Search Contact
About
Research
Scientists
Resources
Events
Education
Data & Models

Data

Models and Web Resources

CAMV: The Computer-Assisted Manual Validation (CAMV) tool expedites the manual validation process for LC-MSMS data as well as collects and summarizes quantitative information from iTRAQ or SILAC experiments.

The MIT/ICBP siRNA Database: An on-line database of experimentally validated siRNAs and shRNAs against target genes, with a focus on genes thought to be involved in cancer.

NetPhorest: NetPhorest integrates in vitro kinase and phosphopeptide-binding domain specificity assays with publically accessible known in vivo substrate lists in order to generate substrate specificity descriptions for individual proteins as well as protein families.

NetworKIN: NetworKIN predicts the kinase responsible for sites of protein phosphorylation using motif analysis to identify the likely kinase family, and then protein-protein interaction network analysis to identify the most likely individual kinase.

phoMSVal: phoMSVal is an open-source platform developed for managing MS/MS data and automatically validating identified phosphopeptides.

PTMScout: PTMScout is a tool for viewing and analyzing high-throughput post-translational modification proteomic data, with a particular eye towards novel hypothesis generation.

Q2LM: Querying Quantitative Logic Models (Q2LM) is a MATLAB library that uses constrained fuzzy logic models based on prior knowledge networks to address two questions about a biological system: 1) What perturbation results in a specified downstream effect? and 2) In what environments do those perturbations produce that effect?

Scansite: Scansite contains substrate specificity matrices determined by in vitro peptide library experiments for a number of kinases and phosphopeptide-binding domains.  These are used to predict likely interactors with putative substrate sequences of interest.



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.


Alexander J, Lim D, Joughin BA, Hegemann B, Hutchins JRA, Ehrenberger T, Ivins F, Sessa F, Hudecz O, Nigg EA, Fry AM, Musacchio A, Stukenberg PT, Mechtler K, Peters J-M, Smerdon S-J, Yaffe MB. Spatial Exclusivity Combined with Positive and Negative Selection of Phosphorylation Motifs Is the Basis for Context-Dependent Mitotic Signaling. Sci. Signal. 2011 Jun 28; 4(179): ra42.


Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK. Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol Cell Proteomics. 2010 Sep;9(9):1849-65.


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.


Apgar JF, Witmer DK, White FM, Tidor B. Sloppy models, parameter uncertainty, and the role of experimental design. Mol Biosyst. 2010 Oct;6(10):1890-900.


Bagheri N, Shiina M, Lauffenburger DA, Korn WM.  A dynamical systems model for combinatorial cancer therapy enhances oncolytic adenovirus efficacy by MEK-inhibition.  PLoS Comput Biol. 2011 Feb;7(2):e1001085.


Carlson SM, Chouinard CR, Labadorf A, Lam CJ, Schmelzle K, Fraenkel E, White FM. Large-Scale Discovery of ERK2 Substrates Identifies ERK-Mediated Transcriptional Regulation by ETV3. Sci Signal. 2011 Oct 25;4(196):rs11.


Carlson SM, White FM. Expanding applications of chemical genetics in signal transduction. Cell Cycle. 2012 May 15;11(10):1903-9.


Chen CH, Miller MA, Sarkar A, Beste MT, Isaacson KB, Lauffenburger DA, Griffith LG, Han J. Multiplexed Protease Activity Assay for Low-Volume Clinical Samples Using Droplet-Based Microfluidics and Its Application to Endometriosis. J Am Chem Soc. 2012 Nov 29.


Chen CH, Sarkar A, Song YA, Miller MA, Kim SJ, Griffith LG, Lauffenburger DA, Han J.  Enhancing protease activity assay in droplet-based microfluidics using a biomolecule concentrator.  J Am Chem Soc. 2011 Jul 13;133(27):10368-71.


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, Niepel M, Sorger PK.  Classic and contemporary approaches to modeling biochemical reactions.  Genes Dev. 2010 Sep 1;24(17):1861-75. Review.


