{"id":115,"date":"2017-03-21T15:49:34","date_gmt":"2017-03-21T22:49:34","guid":{"rendered":"https:\/\/genome.ucsd.edu\/?page_id=115"},"modified":"2018-03-05T11:52:27","modified_gmt":"2018-03-05T19:52:27","slug":"publications","status":"publish","type":"page","link":"https:\/\/genome.ucsd.edu\/index.php\/research\/informatics-infrastructure\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
INFORMATICS INFRASTRUCTURE<\/h5>\n

Metabolomics Workbench: An international repository for metabolomics data, metadata, metabolite standards, protocols, tutorials and training, and analysis tools.<\/b><\/span>
\nNucleic Acids Research. 2016 Jan 4; 44 (D1): D463-D470 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C, Edison A, Fiehn O, Higashi R, Nair KS, Sumner S, Subramaniam S.<\/p>\n

Drug discovery and the maze of biological complexity: an editorial essay.<\/b><\/span>
\nWiley Interdisciplinary Review Systems Biology & Medicine. 2014 May-Jun;6 (3): 225-266 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Subramaniam S.<\/p>\n

Bioinformatics and systems biology of the lipidome.<\/b><\/span>
\nChemical Reviews. 2011 Oct 12; 111 (10): 6452-6490 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR.<\/p>\n

LIPID MAPS-Nature Lipidomics Gateway: An Online Resource for Students and Educators Interested in Lipids.<\/b><\/span>
\nJournal of Chemical Education. 2012 Jan 10; 89 (2): 291-29 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Sud M, Fahy E, Cotter D, Dennis E, Subramaniam S.<\/p>\n

Template-based combinatorial enumeration of virtual compound libraries for lipids.<\/b><\/span>
\nJournal of Cheminformatics. 2012 Sep 25; 4 (1): 23\u00a0 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Sud M, Fahy E, Subramaniam S.<\/p>\n

Signaling gateway molecule pages–a data model perspective.<\/b><\/span>
\nBioinformatics. 2011 Jun 15; 27 (12): 1736-1738 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Dinasarapu AR, Saunders B, Ozerlat I, Azam K, Subramaniam S.<\/p>\n

Lipid classification, structures and tools.<\/b><\/span>
\nBiochimica et Biopysica Acta (BBA) \u2013 Molecular and Cell Biology Lipids. 2011 Nov; 1811 (11): 637-647 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Fahy E, Cotter D, Sud M, Subramaniam S.<\/p>\n

An editor for pathway drawing and data visualization in the Biopathways Workbench.<\/b><\/span>
\nBMC Systems Biology. 2009 Oct 2; 3: 99 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Byrnes RW, Cotter D, Maer A, Li J, Nadeau D, Subramaniam S.<\/p>\n

The Molecule Pages database.<\/b><\/span>
\nNucleic Acids Research. 2008 Jan; 36 (Database issue): D700-D706. PubMed<\/span><\/a><\/b><\/span><\/p>\n

Saunders B, Lyon S, Day M, Riley B, Chenette E, Vadivelu I, Subramaniam S.<\/p>\n

Bioinformatics for lipidomics.<\/b><\/span>
\nMethods in Enzymology. 2007; 432: 247-273 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Fahy E, Cotter D, Byrnes R, Sud M, Maer A, Li J, Nadeau D, Zhau Y, Subramaniam S.<\/p>\n

LIPID MAPS online tools for lipid research.<\/b><\/span>
\nNucleic Acids Research. 2007 Jul; 35(Web Server issue): W606-W612 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Fahy E, Sud M, Cotter D, Subramaniam S.<\/p>\n

Towards a workbench for rodent brain image data: systems architecture and design.<\/b><\/span>
\nNeuroinformatics. 2007 Spring; 5 (1): 35-58 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Moene IA, Subramaniam S, and Bjaalie JG.<\/p>\n

LMPD: LIPID MAPS proteome database.<\/b><\/span>
\nNucleic Acids Research. 2006 Jan 1; 34 (Database issue): D507-D510 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Cotter D, Maer A, Guda C, Saunders B, Subramaniam S.<\/p>\n

pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes.<\/b><\/span>
\nBioinformatics. 2005 Nov 1; 21 (21): 3963-3969 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Guda C, Subramaniam S.<\/p>\n

