Publications

Found 46 results
Title Type [ Year(Desc)]
Filters: Keyword is Models, Biological  [Clear All Filters]
2005
Zaman MH, Kamm RD, Matsudaira P, Lauffenburger DA. Computational model for cell migration in three-dimensional matrices. Biophys J. 2005;89(2):1389-97.
Sorger PK. A reductionist's systems biology: opinion. Curr Opin Cell Biol. 2005;17(1):9-11.
2006
Janes KA, Yaffe MB. Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol. 2006;7(11):820-8.
2007
Kharait S, Hautaniemi S, Wu S, Iwabu A, Lauffenburger DA, Wells A. Decision tree modeling predicts effects of inhibiting contractility signaling on cell motility. BMC Syst Biol. 2007;1:9.
Kumar N, Wolf-Yadlin A, White FM, Lauffenburger DA. Modeling HER2 effects on cell behavior from mass spectrometry phosphotyrosine data. PLoS Comput Biol. 2007;3(1):e4.
Wilkins AK, Barton PI, Tidor B. The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS Comput Biol. 2007;3(12):e242.
Zaman MH, Matsudaira P, Lauffenburger DA. 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.
2008
Janes KA, Reinhardt HC, Yaffe MB. Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell. 2008;135(2):343-54.
Kim H-D, Guo TW, Wu AP, Wells A, Gertler FB, Lauffenburger DA. Epidermal growth factor-induced enhancement of glioblastoma cell migration in 3D arises from an intrinsic increase in speed but an extrinsic matrix- and proteolysis-dependent increase in persistence. Mol Biol Cell. 2008;19(10):4249-59.
Xu L, Shen SS, Hoshida Y, Subramanian A, Ross K, Brunet J-P, Wagner SN, Ramaswamy S, Mesirov JP, Hynes RO. Gene expression changes in an animal melanoma model correlate with aggressiveness of human melanoma metastases. Mol Cancer Res. 2008;6(5):760-9.
Philippar U, Roussos ET, Oser M, Yamaguchi H, Kim H-D, Giampieri S, Wang Y, Goswami S, Wyckoff JB, Lauffenburger DA, Sahai E, Condeelis JS, Gertler FB. A Mena invasion isoform potentiates EGF-induced carcinoma cell invasion and metastasis. Dev Cell. 2008;15(6):813-28.
Apgar JF, Toettcher JE, Endy D, White FM, Tidor B. Stimulus design for model selection and validation in cell signaling. PLoS Comput Biol. 2008;4(2):e30.
2009
Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol. 2009;5:331.
Toettcher JE, Loewer A, Ostheimer GJ, Yaffe MB, Tidor B, Lahav G. Distinct mechanisms act in concert to mediate cell cycle arrest. Proc Natl Acad Sci U S A. 2009;106(3):785-90.
Hori Y, Stern PJ, Hynes RO, Irvine DJ. Engulfing tumors with synthetic extracellular matrices for cancer immunotherapy. Biomaterials. 2009;30(35):6757-67.
Kishi K, van Vugt MATM, Okamoto K, Hayashi Y, Yaffe MB. Functional dynamics of Polo-like kinase 1 at the centrosome. Mol Cell Biol. 2009;29(11):3134-50.
Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA. Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling. PLoS Comput Biol. 2009;5(4):e1000340.
Huang S-SC, Fraenkel E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal. 2009;2(81):ra40.
Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature. 2009;459(7245):428-32.
Lazzara MJ, Lauffenburger DA. Quantitative modeling perspectives on the ErbB system of cell regulatory processes. Exp Cell Res. 2009;315(4):717-25.
2010
Kreeger PK, Lauffenburger DA. Cancer systems biology: a network modeling perspective. Carcinogenesis. 2010;31(1):2-8.
Radhakrishnan ML, Tidor B. Cellular level models as tools for cytokine design. Biotechnol Prog. 2010;26(4):919-37.
Chen WW, Niepel M, Sorger PK. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev. 2010;24(17):1861-75.
Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA. Logic-based models for the analysis of cell signaling networks. Biochemistry. 2010;49(15):3216-24.
Huang PH, Miraldi ER, Xu AM, Kundukulam VA, Del Rosario AM, Flynn RA, Cavenee WK, Furnari FB, White FM. Phosphotyrosine signaling analysis of site-specific mutations on EGFRvIII identifies determinants governing glioblastoma cell growth. Mol Biosyst. 2010;6(7):1227-37.

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