Publications
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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.
. Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology. PLoS Comput Biol. 2013;9(3):e1002960.
. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol. 2013;9(2):e1002887.
. 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.
. Computational approaches for analyzing information flow in biological networks. Sci Signal. 2012;5(220):re1.
. A hybrid model of mammalian cell cycle regulation. PLoS Comput Biol. 2011;7(2):e1001077.
. Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities. Integr Biol (Camb). 2011;3(4):422-38.
. Quantitative phospho-proteomics to investigate the polo-like kinase 1-dependent phospho-proteome. Mol Cell Proteomics. 2011;10(11):M111.008540.
. 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.
. Cellular level models as tools for cytokine design. Biotechnol Prog. 2010;26(4):919-37.
. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One. 2010;5(2):e9202.
. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol. 2009;5:331.
. An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Mol Biosyst. 2009;5(1):59-67.
. MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. Bioinformatics. 2009;25(9):1165-72.
. . Systematic discovery of in vivo phosphorylation networks. Cell. 2007;129(7):1415-26.
. A reductionist's systems biology: opinion. Curr Opin Cell Biol. 2005;17(1):9-11.
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