Shankar Subramaniam - Publications

Bioengineering University of California, San Diego, La Jolla, CA 
Biomedical Engineering, Biomechanics Biophysics

133 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Masnadi-Shirazi M, Maurya MR, Pao G, Ke E, Verma IM, Subramaniam S. Time varying causal network reconstruction of a mouse cell cycle. Bmc Bioinformatics. 20: 294. PMID 31142274 DOI: 10.1186/s12859-019-2895-1  0.72
2019 Rahiminejad S, Maurya MR, Subramaniam S. Topological and functional comparison of community detection algorithms in biological networks. Bmc Bioinformatics. 20: 212. PMID 31029085 DOI: 10.1186/s12859-019-2746-0  0.72
2018 Diez-Cuñado M, Wei K, Bushway PJ, Maurya MR, Perera R, Subramaniam S, Ruiz-Lozano P, Mercola M. miRNAs that Induce Human Cardiomyocyte Proliferation Converge on the Hippo Pathway. Cell Reports. 23: 2168-2174. PMID 29768213 DOI: 10.1016/j.celrep.2018.04.049  0.72
2018 Miao Y, Ajami NE, Huang TS, Lin FM, Lou CH, Wang YT, Li S, Kang J, Munkacsi H, Maurya MR, Gupta S, Chien S, Subramaniam S, Chen Z. Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function. Nature Communications. 9: 292. PMID 29348663 DOI: 10.1038/s41467-017-02113-y  0.72
2017 Ajami NE, Gupta S, Maurya MR, Nguyen P, Li JY, Shyy JY, Chen Z, Chien S, Subramaniam S. Systems biology analysis of longitudinal functional response of endothelial cells to shear stress. Proceedings of the National Academy of Sciences of the United States of America. PMID 28973892 DOI: 10.1073/pnas.1707517114  0.72
2017 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, ... ... Subramaniam S, et al. KLF4 Regulation of Ch25h and LXR Mitigates Atherosclerosis Susceptibility. Circulation. PMID 28794002 DOI: 10.1161/CIRCULATIONAHA.117.027462  0.72
2016 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. 30: 595-609. PMID 27728806 DOI: 10.1016/j.ccell.2016.09.004  1
2016 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. Journal of Immunology (Baltimore, Md. : 1950). PMID 27511733 DOI: 10.4049/jimmunol.1600628  1
2016 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, et al. p62, Upregulated during Preneoplasia, Induces Hepatocellular Carcinogenesis by Maintaining Survival of Stressed HCC-Initiating Cells. Cancer Cell. PMID 27211490 DOI: 10.1016/j.ccell.2016.04.006  1
2016 Gupta S, Kihara Y, Maurya MR, Norris PC, Dennis EA, Subramaniam S. Computational Modeling of Competitive Metabolism Between ω3- and ω6 Polyunsaturated Fatty Acids in Inflammatory Macrophages. The Journal of Physical Chemistry. B. PMID 27063350 DOI: 10.1021/acs.jpcb.6b02036  1
2015 Mohammadi S, Saberidokht B, Subramaniam S, Grama A. Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. Bmc Systems Biology. 9: 96. PMID 26714768 DOI: 10.1186/s12918-015-0253-0  1
2015 Nakaya HI, Hagan T, Duraisingham SS, Lee EK, Kwissa M, Rouphael N, Frasca D, Gersten M, Mehta AK, Gaujoux R, Li GM, Gupta S, Ahmed R, Mulligan MJ, Shen-Orr S, ... ... Subramaniam S, et al. Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures. Immunity. 43: 1186-98. PMID 26682988 DOI: 10.1016/j.immuni.2015.11.012  1
2015 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 Research. PMID 26467476 DOI: 10.1093/nar/gkv1042  1
2015 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, ... ... Subramaniam S, et al. The Role of ARF6 in Biliary Atresia. Plos One. 10: e0138381. PMID 26379158 DOI: 10.1371/journal.pone.0138381  1
2015 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. PMID 26002934 DOI: 10.1136/gutjnl-2015-309456  1
2015 Mukund K, Subramaniam S. Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis. Bmc Research Notes. 8: 182. PMID 25935398 DOI: 10.1186/s13104-015-1141-9  1
