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Publications
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 Apr;5(4):e1000340.
Aldridge BB, Gaudet S, Lauffenburfer DA, Sorger PK. Caspase-to-inhibitor ratios determine whether mitochondrial outer membrane permeabilization is required for receptor-mediated cell death. Submitted.
Alexopoulos L, Saez-Rodriguez J, Cosgrove B, Lauffenburger DA, Sorger PK. Networks reconstructed from cell response data reveal profound differences in signaling by Toll-like receptors and NFkB in normal and transformed human hepatocytes. Submitted.
Apgar JF, Toettcher JE, Endy D, White FM, Tidor B. Stimulus design for model selection and validation in cell signaling. PLoS Comput Biol. 2008 Feb 15; 4(2): e30.
Chen J, Chen SC, Stern P, Scott BB, Lois C. Genetic strategy to prevent influenza virus infections in animals. J Infect Dis. 2008 Feb 15;197 Suppl 1:S25-8.
Chen WW, Schoeberl B, Jasper PJ, Niepel M, Nielsen UB, Lauffenburger DA, Sorger PK. Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol. 2009;5:239.
Cheng C, Yaffe MB, Sharp PA. A positive feedback loop couples Ras activation and CD44 alternative splicing. Genes Dev. 2006 Jul 1;20(13):1715-20.
Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods. 2007 Sep;4(9):721-6.
Fry RC, Svensson JP, Valiathan C, Wang E, Hogan BJ, Bhattacharya S, Bugni JM, Whittaker CA, Samson LD. Genomic predictors of interindividual differences in response to DNA damaging agents. Genes Dev. 2008 Oct 1;22(19):2621-6.
Gardino AK, Smerdon SJ, Yaffe MB. Structural determinants of 14-3-3 binding specificities and regulation of subcellular localization of 14-3-3-ligand complexes: a comparison of the X-ray crystal structures of all human 14-3-3 isoforms. Semin Cancer Biol. 2006 Jun;16(3):173-82.
Ge Q, Pastey M, Kobasa D, Puthavathana P, Lupfer C, Bestwick RK, Iversen PL, Chen J, Stein DA. Inhibition of multiple subtypes of influenza A virus in cell cultures with morpholino oligomers. Antimicrob Agents Chemother. 2006 Nov;50(11):3724-33.
Goswami S, Philippar U, Sun D, Patsialou A, Avraham J, Wang W, Di Modugno F, Nistico P, Gertler FB, Condeelis JS. Identification of invasion specific splice variants of the cytoskeletal protein Mena present in mammary tumor cells during invasion in vivo. Clin Exp Metastasis. 2009;26(2):153-9.
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 May;40(5):600-8.
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 Apr 13;10(4):756-65.
Huang PH, Cavenee WK, Furnari FB, White FM. Uncovering therapeutic targets for glioblastoma: a systems biology approach. Cell Cycle. 2007 Aug 20; 6(22): 2750-4.
Huang PH, Mukasa A, Bonavia R, Flynn R, Brewer ZE, Cavenee WK, Furnari FB, White FM. Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma. Proc Natl Acad Sci U.S.A. 2007 Jul 31; 104(31):12867-72.
Huang SS, Fraenkel E. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal. 2009 Jul 28;2(81):ra40.
Janes KA, Reinhardt HC, Yaffe MB. Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell. 2008 Oct 17;135(2):343-54.
Joslin EJ, Opresko LK, Wells A, Wiley HS, Lauffenburger DA. EGF-receptor-mediated mammary epithelial cell migration is driven by sustained ERK signaling from autocrine stimulation. J Cell Sci 2007 Sep 25; 120(20): 3688-99.
Joughin BA, Naegle KM, Huang PH, Yaffe MB, Lauffenburger DA, White FM. An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells. Mol Biosyst. 2009 Jan;5(1):59-67.
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 Jan 29;1:9.
Kim HD, 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 Oct;19(10):4249-59.
King BM, Tidor B. MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. Bioinformatics. 2009 May 1;25(9):1165-72.
