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

Machine Approaches to Protein Feature Prediction. - David K. Tcheng; Shankar Subramaniam (Int. J. Neural Syst., 1992)

Constructive Induction and Protein Tertiary Structure Prediction. - Thomas R. Ioerger; Larry A. Rendell; Shankar Subramaniam (ISMB, 1993)

An Efficient Storage Scheme for Aligned Genetic Sequences. - Yi-Wen Guu; Shankar Subramaniam (SAC, 1993)

Conformational Study of Dipeptides: A Sensitivity Analysis Approach. - Roberta Susnow; Clarence Schutt; Herschel Rabitz; Shankar Subramaniam (J. Comput. Chem., 1994)

Searching for Representations to Improve Protein Sequence Fold-Class Prediction. - Thomas R. Ioerger; Larry A. Rendell; Shankar Subramaniam (Mach. Learn., 1995)

A Knowledge-Based Method for Protein Structure Refinement and Prediction. - Shankar Subramaniam; David K. Tcheng; James M. Fenton (ISMB, 1996)

Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer. - See-Wing Chiu; Michael M. Clark; Eric Jakobsson; Shankar Subramaniam; H. Larry Scott (J. Comput. Chem., 1999)

Collective motion artifacts arising in long-duration molecular dynamics simulations. - See-Wing Chiu; Michael M. Clark; Shankar Subramaniam; Eric Jakobsson (J. Comput. Chem., 2000)

Neuroscience data and tool sharing - A legal and policy framework for 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; et al. (Neuroinformatics, 2003)

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

MITOPRED: a genome-scale method for prediction of nucleus-encoded mitochondrial proteins. - Chittibabu Guda; Eoin Fahy; Shankar Subramaniam (Bioinform., 2004)

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

SledgeHMMER: a web server for batch searching the Pfam database. - Giridhar Chukkapalli; Chittibabu Guda; Shankar Subramaniam (Nucleic Acids Res., 2004)

MitoProteome: mitochondrial protein sequence database and annotation system. - Dawn Cotter; Purnima Guda; Eoin Fahy; Shankar Subramaniam (Nucleic Acids Res., 2004)

MITOPRED: a web server for the prediction of mitochondrial proteins. - Chittibabu Guda; Purnima Guda; Eoin Fahy; Shankar Subramaniam (Nucleic Acids Res., 2004)

Challenges in Biological Data Integration in the Post-genome Sequence Era. - Shankar Subramaniam (DILS, 2005)

Analysis of the Effects of Multiple Sequence Alignments in Protein Secondary Structure Prediction. - Georgios Joannis Pappas Jr.; Shankar Subramaniam (BSB, 2005)

TARGET: a new method for predicting protein subcellular localization in eukaryotes. - Chittibabu Guda; Shankar Subramaniam (Bioinform., 2005)

VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data. - Albert Hsiao; Trey Ideker; Jerrold M. Olefsky; Shankar Subramaniam (Nucleic Acids Res., 2005)

Inferring functional information from domain co-evolution. - Yohan Kim; Mehmet Koyutürk; Umut Topkara; Ananth Grama; Shankar Subramaniam (Bioinform., 2006)

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. - 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 (BMC Bioinform., 2006)

Detecting Conserved Interaction Patterns in Biological Networks. - Mehmet Koyutürk; Yohan Kim; Shankar Subramaniam; Wojciech Szpankowski; Ananth Grama (J. Comput. Biol., 2006)

Pairwise Alignment of Protein Interaction Networks. - Mehmet Koyutürk; Yohan Kim; Umut Topkara; Shankar Subramaniam; Wojciech Szpankowski; Ananth Grama (J. Comput. Biol., 2006)

LMPD: LIPID MAPS proteome database. - Dawn Cotter; Andreia Maer; Chittibabu Guda; Brian Saunders; Shankar Subramaniam (Nucleic Acids Res., 2006)

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

Reconstruction of Pathways Associated with Amino Acid Metabolism in Human Mitochondria. - Purnima Guda; Chittibabu Guda; Shankar Subramaniam (Genom. Proteom. Bioinform., 2007)

LIPID MAPS online tools for lipid research. - Eoin Fahy; Manish Sud; Dawn Cotter; Shankar Subramaniam (Nucleic Acids Res., 2007)

LMSD: LIPID MAPS structure database. - 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 (Nucleic Acids Res., 2007)

Toward a workbench for rodent brain image data systems architecture and design. - Ivar A. Moene; Shankar Subramaniam; Dmitri Darine; Trygve B. Leergaard; Jan G. Bjaalie (Neuroinformatics, 2007)

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

Functional coherence in domain interaction networks. - Jayesh Pandey; Mehmet Koyutürk; Shankar Subramaniam; Ananth Grama (ECCB, 2008)

The Molecule Pages database. - Brian Saunders; Stephen Lyon; Matthew Day; Brenda Riley; Emily Chenette; Shankar Subramaniam (Nucleic Acids Res., 2008)

An editor for pathway drawing and data visualization in the Biopathways Workbench. - Robert W. Byrnes; Dawn Cotter; Andreia Maer; Joshua Li 001; David Nadeau; Shankar Subramaniam (BMC Syst. Biol., 2009)