2015 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 Systems Biology. 9: 13. PMID 25890336 DOI: 10.1186/s12918-015-0156-0  1
2015 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, ... ... Subramaniam S, et al. Biomarkers of NAFLD progression: a lipidomics approach to an epidemic. Journal of Lipid Research. 56: 722-36. PMID 25598080 DOI: 10.1194/jlr.P056002  1
2014 Tsai AG, Salazar 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. Journal of Functional Biomaterials. 5: 232-45. PMID 25350267 DOI: 10.3390/jfb5040232  0.44
2014 Gersten M, Zhou D, Azad P, Haddad GG, Subramaniam S. Wnt pathway activation increases hypoxia tolerance during development. Plos One. 9: e103292. PMID 25093834 DOI: 10.1371/journal.pone.0103292  1
2014 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 Systems Biology. 8: 77. PMID 24964861 DOI: 10.1186/1752-0509-8-77  1
2014 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. Arteriosclerosis, Thrombosis, and Vascular Biology. 34: 1437-45. PMID 24855060 DOI: 10.1161/ATVBAHA.114.303473  1
2014 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. Vascular Health and Risk Management. 10: 271-7. PMID 24851053 DOI: 10.2147/VHRM.S60130  1
2014 Masnadi-Shirazi M, Maurya MR, Subramaniam S. Time-varying causal inference from phosphoproteomic measurements in macrophage cells. Ieee Transactions On Biomedical Circuits and Systems. 8: 74-86. PMID 24681921 DOI: 10.1109/TBCAS.2013.2288035  0.72
2014 Narayanan T, Subramaniam S. A Newtonian framework for community detection in undirected biological networks. Ieee Transactions On Biomedical Circuits and Systems. 8: 65-73. PMID 24681920 DOI: 10.1109/TBCAS.2013.2288155  1
2014 Subramaniam S. Drug discovery and the maze of biological complexity: an editorial essay. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 6: 225-6. PMID 24648390 DOI: 10.1002/wsbm.1266  1
2014 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. Biophysical Journal. 106: 966-75. PMID 24559999 DOI: 10.1016/j.bpj.2014.01.015  1
2014 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. 50: 744-58. PMID 24536034 DOI: 10.1002/mus.24211  1
2014 Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. Technical variations in low-input RNA-seq methodologies. Scientific Reports. 4: 3678. PMID 24419370 DOI: 10.1038/srep03678  1
2014 Ramarathnam R, Subramaniam S. Phylogenomics of orthologous protein families in prokaryotes: Comparison of evolutionary profiles Current Bioinformatics. 9: 113-131. DOI: 10.2174/157489360902140313105531  1
2013 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, ... ... Subramaniam S, et al. 25-Hydroxycholesterol activates the integrated stress response to reprogram transcription and translation in macrophages. The Journal of Biological Chemistry. 288: 35812-23. PMID 24189069 DOI: 10.1074/jbc.M113.519637  1
2013 Mohammadi S, Subramaniam S, Grama A. Inferring the effective TOR-dependent network: a computational study in yeast. Bmc Systems Biology. 7: 84. PMID 24005029 DOI: 10.1186/1752-0509-7-84  0.32
2013 Lemons D, Maurya MR, Subramaniam S, Mercola M. Developing microRNA screening as a functional genomics tool for disease research. Frontiers in Physiology. 4: 223. PMID 23986717 DOI: 10.3389/fphys.2013.00223  1
2013 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 (Oxford, England). 29: 2735-43. PMID 23981351 DOI: 10.1093/bioinformatics/btt469  1
2013 Narayanan T, Subramaniam S. Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy. Plos One. 8: e67237. PMID 23840633 DOI: 10.1371/journal.pone.0067237  1
