Publications

Found 220 results
Title [ Type(Asc)] Year
Journal Article
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.
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.
Yu M, Mazor T, Huang H, Huang H-T, Kathrein KL, Woo AJ, Chouinard CR, Labadorf A, Akie TE, Moran TB, Xie H, Zacharek S, Taniuchi I, Roeder RG, Kim CF, Zon LI, Fraenkel E, Cantor AB. Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. Mol Cell. 2012;45(3):330-43.
Haigis KM, Kendall KR, Wang Y, Cheung A, Haigis MC, Glickman JN, Niwa-Kawakita M, Sweet-Cordero A, Sebolt-Leopold J, Shannon KM, Settleman J, Giovannini M, Jacks T. Differential effects of oncogenic K-Ras and N-Ras on proliferation, differentiation and tumor progression in the colon. Nat Genet. 2008;40(5):600-8.
Berchowitz LE, Gajadhar AS, van Werven FJ, De Rosa AA, Samoylova ML, Brar GA, Xu Y, Xiao C, Futcher B, Weissman JS, White FM, Amon A. A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Genes Dev. 2013;27(19):2147-63.
Pritchard JR, Bruno PM, Gilbert LA, Capron KL, Lauffenburger DA, Hemann MT. Defining principles of combination drug mechanisms of action. Proc Natl Acad Sci U S A. 2013;110(2):E170-9.
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.
Janes KA, Yaffe MB. Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol. 2006;7(11):820-8.
Hu Y, Atukorale PU, Lu JJ, Moon JJ, Um SH, Cho EC, Wang Y, Chen J, Irvine DJ. Cytosolic delivery mediated via electrostatic surface binding of protein, virus, or siRNA cargos to pH-responsive core-shell gel particles. Biomacromolecules. 2009;10(4):756-65.
Janes KA, Reinhardt HC, Yaffe MB. Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell. 2008;135(2):343-54.
Liu H, Ong S-E, Badu-Nkansah K, Schindler J, White FM, Hynes RO. CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma metastasis. Proc Natl Acad Sci U S A. 2011;108(4):1379-84.
Buck LD, Inman SW, Rusyn I, Griffith LG. Co-regulation of primary mouse hepatocyte viability and function by oxygen and matrix. Biotechnol Bioeng. 2014;111(5):1018-27.
Hagen DR, White JK, Tidor B. Convergence in parameters and predictions using computational experimental design. Interface Focus. 2013;3(4):20130008.
Curran TG, Bryson BD, Reigelhaupt M, Johnson H, White FM. Computer aided manual validation of mass spectrometry-based proteomic data. Methods. 2013;61(3):219-26.
Zaman MH, Kamm RD, Matsudaira P, Lauffenburger DA. Computational model for cell migration in three-dimensional matrices. Biophys J. 2005;89(2):1389-97.
Kholodenko B, Yaffe MB, Kolch W. Computational approaches for analyzing information flow in biological networks. Sci Signal. 2012;5(220):re1.
Saez-Rodriguez J, Alexopoulos LG, Zhang M, Morris MK, Lauffenburger DA, Sorger PK. Comparing signaling networks between normal and transformed hepatocytes using discrete logical models. Cancer Res. 2011;71(16):5400-11.
Jiang H, Reinhardt HC, Bartkova J, Tommiska J, Blomqvist C, Nevanlinna H, Bartek J, Yaffe MB, Hemann MT. The combined status of ATM and p53 link tumor development with therapeutic response. Genes Dev. 2009;23(16):1895-909.
Toni T, Tidor B. Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology. PLoS Comput Biol. 2013;9(3):e1002960.
Tentner AR, Lee MJ, Ostheimer GJ, Samson LD, Lauffenburger DA, Yaffe MB. 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.
Reticker-Flynn NE, Braga Malta DF, Winslow MM, Lamar JM, Xu MJ, Underhill GH, Hynes RO, Jacks TE, Bhatia SN. A combinatorial extracellular matrix platform identifies cell-extracellular matrix interactions that correlate with metastasis. Nat Commun. 2012;3:1122.
Levin VA, Tonge PJ, Gallo JM, Birtwistle MR, Dar AC, Iavarone A, Paddison PJ, Heffron TP, Elmquist WF, Lachowicz JE, Johnson TW, White FM, Sul J, Smith QR, Shen W, Sarkaria JN, Samala R, Wen PY, Berry DA, Petter RC. CNS Anticancer Drug Discovery and Development Conference White Paper. Neuro Oncol. 2015;17 Suppl 6:vi1-26.
Chen WW, Niepel M, Sorger PK. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev. 2010;24(17):1861-75.
Oudin MJ, Hughes SK, Rohani N, Moufarrej MN, Jones JG, Condeelis JS, Lauffenburger DA, Gertler FB. Characterization of the expression of the pro-metastatic Mena(INV) isoform during breast tumor progression. Clin Exp Metastasis. 2016;33(3):249-61.
Radhakrishnan ML, Tidor B. Cellular level models as tools for cytokine design. Biotechnol Prog. 2010;26(4):919-37.

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