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data.<\/b><\/span>
\nNucleic Acids Res. 2005 Jul 1; 33 (Web Server issue): W627-W632 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Hsiao A, Ideker T, Olefsky JM, Subramaniam S.<\/p>\n

Reconstruction of cellular signalling networks and analysis of their properties.<\/b><\/span>
\nNature Reviews: Molecular Cell Biolology. 2005 Feb; 6 (2): 99-111 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Papin JA, Hunter T, Palsson BO, Subramaniam S.<\/p>\n

“Biology Workbenches” Databasing the Brain: From Data to Knowledge (Neuroinformatics)<\/em><\/b>
\n(Koslow S and Subramaniam S, eds.)<\/span><\/p>\n

John Wiley & Sons Inc. Hoboken NJ, 2005;\u00a0 9: 153-168 ISBN: 0-471-30921-4<\/span><\/p>\n

Maer A, Saunders B, Unwin R and Subramaniam S.<\/p>\n

SledgeHMMER: a web server for batch searching the Pfam database.<\/b><\/span>
\nNucleic Acids Research. 2004 Jul 1; 32 (Web Server issue): W542-W544 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Chukkapalli G, Guda C, Subramaniam S.<\/p>\n

MITOPRED: a web server for the prediction of mitochondrial proteins.<\/b><\/span>
\nNucleic Acids Research. 2004 Jul 1; 32 (Web Server issue): W372-W374 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Guda C, Guda P, Fahy E, Subramaniam S.<\/p>\n

MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins.<\/b><\/span>
\nBioinformatics. 2004 Jul 22;20 (11): 1785-1794. Epub 2004 Mar 22 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Guda C, Fahy E, Subramaniam S.<\/p>\n

MitoProteome: mitochondrial protein sequence database and annotation system.<\/b><\/span>
\nNucleic Acids Research. 2004 Jan 1; 32 (Database issue): D463-D467 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Cotter D, Guda P, Fahy E, Subramaniam S.<\/p>\n

The Molecule Pages Database.<\/b><\/span>
\nNature. 2002 Dec 12; 420 (6916): 716-717 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T, Subramaniam S.<\/p>\n

Overview of the Alliance for Cellular Signaling.<\/b><\/span>
\nNature. 2002 Dec 12; 420 (6916):703-706 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Gilman, AG; Simon, MI; Bourne, HR; Harris, BA; Long, R; Ross, EM; Stull, JT; Taussig, R; Bourne, HR; Arkin, AP; Cobb, MH; Cyster, JG; Devreotes, PN; Ferrell, JE; Fruman, D; Gold, M; Weiss, A; Stull, JT; Berridge, MJ; Cantley, LC; Catterall, WA; Coughlin, SR; Olson, EN; Smith, TF; Brugge, JS; Botstein, D; Dixon, JE; Hunter, T; Lefkowitz, RJ; Pawson, AJ; Sternberg, PW; Varmus, H; Subramaniam, S.et.al ; Sinkovits, RS; Li, J; Mock, D; Ning, YH; Saunders, B; Sternweis, PC; Hilgemann, D; Scheuermann, RH; DeCamp, D; Hsueh, R; Lin, KM; Ni, Y; Seaman, WE; Simpson, PC; O’Connell, TD; Roach, T; Simon, MI; Choi, S; Eversole-Cire, P; Fraser, I; Mumby, MC; Zhao, YM; Brekken, D; Shu, HJ; Meyer, T; Chandy, G; Do Heo, W; Liou, J; O’Rourke, N; Verghese, M; Mumby, SM; Han, HP; Brown, HA; Forrester, JS; Ivanova, P; Milne, SB; Casey, PJ; Harden, TK; Arkin, AP; Doyle, J; Gray, ML; Meyer, T; Michnick, S; Schmidt, MA; Toner, M; Tsien, RY; Natarajan, M; Ranganathan, R; Sambrano, GR.<\/p>\n","protected":false},"excerpt":{"rendered":"

INFORMATICS INFRASTRUCTURE Metabolomics Workbench: An international repository for metabolomics data, metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids […]<\/p>\n","protected":false},"author":10,"featured_media":0,"parent":90,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/page_fullwidth.php","meta":{"footnotes":""},"class_list":["post-115","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/115","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/comments?post=115"}],"version-history":[{"count":21,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/115\/revisions"}],"predecessor-version":[{"id":847,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/115\/revisions\/847"}],"up":[{"embeddable":true,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/90"}],"wp:attachment":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/media?parent=115"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}