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    Shankar Subramaniam

    TitleProfessor
    SchoolUniversity of California, San Diego
    DepartmentComputer Science and Engineering
    Address9500 Gilman Drive #0412
    CA La Jolla 92093
    Phone858-822-0986
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      Collapse Research 
      Collapse Research Activities and Funding
      Mapping Disease Pathways for Biliary Atresia
      NIH/NIDDK R01DK109365Apr 1, 2017 - Mar 31, 2021
      Role: Co-Principal Investigator
      The Organizational Hub and Web Portal for the 4D Nucleome Network
      NIH/NCI U01CA200147Sep 1, 2015 - Aug 31, 2020
      Role: Principal Investigator
      The Metabolomics Data Center and Workbench (MDCW)
      NIH/NIDDK U01DK097430Sep 6, 2012 - Aug 31, 2017
      Role: Principal Investigator
      Systems Biology Analyses for Hemodynamic Regulation of Vascular Homeostasis
      NIH/NHLBI R01HL108735Aug 24, 2012 - Jun 30, 2021
      Role: Principal Investigator
      Shear Regulation of MicroRNA Transportomes and Targetomes in Vascular Homeostasis
      NIH/NHLBI R01HL106579Jan 1, 2011 - Nov 30, 2018
      Role: Principal Investigator
      System Biological Analyses of Innate and Adaptive Responses to Vaccination
      NIH U19AI090023Jul 12, 2010 - Jun 30, 2020
      Role: Co-Investigator
      Reconstruction and Modeling of Networks Involved in Cardiomyoctye Differentiation
      NIH/NHLBI R33HL087375Aug 1, 2007 - Jul 31, 2011
      Role: Principal Investigator
      Signaling Gateway
      NIH/NIGMS R01GM078005Sep 30, 2006 - Aug 31, 2013
      Role: Principal Investigator
      Center of Nanotechnology for Treatment, Understanding, *
      NIH/NCI U54CA119335Sep 30, 2005 - Dec 31, 2011
      Role: Co-Investigator
      LIPID MAPS
      NIH/NIGMS U54GM069338Aug 12, 2003 - Jul 31, 2014
      Role: Co-Investigator
      Graduate Training Program in Bioinformatics
      NIH/NIGMS T32GM008806Jul 1, 2001 - Jun 30, 2021
      Role: Principal Investigator
      JOINT CENTER FOR STRUCTURAL GENOMICS
      NIH P50GM062411Sep 30, 2000 - Aug 31, 2006
      Role: Co-Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Li Z, Martin M, Zhang J, Huang HY, Bai L, Zhang J, Kang J, He M, Li J, Maurya MR, Gupta S, Zhou G, Sangwung P, Xu YJ, Lei T, Huang HD, Jain M, Jain MK, Subramaniam S, Shyy JY. KLF4 Regulation of Ch25h and LXR Mitigates Atherosclerosis Susceptibility. Circulation. 2017 Aug 09. PMID: 28794002.
        View in: PubMed
      2. Huang TS, Wang KC, Quon S, Nguyen P, Chang TY, Chen Z, Li YS, Subramaniam S, Shyy J, Chien S. LINC00341 exerts an anti-inflammatory effect on endothelial cells by repressing VCAM1. Physiol Genomics. 2017 Jul 01; 49(7):339-345. PMID: 28500253.
        View in: PubMed
      3. Li S, Sullivan NL, Rouphael N, Yu T, Banton S, Maddur MS, McCausland M, Chiu C, Canniff J, Dubey S, Liu K, Tran V, Hagan T, Duraisingham S, Wieland A, Mehta AK, Whitaker JA, Subramaniam S, Jones DP, Sette A, Vora K, Weinberg A, Mulligan MJ, Nakaya HI, Levin M, Ahmed R, Pulendran B. Metabolic Phenotypes of Response to Vaccination in Humans. Cell. 2017 May 18; 169(5):862-877.e17. PMID: 28502771.
        View in: PubMed
      4. Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H. Discovering and linking public omics data sets using the Omics Discovery Index. Nat Biotechnol. 2017 May 09; 35(5):406-409. PMID: 28486464.
        View in: PubMed
      5. Chen Z, Li S, Subramaniam S, Shyy JY, Chien S. Epigenetic Regulation: A New Frontier for Biomedical Engineers. Annu Rev Biomed Eng. 2017 Jun 21; 19:195-219. PMID: 28301736.
        View in: PubMed
      6. Marin TL, Gongol B, Zhang F, Martin M, Johnson DA, Xiao H, Wang Y, Subramaniam S, Chien S, Shyy JY. AMPK promotes mitochondrial biogenesis and function by phosphorylating the epigenetic factors DNMT1, RBBP7, and HAT1. Sci Signal. 2017 Jan 31; 10(464). PMID: 28143904.
