Shankar Subramaniam

61 papers A 2C 4Misc 1Journal 46Unranked 8

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Playbook workflow builder: Interactive construction of bioinformatics workflows. PLoS Comput. Biol. Daniel J. B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano Ram Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Alexandra Agris, Juncheng Pan, Srinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Sherry L. Jenkins, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma'ayan
2024	J	`jnl`	An efficient solution of the multi-term multi-harmonic electron Boltzmann equation for use in global models. Comput. Phys. Commun. Joel E. Lynch, Travis R. Sippel, Shankar Subramaniam
2023	—	`conf`	A Mechanistic Basis for the Analysis of SARS-CoV-2 Omicron Variant Severity. BIBM Aarav Arora, Kavitha Mukund, Shankar Subramaniam
2022	J	`jnl`	Healthcare Innovations to Address the Challenges of the COVID-19 Pandemic. IEEE J. Biomed. Health Informatics Metin Akay, Shankar Subramaniam, Colin Brennan, Paolo Bonato, Charlotte Mae K. Waits, Bruce C. Wheeler, Dimitrios I. Fotiadis
2019	J	`jnl`	Time varying causal network reconstruction of a mouse cell cycle. BMC Bioinform. Maryam Masnadi-Shirazi, Mano Ram Maurya, Gerald M. Pao, Eugene Ke, Inder M. Verma, Shankar Subramaniam
2019	J	`jnl`	Topological and functional comparison of community detection algorithms in biological networks. BMC Bioinform. Sara Rahiminejad, Mano Ram Maurya, Shankar Subramaniam
2018	J	`jnl`	Co-Expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A. IEEE ACM Trans. Comput. Biol. Bioinform. Kavitha Mukund, Samuel R. Ward, Richard L. Lieber, Shankar Subramaniam
2017	J	`jnl`	Doubly Penalized LASSO for Reconstruction of Biological Networks. Proc. IEEE Behrang Asadi, Mano Ram Maurya, Daniel M. Tartakovsky, Shankar Subramaniam
2016	J	`jnl`	Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res. 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
2015	J	`jnl`	Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome. BMC Syst. Biol. Traci L. Marin, Brendan Gongol, Marcy Martin, Stephanie J. King, Lemar Smith, David A. Johnson, Shankar Subramaniam, Shu Chien, John Shyy
2015	J	`jnl`	Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. BMC Syst. Biol. Shahin Mohammadi, Baharak Saberidokht, Shankar Subramaniam, Ananth Grama
2014	J	`jnl`	A Newtonian Framework for Community Detection in Undirected Biological Networks. IEEE Trans. Biomed. Circuits Syst. Tejaswini Narayanan, Shankar Subramaniam
2014	J	`jnl`	Guest Editorial - Special Issue on '-Omics' Based Companion Diagnostics for Personalized Medicine. IEEE Trans. Biomed. Circuits Syst. Jie Chen, Shankar Subramaniam, David S. Wishart, Stephen T. Wong
2014	J	`jnl`	Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages. BMC Syst. Biol. Farzaneh Farhangmehr, Mano Ram Maurya, Daniel M. Tartakovsky, Shankar Subramaniam
2014	J	`jnl`	Time-Varying Causal Inference From Phosphoproteomic Measurements in Macrophage Cells. IEEE Trans. Biomed. Circuits Syst. Maryam Masnadi-Shirazi, Mano Ram Maurya, Shankar Subramaniam
2013	J	`jnl`	A combined omics study on activated macrophages - enhanced role of STATs in apoptosis, immunity and lipid metabolism. Bioinform. Ashok Reddy Dinasarapu, Shakti Gupta, Mano Ram Maurya, Eoin Fahy, Jun Min, Manish Sud, Merril J. Gersten, Christopher K. Glass, Shankar Subramaniam
2013	—	`conf`	An information-theoretic algorithm to data-driven genetic pathway interaction network reconstruction of dynamic systems. BIBM Farzaneh Farhangmehr, Daniel M. Tartakovsky, Parastou Sadatmousavi, Mano Ram Maurya, Shankar Subramaniam