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.


Curran TG, Bryson BD, Reigelhaupt M, Johnson H, White FM. Computer aided manual validation of mass spectrometry-based proteomic data. Methods. 2013 Jun 15;61(3):219-26.


Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods. 2007 Sep;4(9):721-6.


Floyd SR, Pacold ME, Huang Q, Clarke SM, Lam FC, Cannell IG, Bryson BD, Rameseder J, Lee MJ, Blake EJ, Fydrych A, Ho R, Greenberger BA, Chen GC, Maffa A, Del Rosario AM, Root DE, Carpenter AE, Hahn WC, Sabatini DM, Chen CC, White FM, Bradner JE, Yaffe MB. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature. 2013 Jun 13;498(7453):246-50.


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.


Fu D, Calvo JA, Samson LD. Balancing repair and tolerance of DNA damage caused by alkylating agents. Nat Rev Cancer. 2012 Jan 12;12(2):104-20.


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.


Gardino AK, Yaffe MB. 14-3-3 proteins as signaling integration points for cell cycle control and apoptosis. Semin Cell Dev Biol. 2011 Sep;22(7):688-95.


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.


Gosline SJ, Spencer SJ, Ursu O, Fraenkel E. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol (Camb). 2012 Oct 22;4(11):1415-27.


Grácio F, Cabral J, Tidor B. Modeling stem cell induction processes. PLoS One. 2013 May 8;8(5):e60240.


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.


Grosstessner-Hain K, Hegemann B, Novatchkova M, Rameseder J, Joughin BA, Hudecz O, Roitinger E, Pichler P, Kraut N, Yaffe MB, Peters JM, Mechtler K. Quantitative Phospho-proteomics to Investigate the Polo-like Kinase 1-Dependent Phospho-proteome. Mol Cell Proteomics. 2011 Nov;10(11):M111.008540.


Gupton SL, Riquelme D, Hughes-Alford SK, Tadros J, Rudina SS, Hynes RO, Lauffenburger DA, Gertler FB. Mena binds α5 integrin directly and modulates α5β1 function. J Cell Biol. 2012 Aug 20;198(4):657-76.


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.


Hegemann B, Hutchins JR, Hudecz O, Novatchkova M, Rameseder J, Sykora MM, Liu S, Mazanek M, Lénárt P, Hériché JK, Poser I, Kraut N, Hyman AA, Yaffe MB, Mechtler K, Peters JM. Systematic phosphorylation analysis of human mitotic protein complexes.


Höpker K, Hagmann H, Khurshid S, Chen S, Hasskamp P, Seeger-Nukpezah T, Schilberg K, Heukamp L, Lamkemeyer T, Sos ML, Thomas RK, Lowery D, Roels F, Fischer M, Liebau MC, Resch U, Kisner T, Röther F, Bartram MP, Müller RU, Fabretti F, Kurschat P, Schumacher B, Gaestel M, Medema RH, Yaffe MB, Schermer B, Reinhardt HC, Benzing T. AATF/Che-1 acts as a phosphorylation-dependent molecular modulator to repress p53-driven apoptosis. EMBO J. 2012 Oct 17;31(20):3961-75. Epub 2012 Aug 21.


Hori Y, Stern PJ, Hynes RO, Irvine DJ. Engulfing tumors with synthetic extracellular matrices for cancer immunotherapy.
Biomaterials.
2009 Dec;30(35):6757-67.


Hsu PP, Kang SA, Rameseder J, Zhang Y, Ottina KA, Lim D, Peterson TR, Choi Y, Gray NS, Yaffe MB, Marto JA, Sabatini DM.  The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling.  Science. 2011 Jun 10;332(6035):1317-22.


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, 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 Jul;6(7):1227-37.


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 PH, White FM. Phosphoproteomics: unraveling the signaling web. Mol Cell. 2008 Sep 26;31(6):777-81. Review.


