks279. Epub 2012 Mar 28.

47.

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

Louis A, Roest Crollius H, Robinson-Rechavi M.

Brief Funct Genomics. 2012 Mar;11(2):89-95. doi: 10.1093/bfgp/els003. Epub 2012 Feb 28. Review.

48.

vHOG, a multispecies vertebrate ontology of homologous organs groups.

Niknejad A, Comte A, Parmentier G, Roux J, Bastian FB, Robinson-Rechavi M.

Bioinformatics. 2012 Apr 1;28(7):1017-20. doi: 10.1093/bioinformatics/bts048. Epub 2012 Jan 27.

50.

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

Boeckmann B, Robinson-Rechavi M, Xenarios I, Dessimoz C.

Brief Bioinform. 2011 Sep;12(5):423-35. doi: 10.1093/bib/bbr034. Epub 2011 Jul 7.

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