2013	J	`jnl`	CMAP: Complement Map Database. Bioinform. Kun Yang, Ashok Reddy Dinasarapu, Edimara S. Reis, Robert A. DeAngelis, Daniel Ricklin, Shankar Subramaniam, John D. Lambris
2013	J	`jnl`	Inferring the effective TOR-dependent network: a computational study in yeast. BMC Syst. Biol. Shahin Mohammadi, Shankar Subramaniam, Ananth Grama
2012	J	`jnl`	B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis. Genom. Proteom. Bioinform. Fadi Towfic, Shakti Gupta, Vasant G. Honavar, Shankar Subramaniam
2012	—	`conf`	Doubly Penalized LASSO for Reconstruction of Biological Networks. HISB Behrang Asadi, Daniel M. Tartakovsky, Mano Ram Maurya, Shankar Subramaniam
2012	J	`jnl`	Template-based combinatorial enumeration of virtual compound libraries for lipids. J. Cheminformatics Manish Sud, Eoin Fahy, Shankar Subramaniam
2011	—	`conf`	Community Detection in Biological Networks using a Variational Bayes Approach. BICoB Tejaswini Narayanan, Shankar Subramaniam
2011	J	`jnl`	Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism. BMC Syst. Biol. Shakti Gupta, Mano Ram Maurya, Alfred H. Merrill Jr., Christopher K. Glass, Shankar Subramaniam
2011	J	`jnl`	Signaling gateway molecule pages - a data model perspective. Bioinform. Ashok Reddy Dinasarapu, Brian Saunders, Iley Ozerlat, Kenan Azam, Shankar Subramaniam
2010	C	`conf`	A Clustering Approach to Identify Intergenic Non-coding RNA in Mouse Macrophages. BIBE Lana X. Garmire, Shankar Subramaniam, David G. Garmire, Christopher K. Glass
2010	J	`jnl`	Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells. PLoS Comput. Biol. Shakti Gupta, Mano Ram Maurya, Shankar Subramaniam
2009	J	`jnl`	An editor for pathway drawing and data visualization in the Biopathways Workbench. BMC Syst. Biol. Robert W. Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau, Shankar Subramaniam
2008	C	`conf`	Functional coherence in domain interaction networks. ECCB Jayesh Pandey, Mehmet Koyutürk, Shankar Subramaniam, Ananth Grama
2008	C	`conf`	Peak-Finding Refinement in the Chip-SEQ Experiment. CAINE Lana X. Garmire, David G. Garmire, Chris Benner, Pang Ko, Christopher K. Glass, Shankar Subramaniam
2008	J	`jnl`	The Molecule Pages database. Nucleic Acids Res. Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, Emily Chenette, Shankar Subramaniam
2007	—	`conf`	Functional annotation of regulatory pathways. ISMB/ECCB (Supplement of Bioinformatics) Jayesh Pandey, Mehmet Koyutürk, Yohan Kim, Wojciech Szpankowski, Shankar Subramaniam, Ananth Grama
2007	J	`jnl`	LIPID MAPS online tools for lipid research. Nucleic Acids Res. Eoin Fahy, Manish Sud, Dawn Cotter, Shankar Subramaniam
2007	J	`jnl`	LMSD: LIPID MAPS structure database. Nucleic Acids Res. 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
2007	J	`jnl`	Reconstruction of Pathways Associated with Amino Acid Metabolism in Human Mitochondria. Genom. Proteom. Bioinform. Purnima Guda, Chittibabu Guda, Shankar Subramaniam
2007	J	`jnl`	Toward a workbench for rodent brain image data systems architecture and design. Neuroinformatics Ivar A. Moene, Shankar Subramaniam, Dmitri Darine, Trygve B. Leergaard, Jan G. Bjaalie
2006	J	`jnl`	Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinform. 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
2006	J	`jnl`	Detecting Conserved Interaction Patterns in Biological Networks. J. Comput. Biol. Mehmet Koyutürk, Yohan Kim, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama
2006	J	`jnl`	Inferring functional information from domain co-evolution. Bioinform. Yohan Kim, Mehmet Koyutürk, Umut Topkara, Ananth Grama, Shankar Subramaniam
