INFORMATICS INFRASTRUCTURE
Metabolomics Workbench: An international repository for metabolomics data, metadata, metabolite standards, protocols, tutorials and training, and analysis tools.
Nucleic Acids Research. 2016 Jan 4; 44 (D1): D463-D470 PubMed
Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C, Edison A, Fiehn O, Higashi R, Nair KS, Sumner S, Subramaniam S.
Drug discovery and the maze of biological complexity: an editorial essay.
Wiley Interdisciplinary Review Systems Biology & Medicine. 2014 May-Jun;6 (3): 225-266 PubMed
Subramaniam S.
Bioinformatics and systems biology of the lipidome.
Chemical Reviews. 2011 Oct 12; 111 (10): 6452-6490 PubMed
Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR.
LIPID MAPS-Nature Lipidomics Gateway: An Online Resource for Students and Educators Interested in Lipids.
Journal of Chemical Education. 2012 Jan 10; 89 (2): 291-29 PubMed
Sud M, Fahy E, Cotter D, Dennis E, Subramaniam S.
Template-based combinatorial enumeration of virtual compound libraries for lipids.
Journal of Cheminformatics. 2012 Sep 25; 4 (1): 23 PubMed
Sud M, Fahy E, Subramaniam S.
Signaling gateway molecule pages–a data model perspective.
Bioinformatics. 2011 Jun 15; 27 (12): 1736-1738 PubMed
Dinasarapu AR, Saunders B, Ozerlat I, Azam K, Subramaniam S.
Lipid classification, structures and tools.
Biochimica et Biopysica Acta (BBA) – Molecular and Cell Biology Lipids. 2011 Nov; 1811 (11): 637-647 PubMed
Fahy E, Cotter D, Sud M, Subramaniam S.
An editor for pathway drawing and data visualization in the Biopathways Workbench.
BMC Systems Biology. 2009 Oct 2; 3: 99 PubMed
Byrnes RW, Cotter D, Maer A, Li J, Nadeau D, Subramaniam S.
The Molecule Pages database.
Nucleic Acids Research. 2008 Jan; 36 (Database issue): D700-D706. PubMed
Saunders B, Lyon S, Day M, Riley B, Chenette E, Vadivelu I, Subramaniam S.
Bioinformatics for lipidomics.
Methods in Enzymology. 2007; 432: 247-273 PubMed
Fahy E, Cotter D, Byrnes R, Sud M, Maer A, Li J, Nadeau D, Zhau Y, Subramaniam S.
LIPID MAPS online tools for lipid research.
Nucleic Acids Research. 2007 Jul; 35(Web Server issue): W606-W612 PubMed
Fahy E, Sud M, Cotter D, Subramaniam S.
Towards a workbench for rodent brain image data: systems architecture and design.
Neuroinformatics. 2007 Spring; 5 (1): 35-58 PubMed
Moene IA, Subramaniam S, and Bjaalie JG.
LMPD: LIPID MAPS proteome database.
Nucleic Acids Research. 2006 Jan 1; 34 (Database issue): D507-D510 PubMed
Cotter D, Maer A, Guda C, Saunders B, Subramaniam S.
pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes.
Bioinformatics. 2005 Nov 1; 21 (21): 3963-3969 PubMed
Guda C, Subramaniam S.
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data.
Nucleic Acids Res. 2005 Jul 1; 33 (Web Server issue): W627-W632 PubMed
Hsiao A, Ideker T, Olefsky JM, Subramaniam S.
Reconstruction of cellular signalling networks and analysis of their properties.
Nature Reviews: Molecular Cell Biolology. 2005 Feb; 6 (2): 99-111 PubMed
Papin JA, Hunter T, Palsson BO, Subramaniam S.
“Biology Workbenches” Databasing the Brain: From Data to Knowledge (Neuroinformatics)
(Koslow S and Subramaniam S, eds.)
John Wiley & Sons Inc. Hoboken NJ, 2005; 9: 153-168 ISBN: 0-471-30921-4
Maer A, Saunders B, Unwin R and Subramaniam S.
SledgeHMMER: a web server for batch searching the Pfam database.
Nucleic Acids Research. 2004 Jul 1; 32 (Web Server issue): W542-W544 PubMed
Chukkapalli G, Guda C, Subramaniam S.
MITOPRED: a web server for the prediction of mitochondrial proteins.
Nucleic Acids Research. 2004 Jul 1; 32 (Web Server issue): W372-W374 PubMed
Guda C, Guda P, Fahy E, Subramaniam S.
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins.
Bioinformatics. 2004 Jul 22;20 (11): 1785-1794. Epub 2004 Mar 22 PubMed
Guda C, Fahy E, Subramaniam S.
MitoProteome: mitochondrial protein sequence database and annotation system.
Nucleic Acids Research. 2004 Jan 1; 32 (Database issue): D463-D467 PubMed
Cotter D, Guda P, Fahy E, Subramaniam S.
The Molecule Pages Database.
Nature. 2002 Dec 12; 420 (6916): 716-717 PubMed
Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T, Subramaniam S.
Overview of the Alliance for Cellular Signaling.
Nature. 2002 Dec 12; 420 (6916):703-706 PubMed
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.