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ORCIDShankar Subramaniam
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- affiliation: University of California, San Diego, USA
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2020 – today
- 2024
[j45]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: 109156 (2024)- 2023
- [c15]Aarav Arora, Kavitha Mukund, Shankar Subramaniam:
A Mechanistic Basis for the Analysis of SARS-CoV-2 Omicron Variant Severity. BIBM 2023: 3340-3347 - 2022
- [j44]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): 3294-3302 (2022)
2010 – 2019
- 2019
- [j43]Sara Rahiminejad, Mano Ram Maurya, Shankar Subramaniam:
Topological and functional comparison of community detection algorithms in biological networks. BMC Bioinform. 20(1): 212:1-212:25 (2019) - [j42]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): 294:1-294:22 (2019) - 2018
- [j41]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): 2009-2016 (2018) - 2017
- [j40]Behrang Asadi, Mano Ram Maurya, Daniel M. Tartakovsky, Shankar Subramaniam:
Doubly Penalized LASSO for Reconstruction of Biological Networks. Proc. IEEE 105(2): 319-329 (2017) - 2016
- [j39]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): 463-470 (2016) - 2015
- [j38]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: 13 (2015) - [j37]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: 96 (2015) - 2014
- [j36]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: 77 (2014) - [j35]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): 1-3 (2014) - [j34]Tejaswini Narayanan, Shankar Subramaniam:
A Newtonian Framework for Community Detection in Undirected Biological Networks. IEEE Trans. Biomed. Circuits Syst. 8(1): 65-73 (2014) - [j33]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): 74-86 (2014) - 2013
- [j32]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): 1832-1833 (2013) - [j31]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): 2735-2743 (2013) - [j30]Shahin Mohammadi, Shankar Subramaniam, Ananth Grama:
Inferring the effective TOR-dependent network: a computational study in yeast. BMC Syst. Biol. 7: 84 (2013) - [c14]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: 214-217 - 2012
- [j29]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): 142-152 (2012) - [j28]Manish Sud, Eoin Fahy, Shankar Subramaniam:
Template-based combinatorial enumeration of virtual compound libraries for lipids. J. Cheminformatics 4: 23 (2012) - [c13]Behrang Asadi, Daniel M. Tartakovsky, Mano Ram Maurya, Shankar Subramaniam:
Doubly Penalized LASSO for Reconstruction of Biological Networks. HISB 2012: 129 - 2011
- [j27]Ashok Reddy Dinasarapu, Brian Saunders, Iley Ozerlat, Kenan Azam, Shankar Subramaniam:
Signaling gateway molecule pages - a data model perspective. Bioinform. 27(12): 1736-1738 (2011) - [j26]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: 26 (2011) - [c12]Tejaswini Narayanan, Shankar Subramaniam:
Community Detection in Biological Networks using a Variational Bayes Approach. BICoB 2011: 61-66 - 2010
- [j25]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) - [c11]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
2000 – 2009
- 2009
- [j24]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: 99 (2009) - 2008
- [j23]Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, Shankar Subramaniam:
The Molecule Pages database. Nucleic Acids Res. 36(Database-Issue): 700-706 (2008) - [c10]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 - [c9]Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, Ananth Grama:
Functional coherence in domain interaction networks. ECCB 2008: 28-34 - 2007
- [j22]Purnima Guda, Chittibabu Guda, Shankar Subramaniam:
Reconstruction of Pathways Associated with Amino Acid Metabolism in Human Mitochondria. Genom. Proteom. Bioinform. 5(3-4): 166-176 (2007) - [j21]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): 527-532 (2007) - [j20]Eoin Fahy, Manish Sud, Dawn Cotter, Shankar Subramaniam:
LIPID MAPS online tools for lipid research. Nucleic Acids Res. 35(Web-Server-Issue): 606-612 (2007) - [j19]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): 35-57 (2007) - [c8]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 - 2006
- [j18]Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam:
Inferring functional information from domain co-evolution. Bioinform. 22(1): 40-49 (2006) - [j17]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: 237 (2006) - [j16]Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
Pairwise Alignment of Protein Interaction Networks. J. Comput. Biol. 13(2): 182-199 (2006) - [j15]Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama:
Detecting Conserved Interaction Patterns in Biological Networks. J. Comput. Biol. 13(7): 1299-1322 (2006) - [j14]Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam:
LMPD: LIPID MAPS proteome database. Nucleic Acids Res. 34(Database-Issue): 507-510 (2006) - 2005
- [j13]Chittibabu Guda, Shankar Subramaniam:
TARGET: a new method for predicting protein subcellular localization in eukaryotes. Bioinform. 21(21): 3963-3969 (2005) - [j12]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): 627-632 (2005) - [c7]Shankar Subramaniam:
Challenges in Biological Data Integration in the Post-genome Sequence Era. DILS 2005: 1 - [c6]Georgios Joannis Pappas Jr., Shankar Subramaniam:
Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction. BSB 2005: 128-140 - 2004
- [j11]Chittibabu Guda, Eoin Fahy, Shankar Subramaniam:
MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinform. 20(11): 1785-1794 (2004) - [j10]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): 3108-3127 (2004) - [j9]Dawn Cotter, Purnima Guda, Eoin Fahy, Shankar Subramaniam:
MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. 32(Database-Issue): 463-467 (2004) - [j8]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): 372-374 (2004) - [j7]Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam:
SledgeHMMER: a web server for batch searching the Pfam database. Nucleic Acids Res. 32(Web-Server-Issue): 542-544 (2004) - [c5]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: 98-104 - 2003
- [j6]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): 149-165 (2003) - 2000
- [j5]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): 121-131 (2000)
1990 – 1999
- 1999
- [j4]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): 1153-1164 (1999) - 1996
- [c4]Shankar Subramaniam, David K. Tcheng, James M. Fenton:
A Knowledge-Based Method for Protein Structure Refinement and Prediction. ISMB 1996: 218-229 - 1995
- [j3]Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam:
Searching for Representations to Improve Protein Sequence Fold-Class Prediction. Mach. Learn. 21(1-2): 151-175 (1995) - 1994
- [j2]Roberta Susnow, Clarence Schutt, Herschel Rabitz, Shankar Subramaniam:
Conformational Study of Dipeptides: A Sensitivity Analysis Approach. J. Comput. Chem. 15(9): 947-962 (1994) - 1993
- [c3]Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam:
Constructive Induction and Protein Tertiary Structure Prediction. ISMB 1993: 198-206 - [c2]Yi-Wen Guu, Shankar Subramaniam:
An Efficient Storage Scheme for Aligned Genetic Sequences. SAC 1993: 139-146 - 1992
- [j1]David K. Tcheng, Shankar Subramaniam:
Machine Approaches to Protein Feature Prediction. Int. J. Neural Syst. 3(Supplement): 183-193 (1992) - [c1]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
Coauthor Index
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