Publications

Maurya MR, Bornheimer SJ, Venkatasubramanian V and Subramaniam S. Reduced-ordered modeling in biochemical networks: Application to the GTPase-cycle signaling module. IEE Proceedings Systems Biology December 2005 Volume 152, Issue 4, p. 229-242.

Guda C and Subramaniam S. pTARGET: A new method for predicting protein subcellular localization in eukaryotes. Bioinformatics 2005 21(21):3963-3969.

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.

Maurya MR, Bornheimer SJ, Venkatasubramanian V and Subramaniam S. Reduced-order modeling of biochemical networks by simultaneous determination of network topology and parameters. Foundations of Systems Biology in Engineering (FOSBE); Aug. 7-10; University of California, Santa Barbara, CA, USA. 2005: 281-284.

Hsiao A, Ideker T, Olefsky J, 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.

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. A comprehensive classification system for lipids. J Lipid Res. 2005 May;46(5):839-62.

Papin JA, Subramaniam S, Hunter T and Palsson BO. Reconstruction of cellular signaling networks and analysis of their properties. Nat Rev Mol Cell Biol. 2005 Feb;6(2):99-111.

Papin JA, Gianchandani EP and Subramaniam S. Mapping the genotype-phenotype relationship in cellular signaling networks: building bridges over the unknown. Submitted 2005, Oxford University Press.

Hsiao A and Subramaniam S. Bivariate Microarray Analysis: Statistical Interpretation of Two-Channel Functional Genomics Data. Submitted to Genome Biology 2005.

Ramachandran S, Subramaniam S and La R. Hemichannels Initiate Apoptosis Induced by Oxidative Stress and Cigarette Smoke Extract. Submitted to J. Cell. Biol. 2005.

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.

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. 117(4):527-39, 2004.

Bornheimer SJ, Maurya MR, Farquhar MG and Subramaniam S. Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction. Proc. Natl. Acad. Sci. USA 101: 15899-15904, 2004.

Hsaio A, Worrall DS, Olefsky JM and Subramaniam S. Variance-modeled posterior inference of microarray data: Detecting gene-expression changes in 3T3-L1 adipocytes. Bioinformatics. 2004 Nov 22:20(17):3108-27.

Papin J and Subramaniam S.Bioinformatics and Cellular Signaling.Curr Opin Biotechnol. 2004 Feb;15(1):78-81. Review.

Guda C, Fahy E and Subramaniam S. MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics 20:1-10 2004.

Chukkapalli G, Guda C and Subramaniam S. SledgeHMMER: a web server for batch searching the Pfam database. Nucleic Acids Research 32, Web Server issue 2004.

Guda C, Guda P, Fahy E and Subramaniam S. MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Research 32 2004.

Papin JA and Subramaniam S. Bioinformatics and cellular signaling. Current Opinion in Biotechnology 15:78-81. 2004

Cotter D, Guda P, Fahy E and Subramaniam S. MitoProteome: Mitochondrial Protein Sequence Database and Annotation System. Nucleic Acids Research 32: D463-D467. 2004.

Hunter CG and Subramaniam S. Protein local structure prediction from sequence. Proteins. 2003 Mar 1;50(4):572-9.

Hunter CG and Subramaniam S. Protein fragment clustering and canonical local shapes. Proteins. 2003 Mar 1;50(4):580-8.

Livesay DR, Jambeck P, Rojnuckarin A and Subramaniam S. Conservation of electrostatic properties within enzyme families and superfamilies. Biochemistry. 2003 Apr 1;42(12):3464-73.

Eckersley P, Egan GF, Amari S, Beltrame F, Bennett R, Bjaalie JG, Dalkara T, De Schutter E, Gonzalez C, Grillner S, Herz A, Hoffmann KP, Jaaskelainen IP, Koslow SH, Lee SY, Matthiessen L, Miller PL, da Silva FM, Novak M, Ravindranath V, Ritz R, Ruotsalainen U, Subramaniam S, Toga AW, Usui S, Van Pelt J, Verschure P, Willshaw D, Wrobel A, Tang Y; OECD Working Group on Neuroinformatics. Neuroscience data and tool sharing: a legal and policy framework for neuroinformatics.> Neuroinformatics. 2003;1(2):149-65. Review.

Shealy RT, Murphy AD, Ramarathnam R, Jakobsson E and 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.

Ramarathnam R and Subramaniam S. Are evolutionary relationships in proteins driven by complete sequences or by motifs? Submitted to J Mol Biol., 2003.

