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Results: 1 to 20 of 73

1.

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; the Quest for Orthologs consortium.

Bioinformatics. 2014 Jul 26. pii: btu492. [Epub ahead of print]

PMID:
25064571
[PubMed - as supplied by publisher]
Free Article
2.

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.

PMID:
25009735
[PubMed]
Free PMC Article
3.

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. 2014 May 7. doi: 10.1111/1462-2920.12498. [Epub ahead of print]

PMID:
24803113
[PubMed - as supplied by publisher]
4.

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.

PMID:
24782441
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
24451627
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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 Jan 23. [Epub ahead of print]

PMID:
24389654
[PubMed - as supplied by publisher]
Free PMC Article
7.

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.

PMID:
24319113
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
24225318
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23637639
[PubMed - in process]
Free PMC Article
10.

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
[PubMed - indexed for MEDLINE]
Free Article
11.

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.

PMID:
23558341
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23487185
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23407308
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
23110974
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
22615551
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
22576178
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
22458817
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
22457063
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
22373648
[PubMed - indexed for MEDLINE]
Free PMC Article

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