Publications
A Multivariate Computational Method to Analyze High-Content RNAi Screening Data. J Biomol Screen. 2015;20(8):985-97.
. SAMNetWeb: identifying condition-specific networks linking signaling and transcription. Bioinformatics. 2015;31(7):1124-6.
. Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology. PLoS Comput Biol. 2013;9(3):e1002960.
. Predicting cancer drug mechanisms of action using molecular network signatures. Mol Biosyst. 2013;9(7):1604-19.
. Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol. 2013;20(2):124-36.
. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol (Camb). 2012;4(11):1415-27.
. Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol. 2012;110:57-80.
. MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PLoS Comput Biol. 2011;7(7):e1002119.
. Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities. Integr Biol (Camb). 2011;3(4):422-38.
. Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput Biol. 2011;7(3):e1001099.
. Integrated data management and validation platform for phosphorylated tandem mass spectrometry data. Proteomics. 2010;10(19):3515-24.
. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One. 2010;5(2):e9202.
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Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol. 2006;2:54.
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