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Pearson WR, Li W, Lopez R. Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Nucleic Acids Res. 2016 Dec . PMID: 27923999.Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R. The EMBL-EBI bioinformatics web and programmatic tools framework. Nucleic Acids Res. 2015 Jul;43(W1) W580-4. PMID: 25845596Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7 539. PMID: 21988835UniProt Consortium. UniProt: a hub for protein information. Nucleic Acids Res. 2015 Jan;43(Database issue) D204-12. PMID: 25348405Li W, McWilliam H, de la Torre AR, Grodowski A, Benediktovich I, Goujon M, Nauche S, Lopez R. Non-redundant patent sequence databases with value-added annotations at two levels. Nucleic Acids Res. 2010 Jan;38(Database issue) D52-6. PMID: 19884134 Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR. PSI-Search: iterative HOE-reduced profile SSEARCH searching. Bioinformatics. 2012 Jun;28(12) 1650-1651. PMID: 22539666 Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 2010 Jul;38(Web Server issue) W695-9. PMID: 20439314 McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R. Analysis Tool Web Services from the EMBL-EBI. Nucleic Acids Res. 2013 Jul;41(Web Server issue) W597-600. PMID: 23671338Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S. InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014 May;30(9) 1236-1240. PMID: 24451626Li W, Gracey AY, Mello LV, Brass A, Cossins AR. ExprAlign--the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles. BMC Genomics. 2009;10 560. PMID: 19939286Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R. The annotation-enriched non-redundant patent sequence databases. Database (Oxford). 2013;2013 bat005. PMID: 23396323Silvester N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Ten Hoopen P, Kay S, Leinonen R, Li W, Liu X, Lopez R, Pakseresht N, Pallreddy S, Plaister S, Radhakrishnan R, Rossello M, Senf A, Smirnov D, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Content discovery and retrieval services at the European Nucleotide Archive. Nucleic Acids Res. 2015 Jan;43(Database issue) D23-9. PMID: 25404130Squizzato S, Park YM, Buso N, Gur T, Cowley A, Li W, Uludag M, Pundir S, Cham JA, McWilliam H, Lopez R. The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI. Nucleic Acids Res. 2015 Jul;43(W1) W585-8. PMID: 25855807Pakseresht N, Alako B, Amid C, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Gur T, Jang M, Kay S, Leinonen R, Li W, Liu X, Lopez R, McWilliam H, Oisel A, Pallreddy S, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Squizzato S, ten Hoopen P, Toribio AL, Vaughan D, Zalunin V, Cochrane G. Assembly information services in the European Nucleotide Archive. Nucleic Acids Res. 2014 Jan;42(Database issue) D38-43. PMID: 24214989McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R. Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res. 2009 Jul;37(Web Server issue) W6-10. PMID: 19435877Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass A, Cossins AR. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci U S A. 2004 Nov;101(48) 16970-16975. PMID: 15550548Williams DR, Epperson LE, Li W, Hughes MA, Taylor R, Rogers J, Martin SL, Cossins AR, Gracey AY. Seasonally hibernating phenotype assessed through transcript screening. Physiol Genomics. 2005 Dec;24(1) 13-22. PMID: 16249311Gonzalez SF, Chatziandreou N, Nielsen ME, Li W, Rogers J, Taylor R, Santos Y, Cossins A. Cutaneous immune responses in the common carp detected using transcript analysis. Mol Immunol. 2007 Mar;44(7) 1664-1679. PMID: 17049603.
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