2013 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. Journal of Lipid Research. 54: 2525-42. PMID 23776196 DOI: 10.1194/jlr.M040212  1
2013 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 Radical Biology & Medicine. 64: 61-8. PMID 23727269 DOI: 10.1016/j.freeradbiomed.2013.05.034  1
2013 Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S. Quantitative transcriptomics using designed primer-based amplification. Scientific Reports. 3: 1740. PMID 23624976 DOI: 10.1038/srep01740  1
2013 Garmire LX, Subramaniam S. The poor performance of TMM on microRNA-Seq. Rna (New York, N.Y.). 19: 735-6. PMID 23616641 DOI: 10.1261/rna.039271.113  1
2012 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. Journal of Chemical Education. 89: 291-292. PMID 24764601 DOI: 10.1021/ed200088u  1
2012 Choi T, Maurya MR, Tartakovsky DM, Subramaniam S. Stochastic operator-splitting method for reaction-diffusion systems. The Journal of Chemical Physics. 137: 184102. PMID 23163359 DOI: 10.1063/1.4764108  0.72
2012 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 & Development. 26: 2567-79. PMID 23152446 DOI: 10.1101/gad.200758.112  1
2012 Asadi B, Maurya MR, Tartakovsky DM, Subramaniam S. Comparison of statistical and optimisation-based methods for data-driven network reconstruction of biochemical systems. Iet Systems Biology. 6: 155-63. PMID 23101870 DOI: 10.1049/iet-syb.2011.0052  1
2012 Wang Y, Winters J, Subramaniam S. Functional classification of skeletal muscle networks. I. Normal physiology. Journal of Applied Physiology (Bethesda, Md. : 1985). 113: 1884-901. PMID 23085959 DOI: 10.1152/japplphysiol.01514.2011  1
2012 Wang Y, Winters J, Subramaniam S. Functional classification of skeletal muscle networks. II. Applications to pathophysiology. Journal of Applied Physiology (Bethesda, Md. : 1985). 113: 1902-20. PMID 23085957 DOI: 10.1152/japplphysiol.01515.2011  1
2012 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, ... ... Subramaniam S, et al. Regulated accumulation of desmosterol integrates macrophage lipid metabolism and inflammatory responses. Cell. 151: 138-52. PMID 23021221 DOI: 10.1016/j.cell.2012.06.054  1
2012 Smith LR, Chambers HG, Subramaniam S, Lieber RL. Transcriptional abnormalities of hamstring muscle contractures in children with cerebral palsy. Plos One. 7: e40686. PMID 22956992 DOI: 10.1371/journal.pone.0040686  1
2012 Subramaniam S. Evolution of bioengineering at UCSD: opening new vistas. Ieee Pulse. 3: 49-55. PMID 22850838 DOI: 10.1109/MPUL.2012.2198739  1
2012 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. 7: e39111. PMID 22720043 DOI: 10.1371/journal.pone.0039111  1
2012 Garmire LX, Subramaniam S. Evaluation of normalization methods in mammalian microRNA-Seq data. Rna (New York, N.Y.). 18: 1279-88. PMID 22532701 DOI: 10.1261/rna.030916.111  1
2012 Subramaniam S, Hsiao G. Gene-expression measurement: variance-modeling considerations for robust data analysis. Nature Immunology. 13: 199-203. PMID 22344273 DOI: 10.1038/ni.2244  1
2012 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. Journal of Immunology (Baltimore, Md. : 1950). 188: 641-8. PMID 22184721 DOI: 10.4049/jimmunol.1101925  0.72
2011 Narayanan T, Gersten M, Subramaniam S, Grama A. Modularity detection in protein-protein interaction networks. Bmc Research Notes. 4: 569. PMID 22206604 DOI: 10.1186/1756-0500-4-569  1
2011 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, ... ... Subramaniam S, et al. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. Plos Genetics. 7: e1002401. PMID 22174696 DOI: 10.1371/journal.pgen.1002401  1
2011 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. 6: e24051. PMID 21980340 DOI: 10.1371/journal.pone.0024051  1
