Publications

Moene IA, Subramaniam S, Darin D, Leergaard TB, Bjaalie JG. Toward a workbench for rodent brain image data: systems architecture and design.Neuroinformatics. 2007 Winter;5(1):35-58.

Maurya MR and 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.

Maurya MR and 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.

Pandey J, Koyuturk M, Kim Y, Szpankowski W, Subramaniam S, Grama A. Functional annotation of regulatory pathways Bioinformatics. 2007 Jul 1;23(13):i377-86.

Fahy E, Sud M, Cotter D and Subramaniam S. LIPID MAPS online tools for lipid research. Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W606-12.

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..

Byrnes RW, Fahy E and Subramaniam S. A Laboratory Information Management System for High Throughput Experimental Lipidomics: Minimum Information required for the Analysis of Lipidomics Experiments (MIALE) JALA 2007 Aug ;12(4)230-236. 7

Guda P, Guda C and Subramaniam S. Mitoproteome: human heart mitochondrial protein sequence database. Methods Mol Biol. 2007;357:375-83.

Guda P, Guda C and Subramaniam S. Reconstruction of pathways associated with aminoacid metabolism in human mitochondria. Submitted to Metabolic Engineering. January 2007.

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.The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis. Mol Cell Proteomics 2007.

Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Jr., Murphy RC, Raetz CR, Russell DW and Subramaniam S. LMSD: LIPID MAPS structure database.Nucleic Acids Res 2007;35(Database issue):D527-32.

Koyuturk 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.

Ramachandran S, Xie L-H, John SA, Subramaniam S and Lal R. A novel role for connexin hemichannel in oxidative stress and smoking-induced apoptosis. PLoS ONE 2007 Aug 8;2:e712

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. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics. 2006 May 2;7:237.

Koyuturk 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.

Kim Y and Subramaniam S. Locally defined protein phylogenetic profiles reveal previously missed protein interactions and functional relationships. Proteins. 2006 Mar 1;62(4):1115-24.

Pradervand S, Maurya MR and Subramaniam S. Identification of signaling components required for the prediction of cytokine release in RAW 264.7 macrophages. Genome Biology 2006 Feb 20;7(2):R11.

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. Purification and properties of Escherichia coli Kd02-lipid A, a defined endotoxin that activates macrophages via TLR-4. J Lipid Res. 2006 May;47(5):1097-111. Epub 2006 Feb 14.

Cotter D, Maer AM, Guda C, Saunders B and Subramaniam S. LMPD: LIPID MAPS Proteome Database. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D507-10.

Kim Y, Koyuturk M, Topkara U, Grama A and Subramaniam S. Inferring functional information from domain co-evolution. Bioinformatics 2006 Jan 1;22(1):40-9.