Subramaniam Lab

Bioinformatics, Systems Biology, and Systems Medicine

• Home
• People
• Research
• Projects
• Resources
• Positions
• Publications

Publications

• 2010
|
• 2009
|
• 2008
|
• 2007
|
• 2006
|
• Previous years

2011

• Modularity detection in protein-protein interaction networks.
  Narayanan T, Gersten M, Subramaniam S, Grama A
  BMC Res Notes. 2011 Dec 29;4(1):569.
  
• Bioinformatics and systems biology of the lipidome.
  Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR
  Chem Rev. 2011 Oct 12;111(10):6452-90. Epub 2011 Sep 23
  PMID: 21939287 [PubMed - in process]
  
• Integration of lipidomics and transcriptomics data towards a system biology model of spingolipid metabolism.
  Gupta S, Maurya MR, Merrill AH Jr, Glass CK, Subramaniam
  BMC Syst Biol. 2011, Feb 8:5;26. PMID: 21303545 [PubMed - in process]
• Signaling gateway molecule pages-a data model perspective
  Dinasarapu A, Saunders B, Ozerlat I, Azam K, Subramaniam S
  Bioinformatics. 2011 Jun 15;27(12):1736-8. Epub 2011 Apr 19.
• Community detection in biological networks using a variational bayes approach.
  Narayanan T, Subramaniam S.
  Conf Proc BIcoB. 2011

2010

• Comparison of statistical and optimization-based methods for data-drive network reconstruction of biochemical systems.
  Asadi B, Tartakovsky DM, Maurya MR, Subramaniam S.
  Conf Proc IASTED CompBio 2010
  
• Regulatory network of microRNAs in RAW 264.7 macrophage cells. Conf Proc IEEE Eng Med Biol Soc. 2010;1;6198-201
  Garmire LX, Shen Z, Briggs S, Yeo G, Subramaniam S, Glass C.
  
• Multi-tissue, selective PPAR{gamma} modulation of insulin sensitivity and metabolic pathways in obese rats
  Hsiao G, Chapman J, Ofrecio JM, Wilkes J, Resnik JL, Thapar D, Subramaniam S, Sears DD
  Am J Physiol Endocrinol Metab. 2010 Oct 19. [Epub ahead of print]
• Stochastic hybrid modeling of intracellular calcium dynamics
  Choi T, Maurya MR, Tartakovsky DM, Subramaniam S.
  J Chem Phys. 2010 Oct 28;133(16):165101. PMCID: PMC2998048
• A Mouse Macrophage Lipidome
  Dennis EA, Deems RA, Harkewicz R, Quehenberger O, Brown HA, Milne SB, Myers DS, Glass CK, Hardiman GT, Reichart D, Merrill AH, Sullards MC, Wang E, Murphy RC, Raetz CR, Garrett T, Guan Z, Ryan AC, Russell DW, McDonald JG, Thompson BM, Shaw WA, Sud M, Zhao Y, Gupta S, Maurya MR, Fahy E, Subramaniam S.
  J Biol Chem. 2010 Oct 5. [Epub ahead of print]
• Lipidomics reveals a remarkable diversity of lipids in human plasma
  Quehenberger O, Armando AM, Brown AH, Milne SB, Myers DS, Merrill AH, Bandyopadhyay S, Jones KN, Kelly S, Shaner RL, Sullards CM, Wang E, Murphy RC, Barkley RM, Leiker TJ, Raetz CR, Guan Z, Laird GM, Six DA, Russell DW, McDonald JG, Subramaniam S, Fahy E, Dennis EA.
  J Lipid Res. 2010 Nov;51(11):3299-305. Epub 2010 Jul 29.
• Classification studies based on a spectral representation of DNA
  Bielińska-Waz D, Subramaniam S.
  J Theor Biol. 2010 Oct 21;266(4):667-74. Epub 2010 Aug 4.
• Systems medicine--viewed through the real and computing lenses
  Subramaniam S, Nadeau JH.
  Wiley Interdiscip Rev Syst Biol Med. 2010 Jul-Aug;2(4):383-4.
• Systems biology and medicine--metazoan life and processes
  Subramaniam S, Nadeau JH.
  Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun;2(3):253-4.
• Systems biology--old wine in a new bottle or is the bottle changing the wine?
  Nadeau JH, Subramaniam S.
  Wiley Interdiscip Rev Syst Biol Med. 2010 Jan-Feb;2(1):1-2.
• Subcellular organelle lipidomics in TLR 4-activated macrophages
  Andreyev AY, Fahy E, Guan Z, Kelly S, Li X, McDonald JG, Milne S, Myers D, Park H, Ryan A, Thompson BM, Wang E, Zhao Y, Brown HA, Merrill A, Raetz CR, Russell DW, Subramaniam S, Dennis E.
  
• Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach
  Rodríguez-Flores JL, Zhang K, Kang SW, Wen G, Ghosh S, Friese RS, Mahata SK, Subramaniam S, Hamilton BA, O'Connor DT.
  Mamm Genome. 2010 Apr;21(3-4):195-204. Epub 2010 Mar 5.
• Role of microRNA-23b in flow-regulation of Rb phosphorylation and endothelial cell growth
  Wang KC, Garmire LX, Young A, Nguyen P, Trinh A, Subramaniam S, Wang N, Shyy JY, Li YS, Chien S.
  Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3234-9. Epub 2010 Jan 27.
• Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells
  Gupta S, Maurya MR, Subramaniam S.
  PLoS Comput Biol. 2010 Jan 29;6(1):e1000654.
• Application of proteomic marker ensembles to subcellular organelle identification
  Andreyev AY, Shen Z, Guan Z, Ryan A, Fahy E, Subramaniam S, Raetz CR, Briggs S, Dennis EA.
  Mol Cell Proteomics. 2010 Feb;9(2):388-402. Epub 2009 Nov 2.

2009

• Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization
  Sears DD, Hsiao G, Hsiao A, Yu JG, Courtney CH, Ofrecio JM, Chapman J, Subramaniam S.
  Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18745-50. Epub 2009 Oct 19.
• Systems biology and medicine--plunging into the unknown
  Subramaniam S, Nadeau JH.
  Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):283-4.
• An editor for pathway drawing and data visualization in the Biopathways Workbench
  Byrnes RW, Cotter D, Maer A, Li J, Nadeau D, Subramaniam S.
  BMC Syst Biol. 2009 Oct 2;3(1):99.
• Chemoattractant signaling between tumor cells and macrophages regulates cancer cell migration, metastasis and neovascularization
  Green CE, Liu T, Montel V, Hsiao G, Lester RD, Subramaniam S, Gonias SL, Klemke RL
  PLoS One. 2009 Aug 21;4(8):e6713. PMID: 19696929; PMCID: PMC2725301.
• Diet-induced hepatocellular carcinoma in genetically predisposed mice
  Hill-Baskin AE, Markiewski MM, Buchner DA, Shao H, DeSantis D, Hsiao G, Subramaniam S, Berger NA, Croniger C, Lambris JD, Nadeau JH.
  Hum Mol Genet. 2009 Aug 15;18(16):2975-88. Epub 2009 May 19. PMID: 19454484; PMCID: PMC2714725.
• Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data
  Hsiao A, Subramaniam S.
  Syst Synth Bio. 2008 Dec;2(3-4):95-104. Epub 2009 Aug 13. PMID: 19680790; PMCID: PMC2735646.
• Novel transcriptional profile in wrist muscles from cerebral palsy patients
  Smith LR, Ponten E, Hedstrom Y, Ward SR, Chambers HG, Subramaniam S, Lieber RL.
  BMC Med Genomics. 2009 Jul 14;2:44. PubMed PMID: 19602279; PubMed Central PMCID: PMC2722667.
• Systems biology and medicine: a new take on an old paradigm
  Nadeau JH, Subramaniam S.
  Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug;1(1):1-3.
• An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis
  Gupta S, Maurya MR, Stephens DL, Dennis EA, Subramaniam S.
  Biophys J. 2009 Jun 3;96(11):4542-51. PubMed PMID: 19486676; PubMed Central PMCID: PMC2711499.
• CellML metadata standards, associated tools and repositories
  Beard DA, Britten R, Cooling MT, Garny A, Halstead MD, Hunter PJ, Lawson J, Lloyd CM, Marsh J, Miller A, Nickerson DP, Nielsen PM, Nomura T, Subramaniam S, Wimalaratne SM, Yu T.
  Philos Transact A Math Phys Eng Sci. 2009 May 28;367(1895):1845-67.
• Update of the LIPID MAPS comprehensive classification system for lipids
  Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR, Shimizu T, Spener F, van Meer G, Wakelam MG, Dennis EA.
  J Lipid Res. 2009 Apr;50 Suppl:S9-14. Epub 2008 Dec 19. Review. PubMed PMID: 19098281; PubMed Central PMCID: PMC2674711.
• Mixed-integer nonlinear optimization approach to coarse-graining biochemical networks.
  Maurya MR, Bornheimer SJ, Venkatasubramaniam V, Subramaniam S.
  IET Syst Biol. 2009 Jan;3(1):24-39. PubMed PMID: 19154082; PubMed Central PMCID: PMC2749294.

