{"id":192,"date":"2017-03-23T11:30:31","date_gmt":"2017-03-23T18:30:31","guid":{"rendered":"https:\/\/genome.ucsd.edu\/?page_id=192"},"modified":"2022-10-24T09:01:57","modified_gmt":"2022-10-24T16:01:57","slug":"publications","status":"publish","type":"page","link":"https:\/\/genome.ucsd.edu\/index.php\/research\/systems-computational-modeling\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
SYSTEMS & COMPUTATIONAL MODELING<\/span><\/h5>\n

Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis.<\/b><\/span>
\nBMC Research Notes. 2015 May 3: 8: 182 <\/span> PubMed<\/span><\/a><\/b><\/span><\/p>\n

Mukund K, Subramaniam S.<\/p>\n

Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages.<\/b><\/span>
\nBMC Systems Biology. 2014 Jun 25; 8: 77 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Farhangmehr F, Maurya MR, Tartakovsky DM, Subramaniam S.<\/p>\n

Time-varying causal inference from phosphoproteomic measurements in macrophage cells.<\/b><\/span>
\nIEEE Transaction on Biomedical Circuits Systems. 2014 Feb; 8 (1):74-86 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Masnadi-Shirazi M, Maurya MR, Subramaniam S.<\/p>\n

A Newtonian framework for community detection in undirected biological networks.<\/b><\/span>
\nIEEE Transaction on Biomedical Circuits Systems. 2014 Feb; 8 (1): 65-73 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Narayanan T, Subramaniam S.<\/p>\n

Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy.<\/b><\/span>
\nPLoS One. 2013 Jun 19; 8 (6): e67237 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Narayanan T, Subramaniam S.<\/p>\n

Inferring the effective TOR-dependent network: a computational study in yeast.<\/b><\/span>
\nBMC Systems Biology. 2013 Aug 30; 7: 84 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Mohammadi S, Subramaniam S, Grama A.<\/p>\n

The poor performance of TMM on microRNA-Seq.<\/b><\/span>
\nRNA. 2013 Jun; 19 (6): 735-736 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Garmire LX, Subramaniam S.<\/p>\n

Template-based combinatorial enumeration of virtual compound libraries for lipids.<\/b><\/span>
\nJournal of Cheminformatics. 2012 Sep 25; 4 (1): 23 PubMed<\/span><\/a><\/span><\/p>\n

Sud M, Fahy E, Subramaniam S.<\/p>\n

Evaluation of normalization methods in mammalian microRNA-Seq data.<\/b><\/span>
\nRNA. 2012 Jun; 18 (6): 1279-1288 PubMed<\/span><\/a><\/span><\/p>\n

Garmire LX, Subramaniam S.<\/p>\n

Gene-expression measurement: variance-modeling considerations for robust data analysis.<\/b><\/span>
\nNature Immunology. 2012 Feb 16; 13 (3): 199-203 PubMed<\/span><\/a><\/span><\/p>\n

Subramaniam S, Hsiao G.<\/p>\n

Comparison of statistical and optimisation-based methods for data-driven network reconstruction of biochemical systems.<\/b><\/span>
\nIET Systems Biology. 2012 Oct; 6(5):155-63 PubMed<\/span><\/a><\/span><\/p>\n

Asadi, B, Maurya MR, Tartakovsky DM, Subramaniam S.<\/p>\n

Introduction to Network Biology in “Functional Coherence of Molecular Networks to Bioinformatics.”<\/b><\/span>
\nSpringer (2012) SpringerLink<\/span><\/a><\/span><\/p>\n

Doubly Penalized LASSO Reconstruction of Biological Networks.<\/b><\/span>
\nIEEExplore. 2012 Dec 3; 13154844 IEEEXplore Digital Library<\/span><\/a><\/span><\/p>\n

Asadi B, Tartakovsky DM, Maurya MR, Subramaniam S.<\/p>\n

Stochastic operator-splitting method for reaction-diffusion systems.<\/b><\/span>
\nThe Journal of Chemical Physics. 2012 Nov 14; 137 (18): 184102 PubMed<\/span><\/a><\/span><\/p>\n

