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Shankar Subramaniam
Person information
- 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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last updated on 2024-08-05 20:22 CEST by the dblp team
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