2008

• Functional coherence in domain interaction networks.
  Pandey J, Koyuturk M, Subramaniam S, Grama A.
  Bioinformatics. 2008 Aug 15;24(16):i28-34. PubMed PMID:18689835.
• The Molecule Pages database.
  Saunders B, Lyon S, Day M, Riley B, Chenette E, Vadivelu I., Subramaniam S.
  Nucleic Acids Res.2008 Jan;36(Database issue):D700-6. Epub 2007 Oct 26. Erratum in: Nucleic Acids Res. 2008 Apr;36(7):2457. PubMed PMID: 17965093; PubMed Central PMCID: PMC2238911.

2007

• Toward a workbench for rodent brain image data: systems architecture and design
  Moene IA, Subramaniam S, Darin D, Leergaard TB, Bjaalie JG.
  Neuroinformatics. 2007 Winter;5(1):35-58.
• A Kinetic Model for Calcium Dynamics in RAW 264.7 Cells: 1. Mechanisms, Parameters, and Subpopulational Variability.
  Maurya MR and Subramaniam S.
  Biophys J. 2007 Aug 1;93(3):709-28.
• A kinetic model for calcium dynamics in RAW 264.7 Cells: 2. Knockdown response and long-term response.
  Maurya MR and Subramaniam S.
  Biophys J. 2007 Aug 1;93(3):729-40.
• Functional annotation of regulatory pathways.
  Pandey J, Koyuturk M, Kim Y, Szpankowski W, Subramaniam S, Grama A.
  Bioinformatics 2007 Jul 1;23(13):i377-86.
• LIPID MAPS online tools for lipid research
  Fahy E, Sud M, Cotter D and Subramaniam S.
  Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W606-12
• Macrophage PPAR gamma is required for normal skeletal muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones
  Hevener AL, Olefsky JM, Reichart D, Nguyen MT, Bandyopadyhay G, Leung HY, Watt MJ, Benner C, Febbraio MA, Nguyen AK, Folian B, Subramaniam S, Gonzalez FJ, Glass CK, Ricote M.
  J Clin Invest 2007 Jun;117(6):1658-69.
• A Laboratory Information Management System for High Throughput Experimental Lipidomics: Minimum Information required for the Analysis of Lipidomics Experiments (MIALE)
  Byrnes RW, Fahy E and Subramaniam S.
  JALA 2007 Aug ;12(4)230-236.
• Mitoproteome: human heart mitochondrial protein sequence database.
  Guda P, Guda C and Subramaniam S.
  Methods Mol Biol. 2007;357:375-83.
• Reconstruction of pathways associated with aminoacid metabolism in human mitochondria.
  Guda P, Guda C and Subramaniam S.
  Submitted to Metabolic Engineering. January 2007
• The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis.
  Zavzavadjian JR, Couture S, Sun Park W, Whalen J, Lyon S, Lee G, Fung E, Mi Q, Liu J, Wall E, Santat L, Dhandapani K, Kivork C, Driver A, Zhu X, Sook Chang M, Randhawa B, Gehrig E, Bryan H, Verghese M, Maer A, Saunders B, Ning Y, Subramaniam S, Meyer T, Simon MI, O'rourke N, Chandy G, Fraser ID.
  Mol Cell Proteomics 2007.
• LMSD: LIPID MAPS structure database
  Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Jr., Murphy RC, Raetz CR, Russell DW and Subramaniam S.
  Nucleic Acids Res 2007;35(Database issue):D527-32.
• Detecting conserved interaction patterns in biological networks.
  Koyuturk M, Kim Y, Subramaniam S, Szpankowski W, Grama A.
  J Comput Biol. 2006 Sep;13(7):1299-322.
• A novel role for connexin hemichannel in oxidative stress and smoking-induced apoptosis.
  Ramachandran S, Xie L-H, John SA, Subramaniam S and Lal R.
  PLoS ONE 2007 Aug 8;2:e712

