Publications
Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors. Mol Cell. 2012;45(3):330-43.
. Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements. Cell Rep. 2016;14(2):310-9.
. Extensive changes in DNA methylation are associated with expression of mutant huntingtin. Proc Natl Acad Sci U S A. 2013;110(6):2354-9.
. Integrated network analyses for functional genomic studies in cancer. Semin Cancer Biol. 2013;23(4):213-8.
. Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal. 2009;2(81):ra40.
. Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3. Sci Signal. 2011;4(196):rs11.
. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol. 2013;9(2):e1002887.
. SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets. Integr Biol (Camb). 2012;4(11):1415-27.
. SAMNetWeb: identifying condition-specific networks linking signaling and transcription. Bioinformatics. 2015;31(7):1124-6.
. Sharing information to reconstruct patient-specific pathways in heterogeneous diseases. Pac Symp Biocomput. 2014;:39-50.
. Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem. J Comput Biol. 2013;20(2):124-36.
. 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.
. Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets. Methods Cell Biol. 2012;110:57-80.
. Targeting H3K4 trimethylation in Huntington disease. Proc Natl Acad Sci U S A. 2013;110(32):E3027-36.
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