Ramarathnam R and Subramaniam S. Phlyogenomics of orthologous protein families: comparison of evolutionary profiles. Submitted to Genome Res., 2003.

Hunter CG and Subramaniam S. Natural coordinate representation for the protein backbone structure. Proteins. 2002 Nov 1;49(2):206-15.

Amari SI, Beltrame F, Bjaalie JG, Dalkara T, De Schutter E, Egan GF, Goddard NH, Gonzalez C, Grillner S, Herz A, Hoffmann KP, Jaaskelainen I, Koslow SH, Lee SY, Matthiessen L, Miller PL, Da Silva FM, Novak M, Ravindranath V, Ritz R, Ruotsalainen U, Sebestra V, Subramaniam S, Tang Y, Toga AW, Usui S, Van Pelt J, Verschure, Willshaw D and Wrobel A. Neuroinformatics: The integration of shared databases and tools towards integrative neuroscience. J Integr Neurosci. 2002 Dec;1(2):117-28. Review.

Gilman AG, et al. Overview of the Alliance for Cellular Signaling. Nature. 2002 Dec 12;420(6916):703-6.

Li J, Ning Y, Hedley W, Saunders B, Chen Y, Tindill N, Hannay T and Subramaniam S. The molecule pages database. Nature. 2002 Dec 12;420(6916):716-7.

Subramaniam S. Bioinformatics Core Laboratory. Bioinformatics of cellular signalling. Novartis Found Symp. 2002;247:104-16; discussion 116-8, 119-28, 244-52. Review.

Farnum M and Subramaniam S. Assessment of CASP Models by a Knowledge-based Potential. Submitted to Proteins, 2001.

Fan Y and Subramaniam S. Structure-specific Scoring Matrices. Submitted to J. Comput. Biol. 2001.

Livesay DR and Subramaniam S. Conserved sequence and structural association motifs in antibody-protein and antibody-hapten complexes. Submitted to J Mol Cell Immunol. 2001.

Livesay DR and Subramaniam S. Electrostatics as the leit-motif of structural evolution in the CuZn superoxide dismutase protein family. Submitted to Biophys J. 2001.

Mashl RJ, Scott HL, Subramaniam S and Jakobsson E. Molecular simulation of dioleoylphosphatidylcholine lipid bilayers at differing levels of hydration. Biophys J. 2001 Dec;81(6):3005-15.

Bouzat JL, McNeil LK, Robertson HM, Solter LF, Nixon JE, Beever JE, Gaskins HR, Olsen G , Subramaniam S, Sogin ML, Lewin HA. Phylogenomic analysis of the alpha proteasome gene family from early diverging eukaryotes. J Mol Evol. 2000 Dec;51(6):532-43.

Rojnuckarin A, Livesay D and Subramaniam S. Bimolecular reaction simulation using weighted ensemble brownian dynamics and the university of houston brownian dynamics program. Biophys J. 2000 Aug;79(2):686-93.

Zou G, Skeel RD and Subramaniam S. Biased Brownian Dynamics for Rate Constant Calculation. Biophys J. 2000 Aug;79(2):638-45.

Herrgard S, Jambeck P, Taylor SS, and Subramaniam S. Domain architecture of a Caenorhabditis elegans AKAP suggests a novel AKAP function. FEBS Letters 2000; 486:107-11.

Ramarathnam R and Subramaniam S. A novel microarray strategy for detecting genes and pathways in microbes with unsequenced genomes. Microb Comp Genomics. 2000;5(3):153-61.

Chiu SW, Clark M, Subramaniam S and Jakobsson E. Collective motion artifacts arising in long-duration molecular dynamics. J Comput Chem. 2000 21:121-131.

Altobelli G and Subramaniam S. Kinetics of association of anti-lysozyme monoclonal antibody D44.1 and hen-egg lysozyme. Biophys J. 2000; 79:2954-65, 2000.

Gibas C, Jambeck P and Subramaniam S. Continuum electrostatic methods appied to pH-dependent properties of antibody-antigen association. Methods 2000; 20 292-309.

Linthicum DS and Subramaniam S. Editorial. Methods 2000; Mar;20(3):265-6.

Viswanathan M, Linthicum DS and Subramaniam S. Analysis of correlated motion in antibody combining sites from molecular dynamics simulations. Methods 2000; 20 362-371.

