{"id":90,"date":"2017-03-16T15:18:38","date_gmt":"2017-03-16T22:18:38","guid":{"rendered":"https:\/\/genome.ucsd.edu\/?page_id=90"},"modified":"2026-08-12T12:18:21","modified_gmt":"2026-08-12T19:18:21","slug":"informatics-infrastructure","status":"publish","type":"page","link":"https:\/\/genome.ucsd.edu\/index.php\/research\/informatics-infrastructure\/","title":{"rendered":"Informatics Infrastructure"},"content":{"rendered":"

The importance of curated informatics resources: data and tools – the gateway to knowledge in biology<\/span><\/h4>\n

One of the major challenges in modern systems biology is the integration of diverse high and low throughput measurements on biological systems and deciphering biological mechanisms and pathways. My laboratory has been engaged in multi-omics multi-scale data integration for over a decade. For nearly a decade, we worked on integrating diverse data from measurements on macrophages and the progress in this area is reported across several publications. First, we used time series measurements of phosphoproteins in ligand treated macrophages along with time series cytokine readouts to understand the cellular signaling processes associated with macrophage cells.\u00a0<\/span><\/span><\/p>\n

Transcripts form one of several components, albeit an important one, in a cell. My laboratory had engaged for a few years already in characterizing a few other components, microRNA, lincRNA and phosphoproteins using existing methods. In addition, we participated in a large glue grant effort on lipidomics, which witnessed the development of the state of the art mass spectrometric methods for quantitative measurements of lipid analytes. I was the Director of the Bioinformatics and Systems Biology Cores of this grant and we had a ten-year investigation which led to arguably the best lipid resource in the world, \u201cthe Lipidomics Gateway\u201d (<\/span><\/span>http:\/\/www.lipidmaps.org<\/span><\/span><\/a>). Our efforts in this project resulted in numerous peer-reviewed publications. <\/span><\/span><\/p>\n

Prior to this latest review period we had built a large number of resources (used widely by the scientific community) including the Biology Workbench, the Signaling Gateway (originally, a collaboration with Nature), the Functional Genomics Workbench (based on novel algorithms for gene expression analysis, functional annotation and pathway building), and a number of boutique data resources. Our theme in building networks from data involves identifying pathway modules either dictated by comparative and evolutionary biology consideration or derived by applying various statistical learning strategies augmented by applying biological constraints. We have built numerous methodologies over the past 10 years towards this end. Recently, we have developed algorithms to use various graph theory methods to identify modules as well as reduce complex graphical networks into unique assembly of modules. Visualization and interactive analysis of pathways is a complex problem and we have now built and released a novel pathway editing tool that combines most recent computer science methods along with innovative biological tools.<\/span><\/span><\/p>\n

I was recently awarded a $6 million grant from NIH Common Funds to establish the national metabolomics resource. My laboratory will coordinate activities of 6 other resource centers and numerous individual investigator awards. (<\/span><\/span>http:\/\/www.metabolomicsworkbench.org<\/span><\/span><\/a>)<\/span><\/span><\/p>\n\n\n

RELATED PUBLICATIONS<\/strong><\/summary>\n

<\/p>\n\n\n\n

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

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

Subramaniam S.<\/em><\/p>\n\n\n\n

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

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

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

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

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

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

Signaling gateway molecule pages\u2013a data model perspective.<\/strong>
Bioinformatics. 2011 Jun 15; 27 (12): 1736-1738 PubMed<\/a><\/strong><\/p>\n\n\n\n

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

\u201cBiology Workbenches\u201d Databasing the Brain: From Data to Knowledge (Neuroinformatics)<\/em><\/strong>
(Koslow S and Subramaniam S, eds.)<\/p>\n\n\n\n

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

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

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

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

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

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

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

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

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

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

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

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

Overview of the Alliance for Cellular Signaling.<\/strong>
Nature. 2002 Dec 12; 420 (6916):703-706 PubMed<\/a><\/strong><\/p>\n\n\n\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\u2019Connell, 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\u2019Rourke, 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.<\/em><\/p>\n<\/details>\n\n\n\n

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