Huang SS, Clarke DC, Gosline SJ, Labadorf A, Chouinard CR, Gordon W, Lauffenburger DA, Fraenkel E. Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling. PLoS Comput Biol. 2013 Feb;9(2):e1002887.


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.


Huang SS, Fraenkel E. Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol. 2012;110:57-80.


Hughes-Alford SK, Lauffenburger DA. Quantitative analysis of gradient sensing: towards building predictive models of chemotaxis in cancer. Curr Opin Cell Biol. 2012 Apr;24(2):284-91.


Janes KA, Lauffenburger DA. Models of signalling networks - what cell biologists can gain from them and give to them. J Cell Sci. 2013 May 1;126(Pt 9):1913-21.


Janes KA, Reinhardt HC, Yaffe MB. Cytokine-induced signaling networks prioritize dynamic range over signal strength. Cell. 2008 Oct 17;135(2):343-54.


Janes KA, Yaffe MB. Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Biol. 2006 Nov;7(11):820-8. Review.


Jay SM, Kurtagic E, Alvarez LM, de Picciotto S, Sanchez E, Hawkins JF, Prince RN, Guerrero Y, Treasure CL, Lee RT, Griffith LG. Engineered bivalent ligands to bias ErbB receptor-mediated signaling and phenotypes. J Biol Chem. 2011 Aug 5;286(31):27729-40.


Jay SM, Murthy AC, Hawkins JF, Wortzel JR, Steinhauser ML, Alvarez LM, Gannon J, Macrae CA, Griffith LG, Lee RT. An engineered bivalent neuregulin protects against doxorubicin-induced cardiotoxicity with reduced proneoplastic potential. Circulation. 2013 Jul 9;128(2):152-61.


Jiang H, Pritchard JR, Williams RT, Lauffenburger DA, Hemann MT. A mammalian functional-genetic approach to characterizing cancer therapeutics. Nat Chem Biol. 2011 Feb;7(2):92-100.


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 Aug 15;23(16):1895-909.


Johnson H, Del Rosario AM, Bryson BD, Schroeder MA, Sarkaria JN, White FM. Molecular Characterization of EGFR and EGFRvIII Signaling Networks in Human Glioblastoma Tumor Xenografts. Mol Cell Proteomics. 2012 Dec; 11(12): 1724-40.


Johnson H, White FM. Toward quantitative phosphotyrosine profiling in vivo. Semin Cell Dev Biol. 2012 Oct;23(8):854-62.


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, Cheung E, Karuturi RK, Saez-Rodriguez J, Lauffenburger DA, Liu ET. Cellular Regulatory Networks in Systems Biomedicine: Concepts and Perspectives. Liu ET and Lauffenburger DA, eds., Academic Press. pp. 57-108 (2009).


Joughin BA, Liu C, Lauffenburger DA, Hogue CW, Yaffe MB. Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks. Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19;367(1602):2574-83.


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.


Kang SA, Pacold ME, Cervantes CL, Lim D, Lou HJ, Ottina K, Gray NS, Turk BE, Yaffe MB, Sabatini DM. mTORC1 phosphorylation sites encode their sensitivity to starvation and rapamycin. Science. 2013 Jul 26;341(6144):1236566.


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.


Kholodenko B, Yaffe MB, Kolch W. Computational approaches for analyzing information flow in biological networks. Sci Signal. 2012 Apr 17;5(220):re1.


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.


Kim HD, Meyer AS, Wagner JP, Alford SK, Wells A, Gertler FB, Lauffenburger DA. Signaling network state predicts twist-mediated effects on breast cell migration across diverse growth factor contexts. Mol Cell Proteomics. 2011 Nov;10(11):M111.008433.


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.


Kleiman LB, Maiwald T, Conzelmann H, Lauffenburger DA, Sorger PK.
Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding.  Mol Cell. 2011 Sep 2;43(5):723-37.


Kreeger PK, Lauffenburger DA. Cancer systems biology: a network modeling perspective. Carcinogenesis. 2010 Jan;31(1):2-8. Epub 2009 Oct 27.


