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Lynx web services for annotations and systems analysis of multi-gene disorders.

Sulakhe D, Taylor A, Balasubramanian S, Feng B, Xie B, Börnigen D, Dave UJ, Foster IT, Gilliam TC, Maltsev N.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W473-7. doi: 10.1093/nar/gku517. Epub 2014 Jun 19.


Lynx: a database and knowledge extraction engine for integrative medicine.

Sulakhe D, Balasubramanian S, Xie B, Feng B, Taylor A, Wang S, Berrocal E, Dave U, Xu J, Börnigen D, Gilliam TC, Maltsev N.

Nucleic Acids Res. 2014 Jan;42(Database issue):D1007-12. doi: 10.1093/nar/gkt1166. Epub 2013 Nov 21.


The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.

Yeats C, Lees J, Carter P, Sillitoe I, Orengo C.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W546-50. doi: 10.1093/nar/gkr438. Epub 2011 Jun 6.


GeneTools--application for functional annotation and statistical hypothesis testing.

Beisvag V, Jünge FK, Bergum H, Jølsum L, Lydersen S, Günther CC, Ramampiaro H, Langaas M, Sandvik AK, Laegreid A.

BMC Bioinformatics. 2006 Oct 24;7:470.


BioPP: a tool for web-publication of biological networks.

Viswanathan GA, Nudelman G, Patil S, Sealfon SC.

BMC Bioinformatics. 2007 May 22;8:168.


CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.


Analysis Tool Web Services from the EMBL-EBI.

McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W597-600. doi: 10.1093/nar/gkt376. Epub 2013 May 13.


HPD: an online integrated human pathway database enabling systems biology studies.

Chowbina SR, Wu X, Zhang F, Li PM, Pandey R, Kasamsetty HN, Chen JY.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S5. doi: 10.1186/1471-2105-10-S11-S5.


Recent additions and improvements to the Onto-Tools.

Khatri P, Sellamuthu S, Malhotra P, Amin K, Done A, Draghici S.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W762-5.


A new web-based data mining tool for the identification of candidate genes for human genetic disorders.

van Driel MA, Cuelenaere K, Kemmeren PP, Leunissen JA, Brunner HG.

Eur J Hum Genet. 2003 Jan;11(1):57-63.


Biosphere: the interoperation of web services in microarray cluster analysis.

Cheung KH, de Knikker R, Guo Y, Zhong G, Hager J, Yip KY, Kwan AK, Li P, Cheung DW.

Appl Bioinformatics. 2004;3(4):253-6.


SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models.

Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F.

PLoS One. 2012;7(10):e48053. doi: 10.1371/journal.pone.0048053. Epub 2012 Oct 24.


The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN.

Nucleic Acids Res. 2014 Jan;42(Database issue):D966-74. doi: 10.1093/nar/gkt1026. Epub 2013 Nov 11.


FuncBase: a resource for quantitative gene function annotation.

Beaver JE, Tasan M, Gibbons FD, Tian W, Hughes TR, Roth FP.

Bioinformatics. 2010 Jul 15;26(14):1806-7. doi: 10.1093/bioinformatics/btq265. Epub 2010 May 21.


DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

Sherman BT, Huang da W, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler MW, Lane HC, Lempicki RA.

BMC Bioinformatics. 2007 Nov 2;8:426.


MicrobesFlux: a web platform for drafting metabolic models from the KEGG database.

Feng X, Xu Y, Chen Y, Tang YJ.

BMC Syst Biol. 2012 Aug 2;6:94.


An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

Yang JO, Hwang S, Oh J, Bhak J, Sohn TK.

BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S19. doi: 10.1186/1471-2105-9-S12-S19.


SWS: accessing SRS sites contents through Web Services.

Romano P, Marra D.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S15. doi: 10.1186/1471-2105-9-S2-S15.


Evolution of web services in bioinformatics.

Neerincx PB, Leunissen JA.

Brief Bioinform. 2005 Jun;6(2):178-88. Review.

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