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      7. Ranganathan S, Ningappa M, Ashokkumar C, Higgs BW, Min J, Sun Q, Schmitt L, Subramaniam S, Hakonarson H, Sindhi R. Loss of EGFR-ASAP1 signaling in metastatic and unresectable hepatoblastoma. Sci Rep. 2016 Dec 02; 6:38347. PMID: 27910913.
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      8. Chapman MA, Mukund K, Subramaniam S, Brenner D, Lieber RL. Three Distinct Cell Populations Express Extracellular Matrix Proteins and Increase in Number During Skeletal Muscle Fibrosis. Am J Physiol Cell Physiol. 2016 Nov 23; ajpcell.00226.2016. PMID: 27881411.
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      9. Duran A, Hernandez ED, Reina-Campos M, Castilla EA, Subramaniam S, Raghunandan S, Roberts LR, Kisseleva T, Karin M, Diaz-Meco MT, Moscat J. p62/SQSTM1 by Binding to Vitamin D Receptor Inhibits Hepatic Stellate Cell Activity, Fibrosis, and Liver Cancer. Cancer Cell. 2016 Oct 10; 30(4):595-609. PMID: 27728806.
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      10. Min JS, DeAngelis RA, Reis ES, Gupta S, Maurya MR, Evans C, Das A, Burant C, Lambris JD, Subramaniam S. Systems Analysis of the Complement-Induced Priming Phase of Liver Regeneration. J Immunol. 2016 Sep 15; 197(6):2500-8. PMID: 27511733.
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      11. Umemura A, He F, Taniguchi K, Nakagawa H, Yamachika S, Font-Burgada J, Zhong Z, Subramaniam S, Raghunandan S, Duran A, Linares JF, Reina-Campos M, Umemura S, Valasek MA, Seki E, Yamaguchi K, Koike K, Itoh Y, Diaz-Meco MT, Moscat J, Karin M. p62, Upregulated during Preneoplasia, Induces Hepatocellular Carcinogenesis by Maintaining Survival of Stressed HCC-Initiating Cells. Cancer Cell. 2016 Jun 13; 29(6):935-48. PMID: 27211490.
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      12. Gupta S, Kihara Y, Maurya MR, Norris PC, Dennis EA, Subramaniam S. Computational Modeling of Competitive Metabolism between ?3- and ?6-Polyunsaturated Fatty Acids in Inflammatory Macrophages. J Phys Chem B. 2016 Aug 25; 120(33):8346-53. PMID: 27063350.
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      13. Mohammadi S, Saberidokht B, Subramaniam S, Grama A. Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. BMC Syst Biol. 2015; 9(1):96. PMID: 26714768.
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      14. Sud M, Fahy E, Cotter D, Azam K, Vadivelu I, Burant C, Edison A, Fiehn O, Higashi R, Nair KS, Sumner S, Subramaniam S. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res. 2016 Jan 4; 44(D1):D463-70. PMID: 26467476.
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      15. Ningappa M, So J, Glessner J, Ashokkumar C, Ranganathan S, Min J, Higgs BW, Sun Q, Haberman K, Schmitt L, Vilarinho S, Mistry PK, Vockley G, Dhawan A, Gittes GK, Hakonarson H, Jaffe R, Subramaniam S, Shin D, Sindhi R. The Role of ARF6 in Biliary Atresia. PLoS One. 2015; 10(9):e0138381. PMID: 26379158.
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      16. Zarrinpar A, Gupta S, Maurya MR, Subramaniam S, Loomba R. Serum microRNAs explain discordance of non-alcoholic fatty liver disease in monozygotic and dizygotic twins: a prospective study. Gut. 2016 Sep; 65(9):1546-54. PMID: 26002934.
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      17. Mukund K, Subramaniam S. Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis. BMC Res Notes. 2015; 8(1):182. PMID: 25935398.
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      18. Hagan T, Nakaya HI, Subramaniam S, Pulendran B. Systems vaccinology: Enabling rational vaccine design with systems biological approaches. Vaccine. 2015 Sep 29; 33(40):5294-301. PMID: 25858860.
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      19. Marin TL, Gongol B, Martin M, King SJ, Smith L, Johnson DA, Subramaniam S, Chien S, Shyy JY. Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome. BMC Syst Biol. 2015; 9(1):13. PMID: 25890336.
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      20. Gorden DL, Myers DS, Ivanova PT, Fahy E, Maurya MR, Gupta S, Min J, Spann NJ, McDonald JG, Kelly SL, Duan J, Sullards MC, Leiker TJ, Barkley RM, Quehenberger O, Armando AM, Milne SB, Mathews TP, Armstrong MD, Li C, Melvin WV, Clements RH, Washington MK, Mendonsa AM, Witztum JL, Guan Z, Glass CK, Murphy RC, Dennis EA, Merrill AH, Russell DW, Subramaniam S, Brown HA. Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. J Lipid Res. 2015 Mar; 56(3):722-36. PMID: 25598080.
