Publications

• Fletez-Brant C, Lee D, McCallion AS and Beer MA. 2012. kmer-SVM: a Web-based Toolkit for the Computational Identification of Predictive Regulatory Sequence Features in Genomic Datasets. (submitted)

• Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes. Genome Research (in press)

• Ghandi M, and Beer MA. 2012. Group Normalization for Genomic Data. PLoS ONE 7: e38695. Direct

• Lee D, Karchin R, and Beer MA. 2011. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research 21: 2167 –2180. Pubmed

• Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach. PROTEOMICS 9: 1374–1384. Pubmed

• Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, et al. 2009. Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation. PNAS 106: 3384–3389. Pubmed

• McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b. Genome Research 18: 252 –260. Pubmed

• Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, et al. 2007. Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis. Molecular Cell 26: 745–752. Pubmed

• Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region. Mol Cell Biol 25: 3855–3863. Pubmed

• Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation. Genome Research 14: 99–108. Pubmed

• Beer MA, Tavazoie S. 2004. Predicting Gene Expression from Sequence. Cell 117: 185–198. Pubmed