2011 Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR. Bioinformatics and systems biology of the lipidome. Chemical Reviews. 111: 6452-90. PMID 21939287 DOI: 10.1021/cr200295k  0.72
2011 Subramaniam S, Nadeau JH. Pathways, networks, and systems medicine--the meeting place of the Aegean and the mind. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 3: 253-4. PMID 21462354 DOI: 10.1002/wsbm.153  1
2011 Subramaniam S, Nadeau JH. Systems physiology--the heart of the matter or a bone of contention? Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 3: 127-8. PMID 21305701 DOI: 10.1002/wsbm.146  1
2011 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 Systems Biology. 5: 26. PMID 21303545 DOI: 10.1186/1752-0509-5-26  1
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 2349-54. PMID 21262834 DOI: 10.1073/pnas.1010643108  1
2011 Hsiao G, Chapman J, Ofrecio JM, Wilkes J, Resnik JL, Thapar D, Subramaniam S, Sears DD. Multi-tissue, selective PPARγ modulation of insulin sensitivity and metabolic pathways in obese rats. American Journal of Physiology. Endocrinology and Metabolism. 300: E164-74. PMID 20959535 DOI: 10.1152/ajpendo.00219.2010  1
2010 Garmire LX, Shen Z, Briggs S, Yeo G, Subramaniam S, Glass C. Regulatory network of microRNAs in RAW 264.7 macrophage cells. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2010: 6198-201. PMID 21097158 DOI: 10.1109/IEMBS.2010.5627742  1
2010 Choi T, Maurya MR, Tartakovsky DM, Subramaniam S. Stochastic hybrid modeling of intracellular calcium dynamics. The Journal of Chemical Physics. 133: 165101. PMID 21033822 DOI: 10.1063/1.3496996  0.72
2010 Subramaniam S, Nadeau JH. Systems medicine--viewed through the real and computing lenses. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 383-4. PMID 20836036 DOI: 10.1002/wsbm.103  1
2010 Subramaniam S, Nadeau JH. Systems biology and medicine--metazoan life and processes. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 253-4. PMID 20836027 DOI: 10.1002/wsbm.99  1
2010 Subramaniam S, Nadeau JH. Systems biology and medicine--meta-issues and frameworks. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: i-ii. PMID 20836016 DOI: 10.1002/wsbm.98  1
2010 Nadeau JH, Subramaniam S. Systems biology--old wine in a new bottle or is the bottle changing the wine? Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 2: 1-2. PMID 20836006 DOI: 10.1002/wsbm.91  1
2010 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, ... ... Subramaniam S, et al. Lipidomics reveals a remarkable diversity of lipids in human plasma. Journal of Lipid Research. 51: 3299-305. PMID 20671299 DOI: 10.1194/jlr.M009449  1
2010 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, ... ... Subramaniam S, et al. Subcellular organelle lipidomics in TLR-4-activated macrophages. Journal of Lipid Research. 51: 2785-97. PMID 20574076 DOI: 10.1194/jlr.M008748  1
2010 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. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 21: 195-204. PMID 20204374 DOI: 10.1007/s00335-010-9253-y  1
2010 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. Proceedings of the National Academy of Sciences of the United States of America. 107: 3234-9. PMID 20133741 DOI: 10.1073/pnas.0914825107  1
2010 Gupta S, Maurya MR, Subramaniam S. Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells. Plos Computational Biology. 6: e1000654. PMID 20126526 DOI: 10.1371/journal.pcbi.1000654  0.72
2010 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. Molecular & Cellular Proteomics : McP. 9: 388-402. PMID 19884172 DOI: 10.1074/mcp.M900432-MCP200  1