Kishi K, van Vugt MA, Okamoto K, Hayashi Y, Yaffe MB. Functional dynamics of Polo-like kinase 1 at the centrosome. Mol Cell Biol. 2009 Jun;29(11):3134-50. Epub 2009 Mar 23.
Kreeger P, Mandhana R, Alford SK, Haigis K, Lauffenburger DA. Ras mutations impact TNF-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects. Submitted.
Kumar MS, Erkeland SJ, Pester RE, Chen CY, Ebert MS, Sharp PA, Jacks T. Suppression of non-small cell lung tumor development by the let-7 microRNA family. Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3903-8.
Kumar N, Afeyan R, Kim HD, Lauffenburger DA. Multi-pathway model enables prediction of kinase inhibitor cross-talk effects on migration of HER2-overexpressing mammary epithelial cells. Mol Pharmacol. 2008 Jun;73(6):1668-78.
Kumar N, Wolf-Yadlin A, White FM, Lauffenburger DA. Modeling HER2 Effects on Cell Behavior from Mass Spectrometry Phosphotyrosine Data. PLoS Comput Biol. 2007 Jan 5;3(1):e4
Kumar N, Zaman MH, Kim HD, Lauffenburger, DA. A high-throughput migration assay reveals HER2-mediated cell migration arising from increased directional persistence. Biophys J. 2006 Aug 15;91(4):L32-4.
Lacy-Hulbert A, Smith AM, Tissire H, Barry M, Crowley D, Bronson RT, Roes JT, Savill JS, Hynes RO. Ulcerative colitis and autoimmunity induced by loss of myeloid alphav integrins. Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15823-8.
Lazzara MJ, Lauffenburger DA. Quantitative modeling perspectives on the ErbB system of cell regulatory processes. Exp Cell Res. 2009 Feb 15;315(4):717-25.
Lazzara M, Lane K, Chan R, Jasper P, Sorger PK, Jacks T, Yaffe MB, Neel BG, Lauffenburger DA. Incomplete Shp-2 mediated ERK activation in EGFR-mutant lung cancers leads to increased cellular sensitivity to gefitinib. Submitted.
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MA, Jorgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JG, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T. Systematic discovery of in vivo phosphorylation networks. Cell. 2007 Jun 29;129(7):1415-26.
Linding R, Jensen LJ, Pasculescu A, Olhovsky M, Colwill K, Bork P, Yaffe MB, Pawson T. NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res. 2008 Jan;36(Database issue):D695-9.
Macurek L, Lindqvist A, Lim D, Lampson MA, Klompmaker R, Freire R, Clouin C, Taylor SS, Yaffe MB, Medema RH. Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery. Nature. 2008 Sep 4;455(7209):119-23.
Miller ML, Jensen LJ, Diella F, Jorgensen C, Tinti M, Li L, Hsiung M, Parker SA, Bordeaux J, Sicheritz-Ponten T, Olhovsky M, Pasculescu A, Alexander J, Knapp S, Blom N, Bork P, Li S, Cesareni G, Pawson T, Turk BE, Yaffe MB, Brunak S, Linding R. Linear motif atlas for phosphorylation-dependent signaling. Sci Signal. 2008;1(35):ra2.
Philippar U, Roussos ET, Oser M, Yamaguchi H, Kim HD, 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 Dec;15(6):813-28.
Pino MS, Balsamo M, Di Modugno F, Mottolese M, Alessio M, Melucci E, Milella M, McConkey DJ, Philippar U, Gertler FB, Natali PG, Nistico P. Human Mena+11a isoform serves as a marker of epithelial phenotype and sensitivity to epidermal growth factor receptor inhibition in human pancreatic cancer cell lines. Clin Cancer Res. 2008 Aug 1;14(15):4943-50.
Pritchard J, Cosgrove BD Hemann MT, Griffith LG, Wands J, Lauffenburger DA. Three-kinase inhibitor combination recreates multipathway effects of Geldanamycin analog on hepatocellular carcinoma cell death. Submitted.
