Shankar Subramaniam

Publication Activity (10 Years)

Years Active: 1992-2024
Publications (10 Years): 10

Top Topics

Top Venues

IEEE Trans. Biomed. Circuits Syst.

BMC Syst. Biol.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Joel E. Lynch, Travis R. Sippel, Shankar Subramaniam
An efficient solution of the multi-term multi-harmonic electron Boltzmann equation for use in global models. Comput. Phys. Commun. 299 (2024)
Aarav Arora, Kavitha Mukund, Shankar Subramaniam
A Mechanistic Basis for the Analysis of SARS-CoV-2 Omicron Variant Severity. BIBM (2023)
Metin Akay, Shankar Subramaniam, Colin Brennan, Paolo Bonato, Charlotte Mae K. Waits, Bruce C. Wheeler, Dimitrios I. Fotiadis
Healthcare Innovations to Address the Challenges of the COVID-19 Pandemic. IEEE J. Biomed. Health Informatics 26 (7) (2022)
Maryam Masnadi-Shirazi, Mano Ram Maurya, Gerald M. Pao, Eugene Ke, Inder M. Verma, Shankar Subramaniam
Time varying causal network reconstruction of a mouse cell cycle. BMC Bioinform. 20 (1) (2019)
Sara Rahiminejad, Mano Ram Maurya, Shankar Subramaniam
Topological and functional comparison of community detection algorithms in biological networks. BMC Bioinform. 20 (1) (2019)
Kavitha Mukund, Samuel R. Ward, Richard L. Lieber, Shankar Subramaniam
Co-Expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (6) (2018)
Behrang Asadi, Mano Ram Maurya, Daniel M. Tartakovsky, Shankar Subramaniam
Doubly Penalized LASSO for Reconstruction of Biological Networks. Proc. IEEE 105 (2) (2017)
Manish Sud, Eoin Fahy, Dawn Cotter, Kenan Azam, Ilango Vadivelu, Charles F. Burant, Arthur Edison, Oliver Fiehn, Richard M. Higashi, K. Sreekumaran Nair, Susan Sumner, Shankar Subramaniam
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res. 44 (Database-Issue) (2016)
Traci L. Marin, Brendan Gongol, Marcy Martin, Stephanie J. King, Lemar Smith, David A. Johnson, Shankar Subramaniam, Shu Chien, John Shyy
Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome. BMC Syst. Biol. 9 (2015)
Shahin Mohammadi, Baharak Saberidokht, Shankar Subramaniam, Ananth Grama
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. BMC Syst. Biol. 9 (2015)
Farzaneh Farhangmehr, Mano Ram Maurya, Daniel M. Tartakovsky, Shankar Subramaniam
Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages. BMC Syst. Biol. 8 (2014)
Tejaswini Narayanan, Shankar Subramaniam
A Newtonian Framework for Community Detection in Undirected Biological Networks. IEEE Trans. Biomed. Circuits Syst. 8 (1) (2014)
Maryam Masnadi-Shirazi, Mano Ram Maurya, Shankar Subramaniam
Time-Varying Causal Inference From Phosphoproteomic Measurements in Macrophage Cells. IEEE Trans. Biomed. Circuits Syst. 8 (1) (2014)
Jie Chen, Shankar Subramaniam, David S. Wishart, Stephen T. Wong
Guest Editorial - Special Issue on '-Omics' Based Companion Diagnostics for Personalized Medicine. IEEE Trans. Biomed. Circuits Syst. 8 (1) (2014)
Ashok Reddy Dinasarapu, Shakti Gupta, Mano Ram Maurya, Eoin Fahy, Jun Min, Manish Sud, Merril J. Gersten, Christopher K. Glass, Shankar Subramaniam
A combined omics study on activated macrophages - enhanced role of STATs in apoptosis, immunity and lipid metabolism. Bioinform. 29 (21) (2013)
Shahin Mohammadi, Shankar Subramaniam, Ananth Grama
Inferring the effective TOR-dependent network: a computational study in yeast. BMC Syst. Biol. 7 (2013)
Farzaneh Farhangmehr, Daniel M. Tartakovsky, Parastou Sadatmousavi, Mano Ram Maurya, Shankar Subramaniam
An information-theoretic algorithm to data-driven genetic pathway interaction network reconstruction of dynamic systems. BIBM (2013)
Kun Yang, Ashok Reddy Dinasarapu, Edimara S. Reis, Robert A. DeAngelis, Daniel Ricklin, Shankar Subramaniam, John D. Lambris
CMAP: Complement Map Database. Bioinform. 29 (14) (2013)
Behrang Asadi, Daniel M. Tartakovsky, Mano Ram Maurya, Shankar Subramaniam
Doubly Penalized LASSO for Reconstruction of Biological Networks. HISB (2012)
Fadi Towfic, Shakti Gupta, Vasant G. Honavar, Shankar Subramaniam
B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis. Genom. Proteom. Bioinform. 10 (3) (2012)
Manish Sud, Eoin Fahy, Shankar Subramaniam
Template-based combinatorial enumeration of virtual compound libraries for lipids. J. Cheminformatics 4 (2012)
Shakti Gupta, Mano Ram Maurya, Alfred H. Merrill Jr., Christopher K. Glass, Shankar Subramaniam
Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism. BMC Syst. Biol. 5 (2011)
Tejaswini Narayanan, Shankar Subramaniam
Community Detection in Biological Networks using a Variational Bayes Approach. BICoB (2011)
Ashok Reddy Dinasarapu, Brian Saunders, Iley Ozerlat, Kenan Azam, Shankar Subramaniam
Signaling gateway molecule pages - a data model perspective. Bioinform. 27 (12) (2011)
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)
Shakti Gupta, Mano Ram Maurya, Shankar Subramaniam
Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells. PLoS Comput. Biol. 6 (1) (2010)
Robert W. Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau, Shankar Subramaniam
An editor for pathway drawing and data visualization in the Biopathways Workbench. BMC Syst. Biol. 3 (2009)
Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, Ananth Grama
Functional coherence in domain interaction networks. ECCB (2008)
Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, Shankar Subramaniam
The Molecule Pages database. Nucleic Acids Res. 36 (Database-Issue) (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)
Purnima Guda, Chittibabu Guda, Shankar Subramaniam
Reconstruction of Pathways Associated with Amino Acid Metabolism in Human Mitochondria. Genom. Proteom. Bioinform. 5 (3-4) (2007)
Ivar A. Moene, Shankar Subramaniam, Dmitri Darine, Trygve B. Leergaard, Jan G. Bjaalie
Toward a workbench for rodent brain image data systems architecture and design. Neuroinformatics 5 (1) (2007)
Eoin Fahy, Manish Sud, Dawn Cotter, Shankar Subramaniam
LIPID MAPS online tools for lipid research. Nucleic Acids Res. 35 (Web-Server-Issue) (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 Res. 35 (Database-Issue) (2007)
Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama
Functional annotation of regulatory pathways. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama
Detecting Conserved Interaction Patterns in Biological Networks. J. Comput. Biol. 13 (7) (2006)
Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama
Pairwise Alignment of Protein Interaction Networks. J. Comput. Biol. 13 (2) (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 Bioinform. 7 (2006)
Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam
Inferring functional information from domain co-evolution. Bioinform. 22 (1) (2006)
Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam
LMPD: LIPID MAPS proteome database. Nucleic Acids Res. 34 (Database-Issue) (2006)
Georgios Joannis Pappas Jr., Shankar Subramaniam
Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction. BSB (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 Res. 33 (Web-Server-Issue) (2005)
Shankar Subramaniam
Challenges in Biological Data Integration in the Post-genome Sequence Era. DILS (2005)
Chittibabu Guda, Shankar Subramaniam
TARGET: a new method for predicting protein subcellular localization in eukaryotes. Bioinform. 21 (21) (2005)
Chittibabu Guda, Eoin Fahy, Shankar Subramaniam
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinform. 20 (11) (2004)
Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam
SledgeHMMER: a web server for batch searching the Pfam database. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Dawn Cotter, Purnima Guda, Eoin Fahy, Shankar Subramaniam
MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. 32 (Database-Issue) (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. Bioinform. 20 (17) (2004)
Madhusudan, Ilango 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)
Chittibabu Guda, Purnima Guda, Eoin Fahy, Shankar Subramaniam
MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
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, Raphael Ritz, Viji Ravindranath, Francesco Beltrame, Shun-ichi Amari, Shiro Usui, Soo-Young Lee, Jaap van Pelt, Jan G. Bjaalie, Andrzej Wróbel, Fernando Mira da Silva, Carmen González, Sten Grillner, Paul F. M. J. Verschure, Turgay Dalkara, Robert Bennett, David Willshaw, Stephen H. Koslow, Perry L. Miller, Shankar Subramaniam, Arthur W. Toga
Neuroscience data and tool sharing - A legal and policy framework for neuroinformatics. Neuroinformatics 1 (2) (2003)
See-Wing Chiu, Michael M. Clark, Shankar Subramaniam, Eric Jakobsson
Collective motion artifacts arising in long-duration molecular dynamics simulations. J. Comput. Chem. 21 (2) (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. J. Comput. Chem. 20 (11) (1999)
Shankar Subramaniam, David K. Tcheng, James M. Fenton
A Knowledge-Based Method for Protein Structure Refinement and Prediction. ISMB (1996)
Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam
Searching for Representations to Improve Protein Sequence Fold-Class Prediction. Mach. Learn. 21 (1-2) (1995)
Roberta Susnow, Clarence Schutt, Herschel Rabitz, Shankar Subramaniam
Conformational Study of Dipeptides: A Sensitivity Analysis Approach. J. Comput. Chem. 15 (9) (1994)
Yi-Wen Guu, Shankar Subramaniam
An Efficient Storage Scheme for Aligned Genetic Sequences. SAC (1993)
Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam
Constructive Induction and Protein Tertiary Structure Prediction. ISMB (1993)
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)
David K. Tcheng, Shankar Subramaniam
Machine Approaches to Protein Feature Prediction. Int. J. Neural Syst. 3 (Supplement) (1992)