Publications

Found 23 results
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Gosline SJC, Spencer SJ, Ursu O, Fraenkel E. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol (Camb). 2012;4(11):1415-27.
Gosline SJC, Oh C, Fraenkel E. SAMNetWeb: identifying condition-specific networks linking signaling and transcription. Bioinformatics. 2015;31(7):1124-6.
Peterson LB, Yaffe MB, Imperiali B. Selective mitogen activated protein kinase activity sensors through the application of directionally programmable D domain motifs. Biochemistry. 2014;53(36):5771-8.
Riquelme DN, Meyer AS, Barzik M, Keating A, Gertler FB. Selectivity in subunit composition of Ena/VASP tetramers. Biosci Rep. 2015;35(5).
Lee MJ, Ye AS, Gardino AK, Heijink AMargriet, Sorger PK, MacBeath G, Yaffe MB. Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks. Cell. 2012;149(4):780-94.
Liu F, Park J-E, Qian W-J, Lim D, Gräber M, Berg T, Yaffe MB, Lee KS, Burke TR. Serendipitous alkylation of a Plk1 ligand uncovers a new binding channel. Nat Chem Biol. 2011;7(9):595-601.
Gitter A, Braunstein A, Pagnani A, Baldassi C, Borgs C, Chayes J, Zecchina R, Fraenkel E. Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. Pac Symp Biocomput. 2014;:39-50.
Kim H-D, 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;10(11):M111.008433.
Tuncbag N, Braunstein A, Pagnani A, Huang S-SC, 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;20(2):124-36.
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;12(6):907-15.
Bell EL, Nagamori I, Williams EO, Del Rosario AM, Bryson BD, Watson N, White FM, Sassone-Corsi P, Guarente L. SirT1 is required in the male germ cell for differentiation and fecundity in mice. Development. 2014;141(18):3495-504.
Apgar JF, Witmer DK, White FM, Tidor B. Sloppy models, parameter uncertainty, and the role of experimental design. Mol Biosyst. 2010;6(10):1890-900.
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 SJ, Yaffe MB. Spatial exclusivity combined with positive and negative selection of phosphorylation motifs is the basis for context-dependent mitotic signaling. Sci Signal. 2011;4(179):ra42.
Tuncbag N, McCallum S, Huang S-SC, Fraenkel E. SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways. Nucleic Acids Res. 2012;40(Web Server issue):W505-9.
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.
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;16(3):173-82.
Landry BD, Clarke DC, Lee MJ. Studying Cellular Signal Transduction with OMIC Technologies. J Mol Biol. 2015;427(21):3416-40.
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;105(10):3903-8.
Huang S-SC, 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.
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;105(37):13895-900.
Gajadhar AS, White FM. System level dynamics of post-translational modifications. Curr Opin Biotechnol. 2014;28C:83-87.
Linding R, Jensen LJ, Ostheimer GJ, van Vugt MATM, Jørgensen C, Miron IM, Diella F, Colwill K, Taylor L, Elder K, Metalnikov P, Nguyen V, Pasculescu A, Jin J, Park JGyoon, Samson LD, Woodgett JR, Russell RB, Bork P, Yaffe MB, Pawson T. Systematic discovery of in vivo phosphorylation networks. Cell. 2007;129(7):1415-26.
Hegemann B, Hutchins JRA, Hudecz O, Novatchkova M, Rameseder J, Sykora MM, Liu S, Mazanek M, Lénárt P, Hériché J-K, Poser I, Kraut N, Hyman AA, Yaffe MB, Mechtler K, Peters J-M. Systematic phosphorylation analysis of human mitotic protein complexes. Sci Signal. 2011;4(198):rs12.