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      21. Tsai AG, Vázquez BY, Cabrales P, Kistler EB, Tartakovsky DM, Subramaniam S, Acharya SA, Intaglietta M. Replacing the Transfusion of 1-2 Units of Blood with Plasma Expanders that Increase Oxygen Delivery Capacity: Evidence from Experimental Studies. J Funct Biomater. 2014; 5(4):232-45. PMID: 25350267.
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      22. Gersten M, Zhou D, Azad P, Haddad GG, Subramaniam S. Wnt Pathway Activation Increases Hypoxia Tolerance during Development. PLoS One. 2014; 9(8):e103292. PMID: 25093834.
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      23. Farhangmehr F, Maurya MR, Tartakovsky DM, Subramaniam S. Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages. BMC Syst Biol. 2014; 8(1):77. PMID: 24964861.
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      24. Wang KC, Nguyen P, Weiss A, Yeh YT, Chien HS, Lee A, Teng D, Subramaniam S, Li YS, Chien S. MicroRNA-23b Regulates Cyclin-Dependent Kinase-Activating Kinase Complex Through Cyclin H Repression to Modulate Endothelial Transcription and Growth Under Flow. Arterioscler Thromb Vasc Biol. 2014 Jul; 34(7):1437-45. PMID: 24855060.
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      25. Salazar Vázquez BY, Salazar Vázquez MA, Chávez-Negrete A, Escobedo G, Cabrales P, Subramaniam S, Intaglietta M, Pérez-Tamayo R. Influence of serological factors and BMI on the blood pressure/hematocrit association in healthy young men and women. Vasc Health Risk Manag. 2014; 10:271-7. PMID: 24851053.
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      26. Subramaniam S. Drug discovery and the maze of biological complexity: an editorial essay. Wiley Interdiscip Rev Syst Biol Med. 2014 May; 6(3):225-6. PMID: 24648390.
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      27. Mukund K, Mathewson M, Minamoto V, Ward SR, Subramaniam S, Lieber RL. Systems analysis of transcriptional data provides insights into muscle's biological response to botulinum toxin. Muscle Nerve. 2014 Nov; 50(5):744-58. PMID: 24536034.
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      28. Kihara Y, Gupta S, Maurya MR, Armando A, Shah I, Quehenberger O, Glass CK, Dennis EA, Subramaniam S. Modeling of Eicosanoid Fluxes Reveals Functional Coupling between Cyclooxygenases and Terminal Synthases. Biophys J. 2014 Feb 18; 106(4):966-75. PMID: 24559999.
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      29. Masnadi-Shirazi M, Maurya MR, Subramaniam S. Time-varying causal inference from phosphoproteomic measurements in macrophage cells. IEEE Trans Biomed Circuits Syst. 2014 Feb; 8(1):74-86. PMID: 24681921.
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      30. Narayanan T, Subramaniam S. A newtonian framework for community detection in undirected biological networks. IEEE Trans Biomed Circuits Syst. 2014 Feb; 8(1):65-73. PMID: 24681920.
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      31. Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. Technical Variations in Low-Input RNA-seq Methodologies. Sci Rep. 2014; 4:3678. PMID: 24419370.
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      32. Shibata N, Carlin AF, Spann NJ, Saijo K, Morello CS, McDonald JG, Romanoski CE, Maurya MR, Kaikkonen MU, Lam MT, Crotti A, Reichart D, Fox JN, Quehenberger O, Raetz CR, Sullards MC, Murphy RC, Merrill AH, Brown HA, Dennis EA, Fahy E, Subramaniam S, Cavener DR, Spector DH, Russell DW, Glass CK. 25-hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages. J Biol Chem. 2013 Dec 13; 288(50):35812-23. PMID: 24189069.
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      33. Mohammadi S, Subramaniam S, Grama A. Inferring the effective TOR-dependent network: a computational study in yeast. BMC Syst Biol. 2013; 7:84. PMID: 24005029.
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      34. Lemons D, Maurya MR, Subramaniam S, Mercola M. Developing microRNA screening as a functional genomics tool for disease research. Front Physiol. 2013; 4:223. PMID: 23986717.
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      35. Dinasarapu AR, Gupta S, Ram Maurya M, Fahy E, Min J, Sud M, Gersten MJ, Glass CK, Subramaniam S. A combined omics study on activated macrophages--enhanced role of STATs in apoptosis, immunity and lipid metabolism. Bioinformatics. 2013 Nov 1; 29(21):2735-43. PMID: 23981351.
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      36. Narayanan T, Subramaniam S. Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy. PLoS One. 2013; 8(6):e67237. PMID: 23840633.
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      37. Maurya MR, Gupta S, Li X, Fahy E, Dinasarapu AR, Sud M, Brown HA, Glass CK, Murphy RC, Russell DW, Dennis EA, Subramaniam S. Analysis of inflammatory and lipid metabolic networks across RAW264.7 and thioglycolate-elicited macrophages. J Lipid Res. 2013 Sep; 54(9):2525-42. PMID: 23776196.