Kreeger PK, Mandhana R, Alford SK, Haigis KM, Lauffenburger DA. RAS mutations affect tumor necrosis factor-induced apoptosis in colon carcinoma cells via ERK-modulatory negative and positive feedback circuits along with non-ERK pathway effects. Cancer Res. 2009 Oct 15;69(20):8191-9. Epub 2009 Sep 29.


Kreeger PK, Wang Y, Haigis KM, Lauffenburger DA. Integration of multiple signaling pathway activities resolves K-RAS/N-RAS mutation paradox in colon epithelial cell response to inflammatory cytokine stimulation. Integr. Biol. 2010; 2: 202-8.


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.


Lahesmaa-Korpinen AM, Carlson SM, White FM, Hautaniemi S. Integrated data management and validation platform for phosphorylated tandem mass spectrometry data. Proteomics. 2010 Oct;10(19):3515-24.


Lau KS, Juchheim AM, Cavaliere KR, Philips SR, Lauffenburger DA, Haigis KM. 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, ra16.


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 MJ, Lane K, Chan R, Jasper PJ, Yaffe MB, Sorger PK, Jacks T, Neel BG, Lauffenburger DA. Impaired SHP2-mediated extracellular signal-regulated kinase activation contributes to gefitinib sensitivity of lung cancer cells with epidermal growth factor receptor-activating mutations. Cancer Res. 2010 May 1;70(9):3843-50.


Lee MJ, Ye AS, Gardino AK, Heijink AM, Sorger PK, MacBeath G, Yaffe MB. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell 2012 May 11;149(4):780-94.


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.


Liu F, Park JE, Qian WJ, Lim D, Gräber M, Berg T, Yaffe MB, Lee KS, Burke TR Jr.  Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel.  Nat Chem Biol. 2011 Jul 17;7(9):595-601.


Liu H, Ong SE, 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 USA. 2011 Jan 25;108(4):1379-84.


Lu JJ, Langer R, Chen J. A novel mechanism is involved in cationic lipid-mediated functional siRNA delivery. Mol Pharm. 2009 May-Jun;6(3):763-71.


Machado D, Costa RS, Ferreira EC, Rocha I, Tidor B. Exploring the gap between dynamic and constraint-based models of metabolism. Metab Eng. 2012 Mar;14(2):112-9.


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.


Meacham CE, Ho EE, Dubrovsky E, Gertler FB, Hemann MT.  In vivo RNAi screening identifies regulators of actin dynamics as key determinants of lymphoma progression.  Nat Genet. 2009 Oct;41(10):1133-7.


Meyer AS, Hughes-Alford SK, Kay JE, Castillo A, Wells A, Gertler FB, Lauffenburger DA. 2D protrusion but not motility predicts growth factor-induced cancer cell migration in 3D collagen. J Cell Biol. 2012 Jun 11;197(6):721-9.


Miller MA, Barkal L, Jeng K, Herrlich A, Moss M, Griffith LG, Lauffenburger DA.  Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities.  Integr Biol (Camb). 2011 Apr;3(4):422-38.


Miller MA, Meyer AS, Beste MT, Lasisi Z, Reddy S, Jeng KW, Chen CH, Han J, Isaacson K, Griffith LG, Lauffenburger DA 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 May 28;110(22):E2074-83.


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.


Miraldi ER, Sharfi H, Friedline RH, Johnson H, Zhang T, Lau KS, Ko HJ, Curran TG, Haigis KM, Yaffe MB, Bonneau R, Lauffenburger DA, Kahn BB, Kim JK, Neel BG, Saghatelian A, White FM. Molecular network analysis of phosphotyrosine and lipid metabolism in hepatic PTP1b deletion mice. Integr Biol (Camb). 2013 Jul 24;5(7):940-63.


Mohammad DH, Yaffe MB. Fixin' to divide. Mol Cell. 2012 Feb 10;45(3):273-5.


