Publications

Found 14 results
Title Type [ Year(Desc)]
Filters: Author is Fraenkel, Ernest  [Clear All Filters]
2009
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.
2011
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;4(196):rs11.
2012
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.
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.
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.
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.
2013
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;110(6):2354-9.
Wilson JL, Hemann MT, Fraenkel E, Lauffenburger DA. Integrated network analyses for functional genomic studies in cancer. Semin Cancer Biol. 2013;23(4):213-8.
Huang S-SC, Clarke DC, Gosline SJC, 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;9(2):e1002887.
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.
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;110(32):E3027-36.
2014
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.
2015
Gosline SJC, Oh C, Fraenkel E. SAMNetWeb: identifying condition-specific networks linking signaling and transcription. Bioinformatics. 2015;31(7):1124-6.
2016
Gosline SJC, Gurtan AM, JnBaptiste CK, Bosson A, Milani P, Dalin S, Matthews BJ, Yap YS, Sharp PA, Fraenkel E. Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements. Cell Rep. 2016;14(2):310-9.