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      38. Marin T, Gongol B, Chen Z, Woo B, Subramaniam S, Chien S, Shyy JY. Mechanosensitive microRNAs-role in endothelial responses to shear stress and redox state. Free Radic Biol Med. 2013 Sep; 64:61-8. PMID: 23727269.
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      39. Yang K, Dinasarapu AR, Reis ES, Deangelis RA, Ricklin D, Subramaniam S, Lambris JD. CMAP: Complement Map Database. Bioinformatics. 2013 Jul 15; 29(14):1832-3. PMID: 23661693.
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      40. Garmire LX, Subramaniam S. The poor performance of TMM on microRNA-Seq. RNA. 2013 Jun; 19(6):735-6. PMID: 23616641.
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      41. Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S. Quantitative transcriptomics using designed primer-based amplification. Sci Rep. 2013; 3:1740. PMID: 23624976.
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      42. Colas AR, McKeithan WL, Cunningham TJ, Bushway PJ, Garmire LX, Duester G, Subramaniam S, Mercola M. Whole-genome microRNA screening identifies let-7 and mir-18 as regulators of germ layer formation during early embryogenesis. Genes Dev. 2012 Dec 1; 26(23):2567-79. PMID: 23152446.
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      43. Choi T, Maurya MR, Tartakovsky DM, Subramaniam S. Stochastic operator-splitting method for reaction-diffusion systems. J Chem Phys. 2012 Nov 14; 137(18):184102. PMID: 23163359.
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      44. Wang Y, Winters J, Subramaniam S. Functional classification of skeletal muscle networks. I. Normal physiology. J Appl Physiol (1985). 2012 Dec 15; 113(12):1884-901. PMID: 23085959.
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      45. Wang Y, Winters J, Subramaniam S. Functional classification of skeletal muscle networks. II. Applications to pathophysiology. J Appl Physiol (1985). 2012 Dec 15; 113(12):1902-20. PMID: 23085957.
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      46. Asadi B, Maurya MR, Tartakovsky DM, Subramaniam S. Comparison of statistical and optimisation-based methods for data-driven network reconstruction of biochemical systems. IET Syst Biol. 2012 Oct; 6(5):155-63. PMID: 23101870.
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      47. Spann NJ, Garmire LX, McDonald JG, Myers DS, Milne SB, Shibata N, Reichart D, Fox JN, Shaked I, Heudobler D, Raetz CR, Wang EW, Kelly SL, Sullards MC, Murphy RC, Merrill AH, Brown HA, Dennis EA, Li AC, Ley K, Tsimikas S, Fahy E, Subramaniam S, Quehenberger O, Russell DW, Glass CK. Regulated accumulation of desmosterol integrates macrophage lipid metabolism and inflammatory responses. Cell. 2012 Sep 28; 151(1):138-52. PMID: 23021221.
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      48. Sud M, Fahy E, Subramaniam S. Template-based combinatorial enumeration of virtual compound libraries for lipids. J Cheminform. 2012; 4(1):23. PMID: 23006594.
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      49. Smith LR, Chambers HG, Subramaniam S, Lieber RL. Transcriptional abnormalities of hamstring muscle contractures in children with cerebral palsy. PLoS One. 2012; 7(8):e40686. PMID: 22956992.
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      50. Subramaniam S. Evolution of bioengineering at UCSD: opening new vistas. IEEE Pulse. 2012 Jul; 3(4):49-55. PMID: 22850838.
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      51. Towfic F, Gupta S, Honavar V, Subramaniam S. B-cell ligand processing pathways detected by large-scale comparative analysis. Genomics Proteomics Bioinformatics. 2012 Jun; 10(3):142-52. PMID: 22917187.
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      52. Hightower CM, Salazar Vázquez BY, Acharya SA, Subramaniam S, Intaglietta M. PEG-albumin plasma expansion increases expression of MCP-1 evidencing increased circulatory wall shear stress: an experimental study. PLoS One. 2012; 7(6):e39111. PMID: 22720043.
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      53. Garmire LX, Subramaniam S. Evaluation of normalization methods in mammalian microRNA-Seq data. RNA. 2012 Jun; 18(6):1279-88. PMID: 22532701.
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      54. Subramaniam S, Hsiao G. Gene-expression measurement: variance-modeling considerations for robust data analysis. Nat Immunol. 2012 Mar; 13(3):199-203. PMID: 22344273.
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      55. Sud M, Fahy E, Cotter D, Dennis EA, Subramaniam S. LIPID MAPS-Nature Lipidomics Gateway: An Online Resource for Students and Educators Interested in Lipids. J Chem Educ. 2012 Jan 10; 89(2):291-292. PMID: 24764601.
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      56. Narayanan T, Gersten M, Subramaniam S, Grama A. Modularity detection in protein-protein interaction networks. BMC Res Notes. 2011; 4:569. PMID: 22206604.