Herrgard S, Gibas C and Subramaniam S, Role of an electrostatic network of residues in the enzymatic action of Rhizomucor mihei lipase family. Biochemistry 2000; 39: 2921-2930.

Chiu SW, Subramaniam S and Jakobsson E. Simulation study of gramicidin/lipid bilayer system in excess water and lipid II. Rates and mechanisms of water transport. Biophys J. 1999; 76:1939-50.

Chiu SW, Subramaniam S and Jakobsson E. Simulation study of gramicidin/lipid bilayer system in excess water and lipid I. Structure of the molecular complex. Biophys J. 1999; 76:1929-38.

Rojnuckarin A and Subramaniam S, Knowledge-based potentials for protein structure, Proteins.1999; 36: 54-67.

Wall ME, Subramaniam S and Phillips GN. Protein structure determination using a database of interatomic distance probabilities. Protein Sci. 1999; 8:2720-2727.

Chiu SW, Jakobsson E, Subramaniam S, Scott HL. Combined monte carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers. Biophys J. 1999; 77:2462-9.

Livesay D and Subramaniam S. pH dependence of antibody-hapten association. Molecular Immunol.1999; 36: 397-410.

Chiu SW, Clark M, Jakobsson E, Subramaniam S, and Scott HL. Application of a combined monte carlo and molecular dynamics method to the simulation of a dipalmitoyl phosphatidylcholine lipid bilayer. J Comput Chem. 1999; 20: 1153-1164.

Chiu SW, Clark M, Jakobsson E, Subramaniam S and Scott HL. Optimization of hydrocarbon chain interaction parameters: application to the simulation of fluid phase lipid bilayers. J Phys Chem B. 1999; 103: 6323-6327.

Scott HL, Jakobsson E, Subramaniam S. Simulations of lipid membranes with atomic resolution. Journal of Computational Physics 1998; 12: 328-333.

Liang J, Pamidinghantam S, Edelsbrunner H, Fu P and Subramaniam S. Analytical shape computing in macromolecules. II. Inaccessible voids and interfacial regions in proteins. Proteins.1998; 33:18-29.

Liang J, Pamidinghantam S, Edelsbrunner H, Fu P and Subramaniam S. Analytical shape computing in macromolecules. I. Calculation of surface areas and volumes in proteins. Proteins.1998; 33:1-17.

Rojnuckarin A, Kim S, Subramaniam S. Brownian dynamics simulations of protein folding: access to milliseconds time scale and beyond. Proc Natl Acad Sci U S A 1998; 95:4288-4292.

Sivasankar S, Subramaniam S and Leckband D. Direct measurement of the pH-dependent electrostatic properties of a protein surface. Proc Natl Acad Sci U S A 1998; 95: 12961-12966.

Xiong J, Subramaniam S and Govindjee. A knowledge-based three dimensional model of the Photosystem II reaction center of Chlamydomonas reinhardtii. Photosyn Res. 1998; 56: 229-254.

Subramaniam S. The Biology Workbench: A seamless database and analysis environment for the biologist. Proteins.1998; 32: 1-2.

Pappas G and Subramaniam S. An evaluation of protein secondary structure prediction algorithms. Techniques in Protein Chemistry VII 1997; 783-794.

Gibas C and Subramaniam S. Knowledge-based design of a soluble bacteriorhodopsin. Protein Eng Des Sel.1997; 10: 1175-1190.

Liang J and Subramaniam S. Computation of molecular electrostatics with boundary element methods. Biophys J. 1997; 73: 1830-1841.

Gibas C, Subramaniam S, McCammon JA, Braden B, Poljak RJ.pH dependence of antibody/lysozyme complexation. Biochemistry 1997; 36(50): 15599-15614.

Mandal C, Anchin MM, Subramaniam S and Linthicum DS. ABGEN: A knowledge-based authomated approach for antibody structure modeling. Nat Biotechnol. 1996; 14(3): 323-328.

Gibas C and Subramaniam S. Explicit solvent models in protein pKa calculations. Biophys J. 1996; 71: 138-147.

Subramaniam S, Tcheng DK and Fenton JM.Knowledge-based methods for protein structure refinement and prediction. Proc Int Conf Intell Syst Mol Biol. 1996;4:218-29.

Viswanathan M, Pledger DW, Tetin SY, Linthicum DS and Subramaniam S. Modeling the structure of the combining site of an antisweet taste ligand monoclonal antibody NC 10.14. Biopolymers 1996; 39: 395-406.