2010 Maurya MR, Subramaniam S. Computational Challenges in Systems Biology Systems Biomedicine. 175-223. DOI: 10.1016/B978-0-12-372550-9.00008-0  1
2009 Subramaniam S, Nadeau JH. Systems biology and medicine--plunging into the unknown. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 1: 283-4. PMID 20835997 DOI: 10.1002/wsbm.80  1
2009 Nadeau JH, Subramaniam S. Systems biology and medicine: a new take on an old paradigm. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 1: 1-3. PMID 20835979 DOI: 10.1002/wsbm.34  1
2009 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. Proceedings of the National Academy of Sciences of the United States of America. 106: 18745-50. PMID 19841271 DOI: 10.1073/pnas.0903032106  1
2009 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 Systems Biology. 3: 99. PMID 19799790 DOI: 10.1186/1752-0509-3-99  1
2009 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. 4: e6713. PMID 19696929 DOI: 10.1371/journal.pone.0006713  1
2009 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 Medical Genomics. 2: 44. PMID 19602279 DOI: 10.1186/1755-8794-2-44  1
2009 Gupta S, Maurya MR, Stephens DL, Dennis EA, Subramaniam S. An integrated model of eicosanoid metabolism and signaling based on lipidomics flux analysis. Biophysical Journal. 96: 4542-51. PMID 19486676 DOI: 10.1016/j.bpj.2009.03.011  1
2009 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. Human Molecular Genetics. 18: 2975-88. PMID 19454484 DOI: 10.1093/hmg/ddp236  1
2009 Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. Mixed-integer nonlinear optimisation approach to coarse-graining biochemical networks. Iet Systems Biology. 3: 24-39. PMID 19154082 DOI: 10.1049/iet-syb:20080098  1
2009 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. Journal of Lipid Research. 50: S9-14. PMID 19098281 DOI: 10.1194/jlr.R800095-JLR200  1
2009 Nadeau JH, Subramaniam S. Parts of the whole Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 1: 151-152. DOI: 10.1002/wsbm.66  1
2008 Hsiao A, Subramaniam S. Bivariate microarray analysis: statistical interpretation of two-channel functional genomics data. Systems and Synthetic Biology. 2: 95-104. PMID 19680790 DOI: 10.1007/s11693-009-9033-8  1
2008 Pandey J, Koyutürk M, Subramaniam S, Grama A. Functional coherence in domain interaction networks. Bioinformatics (Oxford, England). 24: i28-34. PMID 18689835 DOI: 10.1093/bioinformatics/btn296  0.32
2008 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 Journal : Official Publication of the Federation of American Societies For Experimental Biology. 22: 4011-21. PMID 18687805 DOI: 10.1096/fj.08-113266  1
2007 Guda P, Guda C, Subramaniam S. Reconstruction of pathways associated with amino acid metabolism in human mitochondria. Genomics, Proteomics & Bioinformatics. 5: 166-76. PMID 18267298 DOI: 10.1016/S1672-0229(08)60004-2  1
2007 Schmelzer K, Fahy E, Subramaniam S, Dennis EA. The lipid maps initiative in lipidomics. Methods in Enzymology. 432: 171-83. PMID 17954217 DOI: 10.1016/S0076-6879(07)32007-7  1
2007 Maurya MR, Benner C, Pradervand S, Glass C, Subramaniam S. Systems biology of macrophages. Advances in Experimental Medicine and Biology. 598: 62-79. PMID 17892205 DOI: 10.1007/978-0-387-71767-8_6  0.72
2007 Pandey J, Koyutürk M, Kim Y, Szpankowski W, Subramaniam S, Grama A. Functional annotation of regulatory pathways. Bioinformatics (Oxford, England). 23: i377-86. PMID 17646320 DOI: 10.1093/bioinformatics/btm203  1
2007 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. The Journal of Clinical Investigation. 117: 1658-69. PMID 17525798 DOI: 10.1172/JCI31561  1
