Difference between revisions of "Publications"

Revision as of 23:25, 29 September 2012

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-based Toolkit for the Computational Identification of 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 (published in advance September 27, 2012)

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, et al. 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, et al. 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, Tavazoie S. 2004. Cell 117:185–198.

@@ Line 1: / Line 1: @@
-* '''Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.''' Karnik, R, and Beer MA. 2012 (submitted)
+* '''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-based Toolkit for the Computational Identification of 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 (submitted)
+* '''Robust k-mer Frequency Estimation Using Gapped k-mers.''' Ghandi M, Mohammad-Noori M, and Beer MA. 2012. (submitted)
 * '''[http://genome.cshlp.org/content/early/2012/09/26/gr.139360.112 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 (published in advance September 27, 2012)