2006	J	`jnl`	LMPD: LIPID MAPS proteome database. Nucleic Acids Res. Dawn Cotter, Andreia Maer, Chittibabu Guda, Brian Saunders, Shankar Subramaniam
2006	J	`jnl`	Pairwise Alignment of Protein Interaction Networks. J. Comput. Biol. Mehmet Koyutürk, Yohan Kim, Umut Topkara, Shankar Subramaniam, Wojciech Szpankowski, Ananth Grama
2005	—	`conf`	Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction. BSB Georgios Joannis Pappas Jr., Shankar Subramaniam
2005	—	`conf`	Challenges in Biological Data Integration in the Post-genome Sequence Era. DILS Shankar Subramaniam
2005	J	`jnl`	TARGET: a new method for predicting protein subcellular localization in eukaryotes. Bioinform. Chittibabu Guda, Shankar Subramaniam
2005	J	`jnl`	VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. Nucleic Acids Res. Albert Hsiao, Trey Ideker, Jerrold M. Olefsky, Shankar Subramaniam
2004	J	`jnl`	MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. Bioinform. Chittibabu Guda, Eoin Fahy, Shankar Subramaniam
2004	J	`jnl`	MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Res. Chittibabu Guda, Purnima Guda, Eoin Fahy, Shankar Subramaniam
2004	J	`jnl`	MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res. Dawn Cotter, Purnima Guda, Eoin Fahy, Shankar Subramaniam
2004	J	`jnl`	SledgeHMMER: a web server for batch searching the Pfam database. Nucleic Acids Res. Giridhar Chukkapalli, Chittibabu Guda, Shankar Subramaniam
2004	—	`conf`	The Laboratory Information Management System (LIMS) for Handling the Heterogeneous Data from High Throughput Experiments in the Post-Genome Sequencing Era. METMBS Madhusudan, Ilango Vadivelu, Lothar Krause, Yuhong Ning, Stephen Lyon, Peter Morrison, Lonnie Sorrells, Ron Taussig, Shankar Subramaniam
2004	J	`jnl`	Variance-modeled posterior inference of microarray data: detecting gene-expression changes in 3T3-L1 adipocytes. Bioinform. Albert Hsiao, D. S. Worrall, Jerrold M. Olefsky, Shankar Subramaniam
2003	J	`jnl`	Neuroscience data and tool sharing - A legal and policy framework for neuroinformatics. Neuroinformatics 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
2000	J	`jnl`	Collective motion artifacts arising in long-duration molecular dynamics simulations. J. Comput. Chem. See-Wing Chiu, Michael M. Clark, Shankar Subramaniam, Eric Jakobsson
1999	J	`jnl`	Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer. J. Comput. Chem. See-Wing Chiu, Michael M. Clark, Eric Jakobsson, Shankar Subramaniam, H. Larry Scott
1996	A	`conf`	A Knowledge-Based Method for Protein Structure Refinement and Prediction. ISMB Shankar Subramaniam, David K. Tcheng, James M. Fenton
1995	J	`jnl`	Searching for Representations to Improve Protein Sequence Fold-Class Prediction. Mach. Learn. Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam
1994	J	`jnl`	Conformational Study of Dipeptides: A Sensitivity Analysis Approach. J. Comput. Chem. Roberta Susnow, Clarence Schutt, Herschel Rabitz, Shankar Subramaniam
1993	Misc	`conf`	An Efficient Storage Scheme for Aligned Genetic Sequences. SAC Yi-Wen Guu, Shankar Subramaniam
1993	A	`conf`	Constructive Induction and Protein Tertiary Structure Prediction. ISMB Thomas R. Ioerger, Larry A. Rendell, Shankar Subramaniam
1992	C	`conf`	Knowledge Engineering for Protein Structure and Motifs: Design of a Prototype System. SEKE Shankar Subramaniam, David K. Tcheng, K. Hu, Harish Ragavan, Larry A. Rendell
1992	J	`jnl`	Machine Approaches to Protein Feature Prediction. Int. J. Neural Syst. David K. Tcheng, Shankar Subramaniam