Mohammad DH, Yaffe MB. 14-3-3 proteins, FHA domains and BRCT domains in the DNA damage response. DNA Repair (Amst). 2009 Sep 2;8(9):1009-17.


Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA.
Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli.  PLoS Comput Biol. 2011 Mar;7(3):e1001099.


Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA.  Logic-based models for the analysis of cell signaling networks. Biochemistry. 2010 Apr 20;49(15):3216-24. Review.


Naegle KM, Gymrek M, Joughin BA, Wagner JP, Welsch RE, Yaffe MB, Lauffenburger DA, White FM.  PTMScout: A web resource for analysis of high-throughput post-translational proteomic studies.  Mol Cell Proteomics. 2010 Nov; 9(11): 2558-2570.


Naegle KM, Welsch RE, Yaffe MB, White FM, Lauffenburger DA.  MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets.  PLoS Comput Biol. 2011 Jul;7(7):e1002119.


Naegle KM, White FM, Lauffenburger DA, Yaffe MB. Robust co-regulation of tyrosine phosphorylation sites on proteins reveals novel protein interactions. Mol Biosyst. 2012 Oct;8(10):2771-82.


Neel NF, Barzik M, Raman D, Sobolik-Delmaire T, Sai J, Ham AJ, Mernaugh RL, Gertler FB, Richmond A.  VASP is a CXCR2-interacting protein that regulates CXCR2-mediated polarization and chemotaxis.  J Cell Sci. 2009 Jun 1;122(Pt 11):1882-94.


Ng CW, Yildirim F, Yap YS, Dalin S, Matthews BJ, Velez PJ, Labadorf A, Housman DE, Fraenkel E. Extensive changes in DNA methylation are associated with expression of mutant huntingtin. Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2354-9.


Nguyen DN, Chen SC, Lu J, Goldberg M, Kim P, Sprague A, Novobrantseva T, Sherman J, Shulga-Morskaya S, de Fougerolles A, Chen J, Langer R, Anderson DG.  Drug delivery-mediated control of RNA immunostimulation. Mol Ther. 2009 Sep;17(9):1555-62.


Niepel M, Spencer SL, Sorger PK.  Non-genetic cell-to-cell variability and the consequences for pharmacology.  Curr Opin Chem Biol. 2009 Dec;13(5-6):556-61.


Noonan EM, Shah D, Yaffe MB, Lauffenburger DA, Samson LD. O6-Methylguanine DNA lesions induce an intra-S-phase arrest from which cells exit into apoptosis governed by early and late multi-pathway signaling network activation. Integr Biol (Camb). 2012 Oct;4(10):1237-55.


Palmer MJ, Mahajan VS, Trajman LC, Irvine DJ, Lauffenburger DA, Chen J. Interleukin-7 receptor signaling network: an integrated systems perspective. Cell Mol Immunol. 2008 Apr;5(2):79-89. Review.


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.


Pines G, Huang PH, Zwang Y, White FM, Yarden Y. EGFRvIV: a previously uncharacterized oncogenic mutant reveals a kinase autoinhibitory mechanism. Oncogene. 2010 Oct 28;29(43):5850-60.


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.


Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, Stolovitzky G.  Towards a rigorous assessment of systems biology models: the DREAM3 challenges.  PLoS One. 2010 Feb 23;5(2):e9202. Erratum in: PLoS One. 2010;5(3).


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 Jan 8; 110(2):E170–E179.


Pritchard JR, Bruno PM, Hemann MT, Lauffenburger DA. Predicting cancer drug mechanisms of action using molecular network signatures. Mol BioSyst. 2013. Ahead of print 20 Dec 2012.


Pritchard JR, Cosgrove BD, Hemann MT, Griffith LG, Wands JR, Lauffenburger DA. Three-kinase inhibitor combination recreates multipathway effects of a geldanamycin analogue on hepatocellular carcinoma cell death. Mol Cancer Ther. 2009 Aug;8(8):2183-92.