2007 Maurya MR, Subramaniam S. A kinetic model for calcium dynamics in RAW 264.7 cells: 2. Knockdown response and long-term response. Biophysical Journal. 93: 729-40. PMID 17483189 DOI: 10.1529/biophysj.106.097501  1
2007 Maurya MR, Subramaniam S. A kinetic model for calcium dynamics in RAW 264.7 cells: 1. Mechanisms, parameters, and subpopulational variability. Biophysical Journal. 93: 709-28. PMID 17483174 DOI: 10.1529/biophysj.106.097469  1
2007 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, ... ... Subramaniam S, et al. The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis. Molecular & Cellular Proteomics : McP. 6: 413-24. PMID 17192258 DOI: 10.1074/mcp.M600437-MCP200  1
2007 Guda P, Subramaniam S, Guda C. Mitoproteome: human heart mitochondrial protein sequence database. Methods in Molecular Biology (Clifton, N.J.). 357: 375-83. PMID 17172703 DOI: 10.1385/1-59745-214-9:375  1
2007 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 Research. 35: D527-32. PMID 17098933 DOI: 10.1093/nar/gkl838  1
2006 Subramaniam S, Abdul R. Surgical audit in day care myringoplasty Medical Journal of Malaysia. 61: 474-476. PMID 17243526  0.56
2006 Koyutürk M, Kim Y, Subramaniam S, Szpankowski W, Grama A. Detecting conserved interaction patterns in biological networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1299-322. PMID 17037960 DOI: 10.1089/cmb.2006.13.1299  1
2006 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. 7: 237. PMID 16670020 DOI: 10.1186/1471-2105-7-237  1
2006 Koyutürk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A. Pairwise alignment of protein interaction networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 182-99. PMID 16597234 DOI: 10.1089/cmb.2006.13.182  1
2006 Pradervand S, Maurya MR, Subramaniam S. Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages. Genome Biology. 7: R11. PMID 16507166 DOI: 10.1186/gb-2006-7-2-r11  0.72
2006 Kim Y, Subramaniam S. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins. 62: 1115-24. PMID 16385560 DOI: 10.1002/prot.20830  1
2006 Kim Y, Koyutürk M, Topkara U, Grama A, Subramaniam S. Inferring functional information from domain co-evolution. Bioinformatics (Oxford, England). 22: 40-9. PMID 16301205 DOI: 10.1093/bioinformatics/bti723  1
2005 Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. Reduced-order modelling of biochemical networks: application to the GTPase-cycle signalling module. Systems Biology. 152: 229-42. PMID 16986265 DOI: 10.1049/ip-syb:20050014  1
2005 Guda C, Subramaniam S. pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics (Oxford, England). 21: 3963-9. PMID 16144808 DOI: 10.1093/bioinformatics/bti650  1
2005 Hsiao A, Ideker T, Olefsky JM, Subramaniam S. VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Research. 33: W627-32. PMID 15980550 DOI: 10.1093/nar/gki443  1
2005 Subramaniam S. Challenges in biological data integration in the post-genome sequence era Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3615: 1.  1
2005 Maurya MR, Subramaniam S. Optimization as a tool for predictive modeling of biological systems and mining of large-scale data sets Aiche Annual Meeting, Conference Proceedings. 3374-3375.  1
2005 Maurya MR, Subramaniam S. Modeling of heterotrimeric G-protein mediated calcium response in raw 264.7 macrophage cells Aiche Annual Meeting, Conference Proceedings. 9252-9253.  1
2004 Bornheimer SJ, Maurya MR, Farquhar MG, Subramaniam S. Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction. Proceedings of the National Academy of Sciences of the United States of America. 101: 15899-904. PMID 15520372 DOI: 10.1073/pnas.0407009101  1
