Difference between revisions of "Publications"

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* '''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)
  
* '''[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)
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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.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038695 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.
 
* '''[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038695 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.
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* '''[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/19253296 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.
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 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.
  
* '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 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.
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 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.
  
* '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029  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.
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029  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.
  
* '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 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.
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 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.
* '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 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.
 
  
* '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 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.  
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 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.
* '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA, Tavazoie S. 2004. Cell 117:185–198.
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 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.
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA, Tavazoie S. 2004. Cell 117:185-198.

Revision as of 00:43, 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-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)