Publications
] . Understanding effects of matrix protease and matrix organization on directional persistence and translational speed in three-dimensional cell migration. Ann Biomed Eng. 2007;35(1):91-100.
. 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.
. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One. 2010;5(2):e9202.
. Stimulus design for model selection and validation in cell signaling. PLoS Comput Biol. 2008;4(2):e30.
. Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol. 2013;20(2):124-36.
. Signaling network state predicts twist-mediated effects on breast cell migration across diverse growth factor contexts. Mol Cell Proteomics. 2011;10(11):M111.008433.
. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell. 2012;149(4):780-94.
. A reductionist's systems biology: opinion. Curr Opin Cell Biol. 2005;17(1):9-11.
. Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding. Mol Cell. 2011;43(5):723-37.
. Quantitative modeling perspectives on the ErbB system of cell regulatory processes. Exp Cell Res. 2009;315(4):717-25.
. Quantitative analysis of gradient sensing: towards building predictive models of chemotaxis in cancer. Curr Opin Cell Biol. 2012;24(2):284-91.
. Predicting cancer drug mechanisms of action using molecular network signatures. Mol Biosyst. 2013;9(7):1604-19.
. Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth. Mol Biosyst. 2010;6(7):1227-37.
. The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS Comput Biol. 2007;3(12):e242.
. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature. 2009;459(7245):428-32.
. A Multivariate Computational Method to Analyze High-Content RNAi Screening Data. J Biomol Screen. 2015;20(8):985-97.
. Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci. 2013;126(Pt 9):1913-21.
. Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol. 2007;3(1):e4.
. A Mena invasion isoform potentiates EGF-induced carcinoma cell invasion and metastasis. Dev Cell. 2008;15(6):813-28.
. MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets. PLoS Comput Biol. 2011;7(7):e1002119.
. Logic-based models for the analysis of cell signaling networks. Biochemistry. 2010;49(15):3216-24.
. Intratumor heterogeneity alters most effective drugs in designed combinations. Proc Natl Acad Sci U S A. 2014;111(29):10773-8.
. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal. 2009;2(81):ra40.
. 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.
. A hybrid model of mammalian cell cycle regulation. PLoS Comput Biol. 2011;7(2):e1001077.