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      57. DeAngelis RA, Markiewski MM, Kourtzelis I, Rafail S, Syriga M, Sandor A, Maurya MR, Gupta S, Subramaniam S, Lambris JD. A complement-IL-4 regulatory circuit controls liver regeneration. J Immunol. 2012 Jan 15; 188(2):641-8. PMID: 22184721.
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      58. Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS Genet. 2011 Dec; 7(12):e1002401. PMID: 22174696.
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      59. Garmire LX, Garmire DG, Huang W, Yao J, Glass CK, Subramaniam S. A global clustering algorithm to identify long intergenic non-coding RNA--with applications in mouse macrophages. PLoS One. 2011; 6(9):e24051. PMID: 21980340.
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      60. Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR. Bioinformatics and systems biology of the lipidome. Chem Rev. 2011 Oct 12; 111(10):6452-90. PMID: 21939287.
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      61. Fahy E, Cotter D, Sud M, Subramaniam S. Lipid classification, structures and tools. Biochim Biophys Acta. 2011 Nov; 1811(11):637-47. PMID: 21704189.
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      62. Zhou J, Wang KC, Wu W, Subramaniam S, Shyy JY, Chiu JJ, Li JY, Chien S. MicroRNA-21 targets peroxisome proliferators-activated receptor-alpha in an autoregulatory loop to modulate flow-induced endothelial inflammation. Proc Natl Acad Sci U S A. 2011 Jun 21; 108(25):10355-60. PMID: 21636785.
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      63. Dinasarapu AR, Saunders B, Ozerlat I, Azam K, Subramaniam S. Signaling gateway molecule pages--a data model perspective. Bioinformatics. 2011 Jun 15; 27(12):1736-8. PMID: 21505029.
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      64. Subramaniam S, Nadeau JH. Pathways, networks, and systems medicine--the meeting place of the Aegean and the mind. Wiley Interdiscip Rev Syst Biol Med. 2011 May-Jun; 3(3):253-4. PMID: 21462354.
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      65. Subramaniam S, Nadeau JH. Systems physiology--the heart of the matter or a bone of contention? Wiley Interdiscip Rev Syst Biol Med. 2011 Mar-Apr; 3(2):127-8. PMID: 21305701.
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      66. Gupta S, Maurya MR, Merrill AH, Glass CK, Subramaniam S. Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism. BMC Syst Biol. 2011; 5:26. PMID: 21303545.
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      67. Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer KA, Posakony JW, Subramaniam S, Bafna V, Haddad GG. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A. 2011 Feb 8; 108(6):2349-54. PMID: 21262834.
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      68. Choi T, Maurya MR, Tartakovsky DM, Subramaniam S. Stochastic hybrid modeling of intracellular calcium dynamics. J Chem Phys. 2010 Oct 28; 133(16):165101. PMID: 21033822.
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      69. Hsiao G, Chapman J, Ofrecio JM, Wilkes J, Resnik JL, Thapar D, Subramaniam S, Sears DD. Multi-tissue, selective PPAR? modulation of insulin sensitivity and metabolic pathways in obese rats. Am J Physiol Endocrinol Metab. 2011 Jan; 300(1):E164-74. PMID: 20959535.
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      70. Dennis EA, Deems RA, Harkewicz R, Quehenberger O, Brown HA, Milne SB, Myers DS, Glass CK, Hardiman G, Reichart D, Merrill AH, Sullards MC, Wang E, Murphy RC, Raetz CR, Garrett TA, Guan Z, Ryan AC, Russell DW, McDonald JG, Thompson BM, Shaw WA, Sud M, Zhao Y, Gupta S, Maurya MR, Fahy E, Subramaniam S. A mouse macrophage lipidome. J Biol Chem. 2010 Dec 17; 285(51):39976-85. PMID: 20923771.
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      71. Bielinska-Waz D, Subramaniam S. Classification studies based on a spectral representation of DNA. J Theor Biol. 2010 Oct 21; 266(4):667-74. PMID: 20691193.
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      72. 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. Lipidomics reveals a remarkable diversity of lipids in human plasma. J Lipid Res. 2010 Nov; 51(11):3299-305. PMID: 20671299.
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      73. Subramaniam S, Nadeau JH. Systems medicine--viewed through the real and computing lenses. Wiley Interdiscip Rev Syst Biol Med. 2010 Jul-Aug; 2(4):383-4. PMID: 20836036.
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      74. 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 AH, Raetz CR, Russell DW, Subramaniam S, Dennis EA. Subcellular organelle lipidomics in TLR-4-activated macrophages. J Lipid Res. 2010 Sep; 51(9):2785-97. PMID: 20574076.
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      75. Subramaniam S, Nadeau JH. Systems biology and medicine--metazoan life and processes. Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun; 2(3):253-4. PMID: 20836027.
