Publications

*, These authors contributed equally to this work
†, To whom correspondence should be addressed

• Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces. Karnik, R, and Beer MA^†. 2012. (submitted)

• kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets. Fletez-Brant C^*, Lee D^*,†, McCallion AS and Beer MA^†. 2012. (submitted)

• Robust k-mer Frequency Estimation Using Gapped k-mers. Ghandi M, Mohammad-Noori M, and Beer MA^†. 2012. (submitted)

• Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes. Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA^†, Pavan WJ^†, and McCallion AS^†. 2012. Genome Research 22:2290-2301.

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

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

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

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

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

• Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis. Chang T-C^*, Wentzel EA^*, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT^†. 2007. Molecular Cell 26: 745-752.

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

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

• Predicting Gene Expression from Sequence. Beer MA and Tavazoie S^†. 2004. Cell 117:185-198.