Singh C, Sankararamakrishnan R, Subramaniam S, and Jakobsson E. Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel. Biophys J. 1996; 71:2276-2288.

Xiong J, Subramaniam S and Govindjee. Modeling of the D1/D2 proteins and cofactors of the photosystem II reaction center: implications for herbicide and bicarbonate binding. Protein Sci. 1996 5: 2054-2073.

Jakobsson E, Subramaniam S and Scott HL. In: Strategic issues in molecular dynamics simulations of membranes in: Membrane Structure and Dynamics. Merz K and Roux B, eds. Birkhauser, Boston, 1995.

Viswanathan M, Anchin JM, Droupadi PR, Mandal C, Linthicum DS, and Subramaniam S. Structural predictions of the binding site architecture for monoclonial antibody NC6.8 using ligand Binding, spectroscopy and computer-aided molecular modeling. Biophys J. 1995; 69(3): 741-753.

Chiu SW, Clark M, Balaji V, Subramaniam S, Scott HL and Jakobsson E.Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys J. 1995; 69(4):1230-1245.

Kozack RE, D'Mello MJ and Subramaniam S. Computer modeling of electrostatic steering and orientational effects in antibody-antigen association. Biophys J. 1995;68(3): 807-814.

Ioerger T, Rendell L and Subramaniam S. Change of representation to improve protein fold-class prediction. Machine Learning Journal 1995; 21:151-176.

Jakobsson E, Subramaniam S and Scott HL. Strategic issues in molecular dynamics simulations of membranes. Beckman Institute Technical Report; June 1995.

Tang L, Ebrey TG, and Subramaniam S. Modeling the structure of visual pigments. Isr J Chem. 1995; 35, 198-209.

Reczko M, Bohr H, Subramaniam S, Pamidinghantam S and Hatzigeorgiou A. Fold-class prediction by neural network. In: Protein Structure Prediction-Past and Present. In: Protein Structure by Distance Analysis, Ed. Bohr H and Brunak S, IOS Press 1994; pp 277-286.

Anchin JM, Mandal C, Culberson C, Subramaniam S and D. S. Linthicum. Computer-aided modeling of the binding site architecture for eight monclonal antibodies that bind a high potency guanidinium sweetener. J Mol Graph. 1994; 12: 257-266.

Susnow R, Schutt C, Rabitz H and Subramaniam S. Conformational analysis of dipeptides - a sensitivity analysis approach. J Comput Chem. 1994 15(9): 947-962.

Slagle SP, Kozack RE and Subramaniam S. Role of electrostatics in antibody-antigen association: anti-hen egg lysozyme/Lysozyme complex (HyHEL-5/HEL) J Biomol Struct Dyn.1994 12: 439-456.

Forsten KE, Kozack RE, Lauffenberger DA and Subramaniam S. Numerical solution of the nonlinear Poisson-Boltzmann equation for a membrane-electrolyte system. J Phys Chem. 1994 98: 5580-5586.

Holst M, Kozack RE, Saied F and Subramaniam S. Protein electrostatics: rapid multigrid-based Newton algorithm for solution of the full nonlinear Poisson-Boltzmann equation. J Biomol Struct Dyn. 1994 11(6): 1437-1445.

Subramaniam S. Protein structure prediction-past and present. In: Protein Structure by Distance Analysis, Ed. Bohr H and Brunak S, IOS Press, 1994, pp 3-14.

Ioerger TR, Rendell LA and Subramaniam S. Searching for representations to improve protein sequence fold-class prediction. Beckman Institute Technical Report; October 1994

Reczko M, Bohr H, Subramaniam S, Pamidinghantam S and Hatzigeorgiou A. Fold-class prediction by neural network. In: Protein Structure Prediction-Past and Present. In: Protein Structure by Distance Analysis, Ed. Bohr H and Brunak S, IOS Press 1994; pp 277-286.

Holst M, Kozack RE, Saied F and Subramaniam S.Treatment of electrostatic effects in proteins: multigrid-based- Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation. Proteins. 1994 18(3): 231-245.

Slagle SP, Kozack RE and Subramaniam S. Role of electrostatics in the association of an electron transfer complex. Beckman Institute Technical Report; November 1994.

Kozack RE and Subramaniam S.Protein Sci, 1993 2: 915-926.

Ioerger TR, Rendell L and Subramaniam S.Constructive induction and protein tertiary structure prediction. Proc Int Conf Intell Syst Mol Biol., 1993;1:198-206.