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      76. Rodríguez-Flores JL, Zhang K, Kang SW, Wen G, Ghosh S, Friese RS, Mahata SK, Subramaniam S, Hamilton BA, O'Connor DT. Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. Mamm Genome. 2010 Apr; 21(3-4):195-204. PMID: 20204374.
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      77. Subramaniam S, Nadeau JH. Systems biology and medicine--meta-issues and frameworks. Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr; 2(2):i-ii. PMID: 20836016.
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      78. Gupta S, Maurya MR, Subramaniam S. Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells. PLoS Comput Biol. 2010 Jan; 6(1):e1000654. PMID: 20126526.
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      79. Wang KC, Garmire LX, Young A, Nguyen P, Trinh A, Subramaniam S, Wang N, Shyy JY, Li YS, Chien S. Role of microRNA-23b in flow-regulation of Rb phosphorylation and endothelial cell growth. Proc Natl Acad Sci U S A. 2010 Feb 16; 107(7):3234-9. PMID: 20133741.
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      80. Garmire LX, Shen Z, Briggs S, Yeo G, Subramaniam S, Glass C. Regulatory network of microRNAs in RAW 264.7 macrophage cells. Conf Proc IEEE Eng Med Biol Soc. 2010; 2010:6198-201. PMID: 21097158.
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      81. Nadeau JH, Subramaniam S. Systems biology--old wine in a new bottle or is the bottle changing the wine? Wiley Interdiscip Rev Syst Biol Med. 2010 Jan-Feb; 2(1):1-2. PMID: 20836006.
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      82. Andreyev AY, Shen Z, Guan Z, Ryan A, Fahy E, Subramaniam S, Raetz CR, Briggs S, Dennis EA. Application of proteomic marker ensembles to subcellular organelle identification. Mol Cell Proteomics. 2010 Feb; 9(2):388-402. PMID: 19884172.
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      83. Subramaniam S, Nadeau JH. Systems biology and medicine--plunging into the unknown. Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec; 1(3):283-4. PMID: 20835997.
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      84. Sears DD, Hsiao G, Hsiao A, Yu JG, Courtney CH, Ofrecio JM, Chapman J, Subramaniam S. Mechanisms of human insulin resistance and thiazolidinedione-mediated insulin sensitization. Proc Natl Acad Sci U S A. 2009 Nov 3; 106(44):18745-50. PMID: 19841271.
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      85. Byrnes RW, Cotter D, Maer A, Li J, Nadeau D, Subramaniam S. An editor for pathway drawing and data visualization in the Biopathways Workbench. BMC Syst Biol. 2009; 3:99. PMID: 19799790.
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      86. Green CE, Liu T, Montel V, Hsiao G, Lester RD, Subramaniam S, Gonias SL, Klemke RL. Chemoattractant signaling between tumor cells and macrophages regulates cancer cell migration, metastasis and neovascularization. PLoS One. 2009; 4(8):e6713. PMID: 19696929.
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      87. Hsiao A, Subramaniam S. Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data. Syst Synth Biol. 2008 Dec; 2(3-4):95-104. PMID: 19680790.
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      88. Smith LR, Pontén E, Hedström Y, Ward SR, Chambers HG, Subramaniam S, Lieber RL. Novel transcriptional profile in wrist muscles from cerebral palsy patients. BMC Med Genomics. 2009; 2:44. PMID: 19602279.
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      89. Nadeau JH, Subramaniam S. Systems biology and medicine: a new take on an old paradigm. Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug; 1(1):1-3. PMID: 20835979.
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      90. Gupta S, Maurya MR, Stephens DL, Dennis EA, Subramaniam S. An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. Biophys J. 2009 Jun 3; 96(11):4542-51. PMID: 19486676.
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      91. Hill-Baskin AE, Markiewski MM, Buchner DA, Shao H, DeSantis D, Hsiao G, Subramaniam S, Berger NA, Croniger C, Lambris JD, Nadeau JH. Diet-induced hepatocellular carcinoma in genetically predisposed mice. Hum Mol Genet. 2009 Aug 15; 18(16):2975-88. PMID: 19454484.
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      92. Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. Mixed-integer nonlinear optimisation approach to coarse-graining biochemical networks. IET Syst Biol. 2009 Jan; 3(1):24-39. PMID: 19154082.
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      93. Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR, Shimizu T, Spener F, van Meer G, Wakelam MJ, Dennis EA. Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res. 2009 Apr; 50 Suppl:S9-14. PMID: 19098281.
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      94. Pandey J, Koyutürk M, Subramaniam S, Grama A. Functional coherence in domain interaction networks. Bioinformatics. 2008 Aug 15; 24(16):i28-34. PMID: 18689835.
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      95. Walsh CT, Radeff-Huang J, Matteo R, Hsiao A, Subramaniam S, Stupack D, Brown JH. Thrombin receptor and RhoA mediate cell proliferation through integrins and cysteine-rich protein 61. FASEB J. 2008 Nov; 22(11):4011-21. PMID: 18687805.