Choi T, Maurya MR, Tartakovsky DM, Subramaniam S.<\/p>\n

Modularity detection in protein-protein interaction networks.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Narayanan T, Gersten M, Subramaniam S, Grama A. (2011)<\/p>\n

A global clustering algorithm to identify long intergenic non-coding RNA–with applications in mouse macrophages.<\/b><\/span>
\nPLoS One. 2011; 6 (9): e24051 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Garmire LX, Garmire DG, Huang W, Yao J, Glass CK, Subramaniam S.<\/p>\n

Community detection in biological networks using a variational bayes approach.<\/b><\/span>
\nConference Proceddings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology, BICoB-2011. 2011 Mar 23<\/span><\/p>\n

Narayanan T, Subramaniam S.<\/p>\n

Comparison of statistical and optimization-based methods for data-drive network reconstruction of biochemical systems.<\/b><\/span><\/p>\n

Asadi B, Tartakovsky DM, Maurya MR, Subramaniam S. (2010)<\/p>\n

Regulatory network of microRNAs in RAW 264.7 macrophage cells.<\/b><\/span>
\n PubMed<\/span><\/a><\/span><\/p>\n

Garmire LX, Shen Z, Briggs S, Yeo G, Subramaniam S, Glass C.\u00a0 (2010)<\/p>\n

Stochastic hybrid modeling of intracellular calcium dynamics.<\/b><\/span>
\nThe Journal of Chemical Physics. 2010 Oct 28; 133 (16): 165101 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Choi T, Maurya MR, Tartakovsky DM, Subramaniam S.<\/p>\n

Classification studies based on a spectral representation of DNA.<\/b><\/span>
\nJournal of Theoretical Biology. 2010 Oct 21; 266 (4): 667-674 PubMed<\/span><\/a><\/b><\/span><\/p>\n

Bieli\u0144ska-Waz D, Subramaniam S.<\/p>\n

Mixed-integer nonlinear optimisation approach to coarse-graining biochemical networks.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. (2009)<\/p>\n

Functional coherence in domain interaction networks.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Pandey J, Koyut\u00fcrk M, Subramaniam S, Grama A. (2008)<\/p>\n

Peak-Finding Refinement in the Chip-SEQ Experiment.<\/b><\/span><\/p>\n

Garmire LX, Garmire DG, Benner C, Ko P, Glass CK, Subramaniam S. (2008)<\/p>\n

A kinetic model for calcium dynamics in RAW 264.7 cells: 2. Knockdown response and long-term response.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Maurya MR, Subramaniam S. (2007)<\/p>\n

A kinetic model for calcium dynamics in RAW 264.7 cells: 1. Mechanisms, parameters, and subpopulational variability.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Maurya MR, Subramaniam S. (2007)<\/p>\n

Detecting conserved interaction patterns in biological networks.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Koyut\u00fcrk M, Kim Y, Subramaniam S, Szpankowski W, Grama A. (2006)<\/p>\n

Reduced-ordered modeling in biochemical networks: Application to the GTPase-cycle signaling module.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Maurya MR, Bornheimer SJ, Venkatasubramanian V, Subramaniam S. (2005)<\/p>\n

Computational modeling reveals how interplay between components of a GTPase-cycle module regulates signal transduction.<\/b><\/span>
\n PubMed<\/span><\/a><\/b><\/span><\/p>\n

Bornheimer SJ, Maurya MR, Farquhar MG, Subramaniam S. (2004)<\/p>\n","protected":false},"excerpt":{"rendered":"

SYSTEMS & COMPUTATIONAL MODELING Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis. BMC Research Notes. 2015 May 3: 8: […]<\/p>\n","protected":false},"author":10,"featured_media":0,"parent":70,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/page_fullwidth.php","meta":{"footnotes":""},"class_list":["post-192","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/192","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/comments?post=192"}],"version-history":[{"count":9,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/192\/revisions"}],"predecessor-version":[{"id":1357,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/192\/revisions\/1357"}],"up":[{"embeddable":true,"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/pages\/70"}],"wp:attachment":[{"href":"https:\/\/genome.ucsd.edu\/index.php\/wp-json\/wp\/v2\/media?parent=192"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}