Forsten KE, Kozack RE, Lauffenburger DA and Subramaniam S. Numerical solution of the nonlinear Posson-Boltzmann equation for membrane-electrolyte system. Beckman Institute Technical Report; December 1993.

Tcheng DK and Subramaniam S. Machine learning approaches to protein feature prediction. Int J Neural Syst.1992 3:183-193.

Lounnas V, Pettitt BM, Findsen L and Subramaniam S. A microscopic view of protein solvation. J Phys Chem 1992 96:7157-7159.

Nell LJ, McCammon JA and Subramaniam S. Anti-insulin antibody. Structure and conformation I. molecular modeling and mechanics. Biopolymers 1992; 32:11-21.

Bassolino D, Bruccoleri RE and Subramaniam S. Modeling the antigen combining site of an anti-dinitrophenyl antibody. Protein Sci. 1992 1:1465-1476.

Subramaniam S, Tcheng D, Hu K, Raghavan H and Rendell L. Knowledge engineering for protein structure and motifs - design of a prototype system. IEEE Computer Society Journal (Proceedings of the Fourth International Conference on Software Engineering and Knowledge Engineering, Capri, Italy), 1992; pp. 420-434.

Rodgers KR, Su C, Subramaniam S and Spiro TG. Hemoglobin T-R quaternary structure and dynamics from simultaneous monitoring of tyrosine and tryptophan UV resonance raman signals. J Am Chem Soc. 1992 114: 3697-3709.

Anchin J, Subramaniam S and Linthicum S. Binding of the neuroleptic drug haloperidol to a monoclonal antibody: refinement of the binding site molecular model using canonical structures. J Mol Recognit 1991 4: 7-15.

Kussie PH, Anchin J, Subramaniam S, Glazel JA and Linthicum DS. Analysis of the binding site architecture of monoclonal antibodies to morphine by using competitive ligand binding and molecular modeling. J Immunol. 1991 Jun 15;146(12):4248-57.

Chiu SW, Jakobsson E, Subramaniam S and McCammon JA. Time correlation analysis of water transport through gramicidin ion channel. Biophys J.; 1991 60: 273-285.

Chiu SW, Nicholson LK, Brenneman MT, Subramaniam S, Teng Q, McCammon JA, Cross TA and Jakobsson E. Molecular dynamics computations and solid state NMR of the gramicidin cation channel. Biophys J. 1991; 60: 974-978.

Shen J, Wong CF, Subramaniam S and McCammon JA. Partial electrostatic charges for the active center of Cu, Zn superoxide dismutase. J Comput Chem. 1990; 11: 346-350.

Shen J, Subramaniam S, Wong CF, and McCammon JA. Superoxide dismutase-fluctuations in the structure and salvation of the active site channel studied by molecular dynamics simulation. Biopolymers 1989; 28: 2085-2096.

Wong CF, Shen J, Subramaniam S, Zheng C, and McCammon JA. Molecular dynamics simulation of protein hydration. J Mol Liq. 1989 41:193-206.

Subramaniam S, McCammon JA and Bacquet RJ. Probing molecular recognition using simulation methods. In: The Immune Response to Structurally Defined Proteins, Ed. S.Smith-Gill and E.Sercarz, pp. 169-176, Adenine Press, 1989.

Chiu SW, Subramaniam S, Jakobsson E and McCammon JA. Water and polypeptide conformations in gramicidin channel-A molecular dynamics study. Biophys J. 1989; 56: 253-261.

Hermans J and Subramaniam S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Isr J Chem. 1988 27:225-227.

Shankar S, Mortier WJ and Ghosh SK. Calculation of atomic charges in large molecules. Ann N Y Acad Sci. 1986; 482: 82- 85.

Mortier WJ, Ghosh SK and Subramaniam S. Electronegativity equalization method and calculation of atomic charges in molecules. J Am Chem Soc. 1986 108: 4315.

Shankar S and Parr RG.Electronegativity and hardness as coordinates in structure stability diagrams. Proc Natl Acad Sci U S A. 1985 82: 264-266.

Subramaniam S and Narasimhan PT. Linear coupled cluster method. I. Exchange-correlation effects in atoms. Phys Rev. 1984; A29: 52-57.

Subramaniam S and Narasimhan PT. Linear coupled cluster method. II. Analysis of exchange-correlation potentials in beryllium and its isoelectronic series. Phys Rev.1984; A29: 58-64.

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