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      96. Guda P, Guda C, Subramaniam S. Reconstruction of pathways associated with amino acid metabolism in human mitochondria. Genomics Proteomics Bioinformatics. 2007 Dec; 5(3-4):166-76. PMID: 18267298.
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      97. Saunders B, Lyon S, Day M, Riley B, Chenette E, Subramaniam S, Vadivelu I. The Molecule Pages database. Nucleic Acids Res. 2008 Jan; 36(Database issue):D700-6. PMID: 17965093.
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      98. Pandey J, Koyutürk M, Kim Y, Szpankowski W, Subramaniam S, Grama A. Functional annotation of regulatory pathways. Bioinformatics. 2007 Jul 1; 23(13):i377-86. PMID: 17646320.
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      99. Fahy E, Sud M, Cotter D, Subramaniam S. LIPID MAPS online tools for lipid research. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W606-12. PMID: 17584797.
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      100. 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. Macrophage PPAR gamma is required for normal skeletal muscle and hepatic insulin sensitivity and full antidiabetic effects of thiazolidinediones. J Clin Invest. 2007 Jun; 117(6):1658-69. PMID: 17525798.
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      101. Maurya MR, Subramaniam S. A kinetic model for calcium dynamics in RAW 264.7 cells: 1. Mechanisms, parameters, and subpopulational variability. Biophys J. 2007 Aug 1; 93(3):709-28. PMID: 17483174.
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      102. Maurya MR, Subramaniam S. A kinetic model for calcium dynamics in RAW 264.7 cells: 2. Knockdown response and long-term response. Biophys J. 2007 Aug 1; 93(3):729-40. PMID: 17483189.
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      103. Fahy E, Cotter D, Byrnes R, Sud M, Maer A, Li J, Nadeau D, Zhau Y, Subramaniam S. Bioinformatics for lipidomics. Methods Enzymol. 2007; 432:247-73. PMID: 17954221.
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      104. Guda P, Subramaniam S, Guda C. Mitoproteome: human heart mitochondrial protein sequence database. Methods Mol Biol. 2007; 357:375-83. PMID: 17172703.
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      105. Moene IA, Subramaniam S, Darin D, Leergaard TB, Bjaalie JG. Toward a workbench for rodent brain image data: systems architecture and design. Neuroinformatics. 2007; 5(1):35-58. PMID: 17426352.
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      106. Maurya MR, Benner C, Pradervand S, Glass C, Subramaniam S. Systems biology of macrophages. Adv Exp Med Biol. 2007; 598:62-79. PMID: 17892205.
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      107. Schmelzer K, Fahy E, Subramaniam S, Dennis EA. The lipid maps initiative in lipidomics. Methods Enzymol. 2007; 432:171-83. PMID: 17954217.
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      108. Zavzavadjian JR, Couture S, Park WS, Whalen J, Lyon S, Lee G, Fung E, Mi Q, Liu J, Wall E, Santat L, Dhandapani K, Kivork C, Driver A, Zhu X, Chang MS, 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. The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis. Mol Cell Proteomics. 2007 Mar; 6(3):413-24. PMID: 17192258.
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      109. Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Murphy RC, Raetz CR, Russell DW, Subramaniam S. LMSD: LIPID MAPS structure database. Nucleic Acids Res. 2007 Jan; 35(Database issue):D527-32. PMID: 17098933.
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      110. Koyutürk M, Kim Y, Subramaniam S, Szpankowski W, Grama A. Detecting conserved interaction patterns in biological networks. J Comput Biol. 2006 Sep; 13(7):1299-322. PMID: 17037960.
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      111. Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics. 2006; 7:237. PMID: 16670020.
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      112. Kim Y, Subramaniam S. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins. 2006 Mar 1; 62(4):1115-24. PMID: 16385560.
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      113. Koyutürk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A. Pairwise alignment of protein interaction networks. J Comput Biol. 2006 Mar; 13(2):182-99. PMID: 16597234.
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      114. Pradervand S, Maurya MR, Subramaniam S. Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages. Genome Biol. 2006; 7(2):R11. PMID: 16507166.
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      115. Raetz CR, Garrett TA, Reynolds CM, Shaw WA, Moore JD, Smith DC, 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. Kdo2-Lipid A of Escherichia coli, a defined endotoxin that activates macrophages via TLR-4. J Lipid Res. 2006 May; 47(5):1097-111. PMID: 16479018.
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      116. Cotter D, Maer A, Guda C, Saunders B, Subramaniam S. LMPD: LIPID MAPS proteome database. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D507-10. PMID: 16381922.
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      117. Kim Y, Koyutürk M, Topkara U, Grama A, Subramaniam S. Inferring functional information from domain co-evolution. Bioinformatics. 2006 Jan 1; 22(1):40-9. PMID: 16301205.