2004 Livesay DR, Subramaniam S. Conserved sequence and structure association motifs in antibody-protein and antibody-hapten complexes Protein Engineering, Design and Selection. 17: 463-472. PMID 15310840 DOI: 10.1093/protein/gzh058  1
2004 Hsiao A, Worrall DS, Olefsky JM, Subramaniam S. Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes. Bioinformatics (Oxford, England). 20: 3108-27. PMID 15217816 DOI: 10.1093/bioinformatics/bth371  1
2004 Papin J, Subramaniam S. Bioinformatics and cellular signaling Current Opinion in Biotechnology. 15: 78-81. PMID 15102471 DOI: 10.1016/j.copbio.2004.01.003  1
2003 Subramaniam S, Abd Majid MD. Eagle's syndrome Medical Journal of Malaysia. 58: 139-141. PMID 14556342  0.56
2003 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. Biophysical Journal. 84: 2929-42. PMID 12719225 DOI: 10.1016/S0006-3495(03)70020-4  1
2003 Hunter CG, Subramaniam S. Protein fragment clustering and canonical local shapes Proteins: Structure, Function and Genetics. 50: 580-588. PMID 12577264 DOI: 10.1002/prot.10309  1
2003 Hunter CG, Subramaniam S. Protein local structure prediction from sequence Proteins: Structure, Function and Genetics. 50: 572-579. PMID 12577263 DOI: 10.1002/prot.10310  1
2002 Hunter CG, Subramaniam S. Natural coordinate representation for the protein backbone structure Proteins: Structure, Function and Genetics. 49: 206-215. PMID 12211001 DOI: 10.1002/prot.10201  1
2000 Ramarathnam R, Subramaniam S. A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes. Microbial & Comparative Genomics. 5: 153-61. PMID 11252352  1
2000 Altobelli G, Subramaniam S. Kinetics of association of anti-lysozyme monoclonal antibody D44.1 and hen-egg lysozyme Biophysical Journal. 79: 2954-2965. PMID 11106603  1
2000 Linthicum DS, Subramaniam S. Antibody-antigen complexes: Editorial Methods. 20: 265-266. DOI: 10.1006/meth.1999.0920  1
1999 Rojnuckarin A, Subramaniam S. Knowledge-based interaction potentials for proteins Proteins: Structure, Function and Genetics. 36: 54-67. PMID 10373006 DOI: 10.1002/(SICI)1097-0134(19990701)36:1<54::AID-PROT5>3.0.CO;2-B  1
1998 Subramaniam S. The biology workbench - A seamless database and analysis environment for the biologist Proteins: Structure, Function and Genetics. 32: 1-2. PMID 9672036 DOI: 10.1002/(SICI)1097-0134(19980701)32:1<1::AID-PROT1>3.0.CO;2-Q  1
1998 Xiong J, Subramaniam S, Govindjee. A knowledge-based three dimensional model of the Photosystem II reaction center of Chlamydomonas reinhardtii Photosynthesis Research. 56: 229-254. DOI: 10.1023/A:1006061918025  1
1997 Gibas C, Subramaniam S. Knowledge-based design of a soluble bacteriorhodopsin Protein Engineering. 10: 1175-1190. PMID 9488142  1
1997 Liang J, Subramaniam S. Computation of molecular electrostatics with boundary element methods Biophysical Journal. 73: 1830-1841. PMID 9336178  1
1997 Pappas G, Subramaniam S. An evaluation of protein secondary structure prediction algorithms Techniques in Protein Chemistry. 8: 783-794. DOI: 10.1016/S1080-8914(97)80076-2  1
1996 Gibas CJ, Subramaniam S. Explicit solvent models in protein pK(a) calculations Biophysical Journal. 71: 138-147. PMID 8804597  1
1993 Kozack RE, Subramaniam S. Brownian dynamics simulations of molecular recognition in an antibody- antigen system Protein Science. 2: 915-926. PMID 8318896  1
1992 Subramaniam S, Boo K. Sudden death in a young adult due to coronary artery aneurysm secondary to suspected Kawasaki disease The Malaysian Journal of Pathology. 14: 49-51. PMID 1469919  0.56
1991 Subramaniam S. Autopsy examination of firearm fatalities The Malaysian Journal of Pathology. 13: 5-15. PMID 1795562  0.56
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