Shankar Subramaniam

Fadi Towfic, Shakti Gupta, Vasant Honavar, Shankar Subramaniam: B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis. Genomics, Proteomics & Bioinformatics 10(3): 142-152 (2012)

Manish Sud, Eoin Fahy, Shankar Subramaniam: Template-based combinatorial enumeration of virtual compound libraries for lipids. J. Cheminformatics 4: 23 (2012)

Behrang Asadi, Daniel M. Tartakovsky, Mano Ram Maurya, Shankar Subramaniam: Doubly Penalized LASSO for Reconstruction of Biological Networks. HISB 2012: 129

Ashok Reddy Dinasarapu, Brian Saunders, Iley Ozerlat, Kenan Azam, Shankar Subramaniam: Signaling gateway molecule pages - a data model perspective. Bioinformatics 27(12): 1736-1738 (2011)

Tejaswini Narayanan, Shankar Subramaniam: Community Detection in Biological Networks using a Variational Bayes Approach. BICoB 2011: 61-66

Shakti Gupta, Mano Ram Maurya, Shankar Subramaniam: Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells. PLoS Computational Biology 6(1) (2010)

Lana X. Garmire, Shankar Subramaniam, David G. Garmire, Christopher K. Glass: A Clustering Approach to Identify Intergenic Non-coding RNA in Mouse Macrophages. BIBE 2010: 1-6

Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, Shankar Subramaniam: The Molecule Pages database. Nucleic Acids Research 36(Database-Issue): 700-706 (2008)

Lana X. Garmire, David G. Garmire, Chris Benner, Pang Ko, Christopher K. Glass, Shankar Subramaniam: Peak-Finding Refinement in the Chip-SEQ Experiment. CAINE 2008: 20-25

Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, Ananth Grama: Functional coherence in domain interaction networks. ECCB 2008: 28-34

Purnima Guda, Chittibabu Guda, Shankar Subramaniam: Reconstruction of Pathways Associated with Amino Acid Metabolism in Human Mitochondria. Genomics, Proteomics & Bioinformatics 5(3-4): 166-176 (2007)

Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward A. Dennis, Christopher K. Glass, Alfred H. Merrill Jr., Robert C. Murphy, Christian R. H. Raetz, David W. Russell, Shankar Subramaniam: LMSD: LIPID MAPS structure database. Nucleic Acids Research 35(Database-Issue): 527-532 (2007)

Eoin Fahy, Manish Sud, Dawn Cotter, Shankar Subramaniam: LIPID MAPS online tools for lipid research. Nucleic Acids Research 35(Web-Server-Issue): 606-612 (2007)

Ivar A. Moene, Shankar Subramaniam, Dmitri Darin, Trygve B. Leergaard, Jan G. Bjaalie: Toward a workbench for rodent brain image data systems architecture and design. Neuroinformatics 5(1): 35-57 (2007)

Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama: Functional annotation of regulatory pathways. ISMB/ECCB (Supplement of Bioinformatics) 2007: 377-386

Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam: Inferring functional information from domain co-evolution. Bioinformatics 22(1): 40-49 (2006)

Jamie A. Lee, Robert S. Sinkovits, Dennis Mock, Eva L. Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C. Hsueh, Sangdun Choi, Shankar Subramaniam, Richard H. Scheuermann: 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 (2006)

Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama: Pairwise Alignment of Protein Interaction Networks. Journal of Computational Biology 13(2): 182-199 (2006)

Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama: Detecting Conserved Interaction Patterns in Biological Networks. Journal of Computational Biology 13(7): 1299-1322 (2006)

Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam: LMPD: LIPID MAPS proteome database. Nucleic Acids Research 34(Database-Issue): 507-510 (2006)

Chittibabu Guda, Shankar Subramaniam: TARGET: a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics 21(21): 3963-3969 (2005)

Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, Shankar Subramaniam: VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Research 33(Web-Server-Issue): 627-632 (2005)