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      118. Ogawa S, Lozach J, Benner C, Pascual G, Tangirala RK, Westin S, Hoffmann A, Subramaniam S, David M, Rosenfeld MG, Glass CK. Molecular determinants of crosstalk between nuclear receptors and toll-like receptors. Cell. 2005 Sep 9; 122(5):707-21. PMID: 16143103.
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      119. Guda C, Subramaniam S. pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics. 2005 Nov 1; 21(21):3963-9. PMID: 16144808.
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      120. Hsiao A, Ideker T, Olefsky JM, 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):W627-32. PMID: 15980550.
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      121. Fahy E, Subramaniam S, Brown HA, Glass CK, Merrill AH, 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. A comprehensive classification system for lipids. J Lipid Res. 2005 May; 46(5):839-61. PMID: 15722563.
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      122. Papin JA, Hunter T, Palsson BO, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol. 2005 Feb; 6(2):99-111. PMID: 15654321.
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      123. 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. Analysis of the major patterns of B cell gene expression changes in response to short-term stimulation with 33 single ligands. J Immunol. 2004 Dec 15; 173(12):7141-9. PMID: 15585835.
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      124. Bornheimer SJ, Maurya MR, Farquhar MG, Subramaniam S. Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction. Proc Natl Acad Sci U S A. 2004 Nov 9; 101(45):15899-904. PMID: 15520372.
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      125. Livesay DR, Subramaniam S. Conserved sequence and structure association motifs in antibody-protein and antibody-hapten complexes. Protein Eng Des Sel. 2004 May; 17(5):463-72. PMID: 15310840.
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      126. Guda C, Guda P, Fahy E, Subramaniam S. MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W372-4. PMID: 15215413.
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      127. Chukkapalli G, Guda C, Subramaniam S. SledgeHMMER: a web server for batch searching the Pfam database. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W542-4. PMID: 15215445.
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      128. Avidor-Reiss T, Maer AM, Koundakjian E, Polyanovsky A, Keil T, Subramaniam S, Zuker CS. Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis. Cell. 2004 May 14; 117(4):527-39. PMID: 15137945.
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      129. Guda C, Fahy E, Subramaniam S. MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics. 2004 Jul 22; 20(11):1785-94. PMID: 15037509.
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      130. Papin J, Subramaniam S. Bioinformatics and cellular signaling. Curr Opin Biotechnol. 2004 Feb; 15(1):78-81. PMID: 15102471.
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      131. Cotter D, Guda P, Fahy E, Subramaniam S. MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D463-7. PMID: 14681458.
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      132. Subramaniam S. Bioinformatics and computational systems biology: at the cross roads of biology, engineering and computation. Conf Proc IEEE Eng Med Biol Soc. 2004; 7:5458. PMID: 17271584.
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      133. Shealy RT, Murphy AD, Ramarathnam R, Jakobsson E, Subramaniam S. Sequence-function analysis of the K+-selective family of ion channels using a comprehensive alignment and the KcsA channel structure. Biophys J. 2003 May; 84(5):2929-42. PMID: 12719225.
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      134. Livesay DR, Jambeck P, Rojnuckarin A, Subramaniam S. Conservation of electrostatic properties within enzyme families and superfamilies. Biochemistry. 2003 Apr 1; 42(12):3464-73. PMID: 12653550.
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      135. Hunter CG, Subramaniam S. Protein local structure prediction from sequence. Proteins. 2003 Mar 1; 50(4):572-9. PMID: 12577263.
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      136. Hunter CG, Subramaniam S. Protein fragment clustering and canonical local shapes. Proteins. 2003 Mar 1; 50(4):580-8. PMID: 12577264.
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      137. 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, Sinkovits RS, Li J, Mock D, Ning Y, 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 Y, Brekken D, Shu H, Meyer T, Chandy G, Heo WD, Liou J, O'Rourke N, Verghese M, Mumby SM, Han H, 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. Overview of the Alliance for Cellular Signaling. Nature. 2002 Dec 12; 420(6916):703-6. PMID: 12478301.
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      138. Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T, Subramaniam S. The Molecule Pages database. Nature. 2002 Dec 12; 420(6916):716-7. PMID: 12478304.
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      139. Hunter CG, Subramaniam S. Natural coordinate representation for the protein backbone structure. Proteins. 2002 Nov 1; 49(2):206-15. PMID: 12211001.
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      140. Subramaniam S. Bioinformatics of cellular signalling. Novartis Found Symp. 2002; 247:104-16; discussion 116-8, 119-28, 244-52. PMID: 12539952.
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      141. Herrgård S, Jambeck P, Taylor SS, Subramaniam S. Domain architecture of a Caenorhabditis elegans AKAP suggests a novel AKAP function. FEBS Lett. 2000 Dec 8; 486(2):107-11. PMID: 11113448.
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      142. Ramarathnam R, Subramaniam S. A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes. Microb Comp Genomics. 2000; 5(3):153-61. PMID: 11252352.
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