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

Identification of Crosstalk between Phosphoprotein Signaling Pathways in RAW 264.7 Macrophage Cells. - Shakti Gupta; Mano Ram Maurya; Shankar Subramaniam (PLoS Comput. Biol., 2010)

Community Detection in Biological Networks using a Variational Bayes Approach. - Tejaswini Narayanan; Shankar Subramaniam (BICoB, 2011)

Signaling gateway molecule pages - a data model perspective. - Ashok Reddy Dinasarapu; Brian Saunders; Iley Ozerlat; Kenan Azam; Shankar Subramaniam (Bioinform., 2011)

Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism. - Shakti Gupta; Mano Ram Maurya; Alfred H. Merrill Jr.; Christopher K. Glass; Shankar Subramaniam (BMC Syst. Biol., 2011)

B-cell Ligand Processing Pathways Detected by Large-scale Comparative Analysis. - Fadi Towfic; Shakti Gupta; Vasant G. Honavar; Shankar Subramaniam (Genom. Proteom. Bioinform., 2012)

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

An information-theoretic algorithm to data-driven genetic pathway interaction network reconstruction of dynamic systems. - Farzaneh Farhangmehr; Daniel M. Tartakovsky; Parastou Sadatmousavi; Mano Ram Maurya; Shankar Subramaniam (BIBM, 2013)

A combined omics study on activated macrophages - enhanced role of STATs in apoptosis, immunity and lipid metabolism. - Ashok Reddy Dinasarapu; Shakti Gupta; Mano Ram Maurya; Eoin Fahy; Jun Min; Manish Sud; Merril J. Gersten; Christopher K. Glass; Shankar Subramaniam (Bioinform., 2013)

CMAP: Complement Map Database. - Kun Yang 003; Ashok Reddy Dinasarapu; Edimara S. Reis; Robert A. DeAngelis; Daniel Ricklin; Shankar Subramaniam; John D. Lambris (Bioinform., 2013)

Inferring the effective TOR-dependent network: a computational study in yeast. - Shahin Mohammadi; Shankar Subramaniam; Ananth Grama (BMC Syst. Biol., 2013)

Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages. - Farzaneh Farhangmehr; Mano Ram Maurya; Daniel M. Tartakovsky; Shankar Subramaniam (BMC Syst. Biol., 2014)

Guest Editorial - Special Issue on '-Omics' Based Companion Diagnostics for Personalized Medicine. - Jie Chen 002; Shankar Subramaniam; David S. Wishart; Stephen T. Wong (IEEE Trans. Biomed. Circuits Syst., 2014)

Time-Varying Causal Inference From Phosphoproteomic Measurements in Macrophage Cells. - Maryam Masnadi-Shirazi; Mano Ram Maurya; Shankar Subramaniam (IEEE Trans. Biomed. Circuits Syst., 2014)

A Newtonian Framework for Community Detection in Undirected Biological Networks. - Tejaswini Narayanan; Shankar Subramaniam (IEEE Trans. Biomed. Circuits Syst., 2014)

Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome. - Traci L. Marin; Brendan Gongol; Marcy Martin; Stephanie J. King; Lemar Smith; David A. Johnson 003; Shankar Subramaniam; Shu Chien; John Shyy (BMC Syst. Biol., 2015)

Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. - Shahin Mohammadi; Baharak Saberidokht; Shankar Subramaniam; Ananth Grama (BMC Syst. Biol., 2015)

Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. - 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 (Nucleic Acids Res., 2016)

Doubly Penalized LASSO for Reconstruction of Biological Networks. - Behrang Asadi; Mano Ram Maurya; Daniel M. Tartakovsky; Shankar Subramaniam (Proc. IEEE, 2017)

Co-Expression Network Approach to Studying the Effects of Botulinum Neurotoxin-A. - Kavitha Mukund; Samuel R. Ward; Richard L. Lieber; Shankar Subramaniam (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Time varying causal network reconstruction of a mouse cell cycle. - Maryam Masnadi-Shirazi; Mano Ram Maurya; Gerald M. Pao; Eugene Ke; Inder M. Verma; Shankar Subramaniam (BMC Bioinform., 2019)

Topological and functional comparison of community detection algorithms in biological networks. - Sara Rahiminejad; Mano Ram Maurya; Shankar Subramaniam (BMC Bioinform., 2019)

Healthcare Innovations to Address the Challenges of the COVID-19 Pandemic. - Metin Akay; Shankar Subramaniam; Colin Brennan; Paolo Bonato; Charlotte Mae K. Waits; Bruce C. Wheeler; Dimitrios I. Fotiadis (IEEE J. Biomed. Health Informatics, 2022)

A Mechanistic Basis for the Analysis of SARS-CoV-2 Omicron Variant Severity. - Aarav Arora; Kavitha Mukund; Shankar Subramaniam (BIBM, 2023)

An efficient solution of the multi-term multi-harmonic electron Boltzmann equation for use in global models. - Joel E. Lynch; Travis R. Sippel; Shankar Subramaniam (Comput. Phys. Commun., 2024)

Playbook workflow builder: Interactive construction of bioinformatics workflows. - 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; et al. (PLoS Comput. Biol., 2025)