Shankar Subramaniam: Challenges in Biological Data Integration in the Post-genome Sequence Era. DILS 2005: 1

Georgios Joannis Pappas Jr., Shankar Subramaniam: Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction. BSB 2005: 128-140

Chittibabu Guda, Eoin Fahy, Shankar Subramaniam: MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinformatics 20(11): 1785-1794 (2004)

Albert Hsiao, D. S. Worrall, Jerrold M. Olefsky, Shankar Subramaniam: Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes. Bioinformatics 20(17): 3108-3127 (2004)

Dawn Cotter, Purnima Guda, Eoin Fahy, Shankar Subramaniam: MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Research 32(Database-Issue): 463-467 (2004)

Chittibabu Guda, Purnima Guda, Eoin Fahy, Shankar Subramaniam: MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Research 32(Web-Server-Issue): 372-374 (2004)

Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam: SledgeHMMER: a web server for batch searching the Pfam database. Nucleic Acids Research 32(Web-Server-Issue): 542-544 (2004)

Madhusudan, Illango Vadivelu, Lothar Krause, Yuhong Ning, Stephen Lyon, Peter Morrison, Lonnie Sorrells, Ron Taussig, Shankar Subramaniam: The Laboratory Information Management System (LIMS) for Handling the Heterogeneous Data from High Throughput Experiments in the Post-Genome Sequencing Era. METMBS 2004: 98-104

Peter Eckersley, Gary F. Egan, Erik De Schutter, Yiyuan Tang, Mirko Novak, Václav Sebesta, Line Matthiessen, Iiro P. Jääskeläinen, Ulla Ruotsalainen, Andreas V. M. Herz, K. Peter Hoffmann, Iiro P. Jaaskelainen, Stephen H. Koslow, Soo-Young Lee, Line Matthiessen, Perry L. Miller, Fernando Mira da Silva, Mirko Novak, Viji Ravindranath, Raphael Ritz, Ulla Ruotsalainen, Shankar Subramaniam, Arthur W. Toga, Shiro Usui, Jaap van Pelt, Paul F. M. J. Verschure, David Willshaw, Andrzej Wróbel, Yiyuan Tang: Neuroscience data and tool sharing - A legal and policy framework for neuroinformatics. Neuroinformatics 1(2): 149-165 (2003)

See-Wing Chiu, Michael M. Clark, Shankar Subramaniam, Eric Jakobsson: Collective motion artifacts arising in long-duration molecular dynamics simulations. Journal of Computational Chemistry 21(2): 121-131 (2000)

See-Wing Chiu, Michael M. Clark, Eric Jakobsson, Shankar Subramaniam, H. Larry Scott: Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer. Journal of Computational Chemistry 20(11): 1153-1164 (1999)

Shankar Subramaniam, David K. Tcheng, James M. Fenton: A Knowledge-Based Method for Protein Structure Refinement and Prediction. ISMB 1996: 218-229

Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam: Searching for Representations to Improve Protein Sequence Fold-Class Prediction. Machine Learning 21(1-2): 151-175 (1995)

Roberta Susnow, Clarence Schutt, Herschel Rabitz, Shankar Subramaniam: Conformational Study of Dipeptides: A Sensitivity Analysis Approach. Journal of Computational Chemistry 15(9): 947-962 (1994)

Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam: Constructive Induction and Protein Tertiary Structure Prediction. ISMB 1993: 198-206

Yi-Wen Guu, Shankar Subramaniam: An Efficient Storage Scheme for Aligned Genetic Sequences. SAC 1993: 139-146

David K. Tcheng, Shankar Subramaniam: Machine Approaches to Protein Feature Prediction. Int. J. Neural Syst. 3(Supplement): 183-193 (1992)

Shankar Subramaniam, David K. Tcheng, K. Hu, Harish Ragavan, Larry A. Rendell: Knowledge Engineering for Protein Structure and Motifs: Design of a Prototype System. SEKE 1992: 420-435