SYSTEMS & COMPUTATIONAL MODELING
Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis.
BMC Research Notes. 2015 May 3: 8: 182 PubMed
Mukund K, Subramaniam S.
Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages.
BMC Systems Biology. 2014 Jun 25; 8: 77 PubMed
Farhangmehr F, Maurya MR, Tartakovsky DM, Subramaniam S.
Time-varying causal inference from phosphoproteomic measurements in macrophage cells.
IEEE Transaction on Biomedical Circuits Systems. 2014 Feb; 8 (1):74-86 PubMed
Masnadi-Shirazi M, Maurya MR, Subramaniam S.
A Newtonian framework for community detection in undirected biological networks.
IEEE Transaction on Biomedical Circuits Systems. 2014 Feb; 8 (1): 65-73 PubMed
Narayanan T, Subramaniam S.
Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy.
PLoS One. 2013 Jun 19; 8 (6): e67237 PubMed
Narayanan T, Subramaniam S.
Inferring the effective TOR-dependent network: a computational study in yeast.
BMC Systems Biology. 2013 Aug 30; 7: 84 PubMed
Mohammadi S, Subramaniam S, Grama A.
The poor performance of TMM on microRNA-Seq.
RNA. 2013 Jun; 19 (6): 735-736 PubMed
Garmire LX, Subramaniam S.
Template-based combinatorial enumeration of virtual compound libraries for lipids.
Journal of Cheminformatics. 2012 Sep 25; 4 (1): 23 PubMed
Sud M, Fahy E, Subramaniam S.
Evaluation of normalization methods in mammalian microRNA-Seq data.
RNA. 2012 Jun; 18 (6): 1279-1288 PubMed
Garmire LX, Subramaniam S.
Gene-expression measurement: variance-modeling considerations for robust data analysis.
Nature Immunology. 2012 Feb 16; 13 (3): 199-203 PubMed
Subramaniam S, Hsiao G.
Comparison of statistical and optimisation-based methods for data-driven network reconstruction of biochemical systems.
IET Systems Biology. 2012 Oct; 6(5):155-63 PubMed
Asadi, B, Maurya MR, Tartakovsky DM, Subramaniam S.
Introduction to Network Biology in “Functional Coherence of Molecular Networks to Bioinformatics.”
Springer (2012) SpringerLink
Doubly Penalized LASSO Reconstruction of Biological Networks.
IEEExplore. 2012 Dec 3; 13154844 IEEEXplore Digital Library
Asadi B, Tartakovsky DM, Maurya MR, Subramaniam S.
Stochastic operator-splitting method for reaction-diffusion systems.
The Journal of Chemical Physics. 2012 Nov 14; 137 (18): 184102 PubMed
Choi T, Maurya MR, Tartakovsky DM, Subramaniam S.
Modularity detection in protein-protein interaction networks.
PubMed
Narayanan T, Gersten M, Subramaniam S, Grama A. (2011)
A global clustering algorithm to identify long intergenic non-coding RNA–with applications in mouse macrophages.
PLoS One. 2011; 6 (9): e24051 PubMed
Garmire LX, Garmire DG, Huang W, Yao J, Glass CK, Subramaniam S.
Community detection in biological networks using a variational bayes approach.
Conference Proceddings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology, BICoB-2011. 2011 Mar 23
Narayanan T, Subramaniam S.
Comparison of statistical and optimization-based methods for data-drive network reconstruction of biochemical systems.
Asadi B, Tartakovsky DM, Maurya MR, Subramaniam S. (2010)
Regulatory network of microRNAs in RAW 264.7 macrophage cells.
PubMed
Garmire LX, Shen Z, Briggs S, Yeo G, Subramaniam S, Glass C. (2010)
Stochastic hybrid modeling of intracellular calcium dynamics.
The Journal of Chemical Physics. 2010 Oct 28; 133 (16): 165101 PubMed
Choi T, Maurya MR, Tartakovsky DM, Subramaniam S.
Classification studies based on a spectral representation of DNA.
Journal of Theoretical Biology. 2010 Oct 21; 266 (4): 667-674 PubMed
Bielińska-Waz D, Subramaniam S.
Mixed-integer nonlinear optimisation approach to coarse-graining biochemical networks.
PubMed
Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. (2009)
Functional coherence in domain interaction networks.
PubMed
Pandey J, Koyutürk M, Subramaniam S, Grama A. (2008)
Peak-Finding Refinement in the Chip-SEQ Experiment.
Garmire LX, Garmire DG, Benner C, Ko P, Glass CK, Subramaniam S. (2008)
A kinetic model for calcium dynamics in RAW 264.7 cells: 2. Knockdown response and long-term response.
PubMed
Maurya MR, Subramaniam S. (2007)
A kinetic model for calcium dynamics in RAW 264.7 cells: 1. Mechanisms, parameters, and subpopulational variability.
PubMed
Maurya MR, Subramaniam S. (2007)
Detecting conserved interaction patterns in biological networks.
PubMed
Koyutürk M, Kim Y, Subramaniam S, Szpankowski W, Grama A. (2006)
Reduced-ordered modeling in biochemical networks: Application to the GTPase-cycle signaling module.
PubMed
Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. (2005)
Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction.
PubMed
Bornheimer SJ, Maurya MR, Farquhar MG, Subramaniam S. (2004)