Reinhardt HC, Aslanian AS, Lees JA, Yaffe MB. p53-deficient cells rely on ATM- and ATR-mediated checkpoint signaling through the p38MAPK/MK2 pathway for survival after DNA damage. Cancer Cell. 2007 Feb;11(2):175-89.
Reinhardt HC, Yaffe MB. Kinases that control the cell cycle in response to DNA damage: Chk1, Chk2, and MK2. Curr Opin Cell Biol. 2009 Apr;21(2):245-55.
Robinson BD, Sica GL, Liu YF, Rohan TE, Gertler FB, Condeelis JS, Jones JG. Tumor microenvironment of metastasis in human breast carcinoma: a potential prognostic marker linked to hematogenous dissemination. Clin Cancer Res. 2009 Apr 1;15(7):2433-41.
Samaga R, Saez-Rodriguez J, Alexopoulos L, Sorger PK, Klamt S. The logic of EGFR/ErbB signaling: theoretical properties and analysis of high-throughput data. PLoS Comp Biol, in press.
Saez-Rodriguez J, Alexopoulos L, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK. Discrete logic models as a means to link pathway maps to functional analysis of signal transduction in mammalian cells. Submitted.
Sobolev O, Stern P, Lacy-Hulbert A, Hynes RO. Natural killer cells require selectins for suppression of subcutaneous tumors. Cancer Res. 2009 Mar 15;69(6):2531-9.
Sorger PK. A reductionist's systems biology: opinion. Curr Opin Cell Biol. 2005 Feb;17(1):9-11.
Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK. Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature. 2009 May 21;459(7245):428-32.
Stern P, Astrof S, Erkeland SJ, Schustak J, Sharp PA, Hynes RO. A system for Cre-regulated RNA interference in vivo. Proc Natl Acad Sci U S A. 2008 Sep 16;105(37):13895-900.
Thomas M, Lu JJ, Zhang C, Chen J, Klibanov AM. Identification of novel superior polycationic vectors for gene delivery by high-throughput synthesis and screening of a combinatorial library. Pharm Res 2007. Aug; 24(8): 1564-71.
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 Jan 20;106(3):785-90.
White FM. Quantitative phosphoproteomic analysis of signaling network dynamics. Curr Opin Biotechnol. 2008 Aug;19(4):404-9.
Wilkins AK, Barton PI, Tidor B. The Per2 negative feedback loop sets the period in the mammalian circadian clock mechanism. PLoS Comput Biol. 2007 Dec 14;3(12):e242.
Wille L, Kemp ML, Sandy P, Lewis CL, Lauffenburger DA. Epi-allelic Erk1 and Erk2 knockdown series for quantitative analysis of T cell Erk regulation and IL-2 production. Mol Immunol. 2007 May;44(12):3085-91.
Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM. Effects of HER2 overexpression on cell signaling networks governing proliferation and migration. Mol Syst Biol. 2006;2:54.
Wong SY, Crowley D, Bronson RT, Hynes RO. Analyses of the role of endogenous SPARC in mouse models of prostate and breast cancer. Clin Exp Metastasis. 2008;25(2):109-18.
Wong SY, Haack H, Kissil JL, Barry M, Bronson RT, Shen S, Whittaker CA, Crowley D, Hynes RO. Protein 4.1B suppresses prostate cancer progression and metastasis. Proc Natl Acad Sci U S A. 2007 Jul 31; 104(31): 12784-9.
Xu L, Shen S, Subramanian A, Ross K, Brunet JP, 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 May;6(5):760-9.
Zaman, MH, Kamm RD, Matsudaira P, Lauffenburger DA. Computational model for cell migration in three-dimensional matrices. Biophys J. 2005 Aug;89(2):1389-97.
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 Jan;35(1):91-100.
Zaman MH, Trapani LM, Sieminski AL, Mackellar D, Gong H, Kamm RD, Wells A, Lauffenburger DA, Matsudaira P. Migration of tumor cells in 3D matrices is governed by matrix stiffness along with cell-matrix adhesion and proteolysis. Proc Natl Acad Sci U S A. 2006 Jul 18;103(29):10889-94.
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