2006

• Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.
  Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH; Alliance for Cellular Signaling.
  BMC Bioinformatics. 2006 May 2;7:237
• Pairwise alignment of protein interaction networks.
  Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A.
  J Comput Biol. 2006 Mar;13(2):182-99.
• Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships.
  Kim Y and Subramaniam S.
  Proteins. 2006 Mar 1;62(4):1115-24.
• Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages. 
  Pradervand S, Maurya MR and Subramaniam S.
  Genome Biology 2006 Feb 20;7(2):R11.
• Purification and properties of Escherichia coli Kd02-lipid A, a defined endotoxin that activates macrophages via TLR-4. J Lipid Res.
  Raetz CR, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC Jr, Ribeiro AA, Murphy RC, Ulevitch RJ, Fearns C, Reichart D, Glass CK, Benner C, Subramaniam S, Harkewicz R, Bowers-Gentry RC, Buczynski MW, Cooper JA, Deems RA, Dennis EA.
  2006 May;47(5):1097-111. Epub 2006 Feb 14.
• LMPD: LIPID MAPS Proteome Database.
  Cotter D, Maer AM, Guda C, Saunders B and Subramaniam S.
  Nucleic Acids Res. 2006 Jan 1;34(Database issue):D507-10.
• Inferring functional information from domain co-evolution.
  Kim Y, Koyuturk M, Topkara U, Grama A and Subramaniam S.
  Bioinformatics 2006 Jan 1;22(1):40-9

Previous years (selected)

• Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module
  Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S.
  Syst Biol (Stevenage). 2005 Dec;152(4):229-42.
• Molecular determinants of crosstalk between nuclear receptors and toll-like receptors
  Ogawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK.
  Cell. 2005 Sep 9;122(5):707-21.
• VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data
  Hsiao A, Ideker T, Olefsky JM, Subramaniam S.
  Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W627-32.
• A comprehensive classification system for lipids
  Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH Jr, Murphy RC, Raetz CR, Russell DW, Seyama Y, Shaw W, Shimizu T, Spener F, van Meer G, VanNieuwenhze MS, White SH, Witztum JL, Dennis EA.
  J Lipid Res. 2005 May;46(5):839-61. Epub 2005 Feb 16.
• Reconstruction of cellular signalling networks and analysis of their properties
  Papin JA, Hunter T, Palsson BO, Subramaniam S.
  Nat Rev Mol Cell Biol. 2005 Feb;6(2):99-111.
• Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands
  Zhu X, Hart R, Chang MS, Kim JW, Lee SY, Cao YA, Mock D, Ke E, Saunders B, Alexander A, Grossoehme J, Lin KM, Yan Z, Hsueh R, Lee J, Scheuermann RH, Fruman DA, Seaman W, Subramaniam S, Sternweis P, Simon MI, Choi S.
  J Immunol. 2004 Dec 15;173(12):7141-9.
• Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes
  Hsiao A, Worrall DS, Olefsky JM, Subramaniam S.
  Bioinformatics. 2004 Nov 22;20(17):3108-27. Epub 2004 Jun 24.
• Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction
  Bornheimer SJ, Maurya MR, Farquhar MG, Subramaniam S.
  Proc Natl Acad Sci U S A. 2004 Nov 9;101(45):15899-904. Epub 2004 Nov 1.
• MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins
  Guda C, Fahy E, Subramaniam S.
  Bioinformatics. 2004 Jul 22;20(11):1785-94. Epub 2004 Mar 22.
• SledgeHMMER: a web server for batch searching the Pfam database
  Chukkapalli G, Guda C, Subramaniam S.
  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W542-4.
• MITOPRED: a web server for the prediction of mitochondrial proteins
  Guda C, Guda P, Fahy E, Subramaniam S.
  Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W372-4.
• Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis
  Avidor-Reiss T, Maer AM, Koundakjian E, Polyanovsky A, Keil T, Subramaniam S, Zuker CS
  Cell. 2004 May 14;117(4):527-39
• Conserved sequence and structure association motifs in antibody-protein and antibody-hapten complexes
  Livesay DR, Subramaniam S.
  Protein Eng Des Sel. 2004 May;17(5):463-72. Epub 2004 Aug 13.
• Bioinformatics and cellular signaling
  Papin J, Subramaniam S.
  Curr Opin Biotechnol. 2004 Feb;15(1):78-81.
• Bioinformatics and computational systems biology: at the cross roads of biology, engineering and computation
  Subramaniam S.
  Conf Proc IEEE Eng Med Biol Soc. 2004;7:5458.
• MitoProteome: mitochondrial protein sequence database and annotation system
  Cotter D, Guda P, Fahy E, Subramaniam S.
  Nucleic Acids Res. 2004 Jan 1;32(Database issue):D463-7.

©University of California, San Diego