Difference between revisions of "Publications"
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* '''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 | + | * '''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) | * '''Robust k-mer Frequency Estimation Using Gapped k-mers.''' Ghandi M, Mohammad-Noori M, and Beer MA. 2012. (submitted) | ||
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 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. | * '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 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. | ||
| − | * '''[http://www. | + | * '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695. |
* '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180. | * '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180. | ||
Revision as of 00:46, 30 December 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 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, 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.