Publications
Efficient Bayesian estimates for discrimination among topologically different systems biology models. Mol Biosyst. 2015;11(2):574-84.
. A Multivariate Computational Method to Analyze High-Content RNAi Screening Data. J Biomol Screen. 2015;20(8):985-97.
. Equilibrium and dynamic design principles for binding molecules engineered for reagentless biosensors. Anal Biochem. 2014;460:9-15.
. Intratumor heterogeneity alters most effective drugs in designed combinations. Proc Natl Acad Sci U S A. 2014;111(29):10773-8.
. ADAM-10 and -17 regulate endometriotic cell migration via concerted ligand and receptor shedding feedback on kinase signaling. Proc Natl Acad Sci U S A. 2013;110(22):E2074-83.
. Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci. 2013;126(Pt 9):1913-21.
. 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.
. Combined experimental and computational analysis of DNA damage signaling reveals context-dependent roles for Erk in apoptosis and G1/S arrest after genotoxic stress. Mol Syst Biol. 2012;8:568.
. Exploring the gap between dynamic and constraint-based models of metabolism. Metab Eng. 2012;14(2):112-9.
. Quantitative analysis of gradient sensing: towards building predictive models of chemotaxis in cancer. Curr Opin Cell Biol. 2012;24(2):284-91.
. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell. 2012;149(4):780-94.
. Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res. 2011;71(16):5400-11.
. A dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition. PLoS Comput Biol. 2011;7(2):e1001085.
. A hybrid model of mammalian cell cycle regulation. PLoS Comput Biol. 2011;7(2):e1001077.
. In vivo systems analysis identifies spatial and temporal aspects of the modulation of TNF-α-induced apoptosis and proliferation by MAPKs. Sci Signal. 2011;4(165):ra16.
. MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PLoS Comput Biol. 2011;7(7):e1002119.
. Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding. Mol Cell. 2011;43(5):723-37.
. Signaling network state predicts twist-mediated effects on breast cell migration across diverse growth factor contexts. Mol Cell Proteomics. 2011;10(11):M111.008433.
. 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.
. Cancer systems biology: a network modeling perspective. Carcinogenesis. 2010;31(1):2-8.
. Cellular level models as tools for cytokine design. Biotechnol Prog. 2010;26(4):919-37.
. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev. 2010;24(17):1861-75.
. Logic-based models for the analysis of cell signaling networks. Biochemistry. 2010;49(15):3216-24.
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