Pritchard JR, Gilbert LA, Meacham CE, Ricks JL, Jiang H, Lauffenburger DA, Hemann MT.  Bcl-2 family genetic profiling reveals microenvironment-specific determinants of chemotherapeutic response. Cancer Res. 2011 Sep 1;71(17):5850-8.


Pritchard JR, Lauffenburger DA, Hemann MT. Understanding resistance to combination chemotherapy. Drug Resist Updat. 2012 Oct;15(5-6):249-57. doi: 10.1016/j.drup.2012.10.003. Epub 2012 Nov 17.


Radhakrishnan ML, Tidor B. Cellular level models as tools for cytokine design. Biotechnol Prog. 2010 Jul-Aug;26(4):919-37.


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, Cannell IG, Morandell S, Yaffe MB.  Is post-transcriptional stabilization, splicing and translation of selective mRNAs a key to the DNA damage response?  Cell Cycle. 2011 Jan 1;10(1):23-7.


Reinhardt HC, Hasskamp P, Schmedding I, Morandell S, van Vugt MA, Wang X, Linding R, Ong SE, Weaver D, Carr SA, Yaffe MB.  DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization.  Mol Cell. 2010 Oct 8;40(1):34-49.


Reinhardt HC, Jiang H, Hemann MT, Yaffe MB.  Exploiting synthetic lethal interactions for targeted cancer therapy.  Cell Cycle. 2009 Oct 1;8(19):3112-9. Review.


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.


Reticker-Flynn NE, 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.


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.


Rock JM, Lim D, Stach L, Ogrodowicz RW, Keck JM, Jones MH, Wong CC, Yates JR 3rd, Winey M, Smerdon SJ, Yaffe MB, Amon A. Activation of the yeast Hippo pathway by phosphorylation-dependent assembly of signaling complexes. Science. 2013 May 17;340(6134):871-5.


Roussos ET, Balsamo M, Alford SK, Wyckoff JB, Gligorijevic B, Wang Y, Pozzuto M, Stobezki R, Goswami S, Segall JE, Lauffenburger DA, Bresnick AR, Gertler FB, Condeelis JS. Mena invasive (MenaINV) promotes multicellular streaming motility and transendothelial migration in a mouse model of breast cancer. J Cell Sci. 2011 Jul 1;124(Pt 13):2120-31.


Roussos ET, Goswami S, Balsamo M, Wang Y, Stobezki R, Adler E, Robinson BD, Jones JG, Gertler FB, Condeelis JS, Oktay MH. Mena invasive (Mena(INV)) and Mena11a isoforms play distinct roles in breast cancer cell cohesion and association with TMEM. Clin Exp Metastasis. 2011 Aug;28(6):515-27.


Roussos ET, Wang Y, Wyckoff JB, Sellers RS, Wang W, Li J, Pollard JW, Gertler FB, Condeelis JS. Mena deficiency delays tumor progression and decreases metastasis in polyoma middle-T transgenic mouse mammary tumors. Breast Cancer Res. 2010;12(6):R101.


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.


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 Aug 15;71(16):5400-11.


Shapiro IM, Cheng AW, Flytzanis NC, Balsamo M, Condeelis JS, Oktay MH, Burge CB, Gertler FB. An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 2011 Aug;7(8):e1002218.


Singh N, Basnet H, Wiltshire TD, Mohammad DH, Thompson JR, Héroux A, Botuyan MV, Yaffe MB, Couch FJ, Rosenfeld MG, Mer G. Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1. Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14381-6.


Singhania R, Sramkoski RM, Jacobberger JW, Tyson JJ. A hybrid model of mammalian cell cycle regulation. PLoS Comput Biol. 2011 Feb 10;7(2):e1001077.


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.


Stains CI, Tedford NC, Walkup TC, Luković E, Goguen BN, Griffith LG, Lauffenburger DA, Imperiali B. Interrogating signaling nodes involved in cellular transformations using kinase activity probes. Chem Biol. 2012 Feb 24;19(2):210-7.


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.


Svensson JP, Fry RC, Wang E, Somoza LA, Samson LD. Identification of novel human damage response proteins targeted through yeast orthology. PLoS One. 2012;7(5):e37368. Epub 2012 May 16.


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 Jan 31;8:568.


Thomas M, Lu JJ, Chen J, Klibanov AM. Non-viral siRNA delivery to the lung. Adv Drug Deliv Rev. 2007 Mar 30;59(2-3):124-33.


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.


Toni T, Tidor B. Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology. PLoS Comput Biol 9(3): e1002960.


Tuncbag N, Braunstein A, Pagnani A, Huang SS, Chayes J, Borgs C, Zecchina R, Fraenkel E. Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol. 2013 Feb;20(2):124-36.


Tuncbag N, McCallum S, Huang SS, Fraenkel E. SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W505-9.


Valiathan C, McFaline JL, Samson LD. A rapid survival assay to measure drug-induced cytotoxicity and cell cycle effects. DNA Repair (Amst). 2012 Jan 2;11(1):92-8.


van Vugt MA, Gardino AK, Linding R, Ostheimer GJ, Reinhardt HC, Ong SE, Tan CS, Miao H, Keezer SM, Li J, Pawson T, Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR, Yaffe MB.  A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint.  PLoS Biol. 2010 Jan 26;8(1):e1000287.


Vashishtha M, Ng CW, Yildirim F, Gipson TA, Kratter IH, Bodai L, Song W, Lau A, Labadorf A, Vogel-Ciernia A, Troncosco J, Ross CA, Bates GP, Krainc D, Sadri-Vakili G, Finkbeiner S, Marsh JL, Housman DE, Fraenkel E, Thompson LM. Targeting H3K4 trimethylation in Huntington disease. Proc Natl Acad Sci U S A. 2013 Aug 6;110(32):E3027-36.


Vasudevan KM, Barbie DA, Davies MA, Rabinovsky R, McNear CJ, Kim JJ, Hennessy BT, Tseng H, Pochanard P, Kim SY, Dunn IF, Schinzel AC, Sandy P, Hoersch S, Sheng Q, Gupta PB, Boehm JS, Reiling JH, Silver S, Lu Y, Stemke-Hale K, Dutta B, Joy C, Sahin AA, Gonzalez-Angulo AM, Lluch A, Rameh LE, Jacks T, Root DE, Lander ES, Mills GB, Hahn WC, Sellers WR, Garraway LA.  AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer.  Cancer Cell. 2009 Jul 7;16(1):21-32.


Wagner JP, Wolf-Yadlin A, Sevecka M, Grenier JK, Root DE, Lauffenburger DA, MacBeath G. Receptor tyrosine kinases fall into distinct classes based on their inferred signaling networks. Sci Signal. 2013 Jul 16;6(284):ra58.


Wang Y, Velho S, Vakiani E, Peng S, Bass AJ, Chu GC, Gierut J, Bugni JM, Der CJ, Philips M, Solit DB, Haigis KM. Mutant N-Ras protects colorectal cancer cells from stress-induced apoptosis and contributes to cancer development and progression. Cancer Discov. 2012 Dec 28.


Weingeist DM, Ge J, Wood DK, Mutamba JT, Huang Q, Rowland EA, Yaffe MB, Floyd S, Engelward BP. Single-cell microarray enables high-throughput evaluation of DNA double-strand breaks and DNA repair inhibitors. Cell Cycle. 2013 Mar 15;12(6):907-15.


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.


Wilson JL, Hemann MT, Fraenkel E, Lauffenburger DA. Integrated network analyses for functional genomic studies in cancer. Semin Cancer Biol. 2013 Aug;23(4):213-8.


Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM. Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5860-5.


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.


Yu M, Mazor T, Huang H, Huang HT, 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 Feb 10;45(3):330-43.


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.


 

MIT
Home Home