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<sup>†</sup>. 2012. (submitted)
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* '''Mammalian Enhancer Prediction.''' Lee D, Beer MA. 2013. Genome Analysis: Current Procedures and Applications (submitted)
  
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* '''kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.''' Fletez-Brant C<sup>*</sup>, Lee D<sup>*,†</sup>, McCallion AS and Beer MA<sup>†</sup>. 2012. (submitted)
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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)
  
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* '''Robust k-mer Frequency Estimation Using Gapped k-mers.''' Ghandi M, Mohammad-Noori M, and Beer MA<sup>†</sup>. 2012. (submitted)
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* '''kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.''' Fletez-Brant C<sup>*</sup>, Lee D<sup>*</sup>, McCallion AS 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<sup>†</sup>, Pavan WJ<sup>†</sup>, and McCallion AS<sup>†</sup>. 2012. Genome Research 22:2290-2301.
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* '''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/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA<sup>†</sup>. 2012. PLoS ONE 7:e38695.
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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.
  
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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<sup>†</sup>. 2011. Genome Research 21:2167-2180.
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.
  
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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<sup>†</sup>. 2009. Proteomics 9:1374-1384.
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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.
  
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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, Thomas-Tikhonenko A, and Mendell JT<sup>†</sup>. 2009. PNAS 106:3384-3389.
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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.
  
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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<sup>†</sup>. 2008. Genome Research 18:252-260.
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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, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.
  
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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<sup>*</sup>, Wentzel EA<sup>*</sup>, 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<sup>†</sup>. 2007. Molecular Cell 26: 745-752.
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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.
  
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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<sup>†</sup>. 2005. Mol Cell Biol 25:3855-3863.
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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,  Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.
  
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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<sup>†</sup>. 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.
  
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S<sup>†</sup>. 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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<nowiki>*, These authors contributed equally to this work</nowiki><br/>
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* '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.
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<nowiki>†, To whom correspondence should be addressed</nowiki>
 

Revision as of 06:27, 27 January 2013

  • Mammalian Enhancer Prediction. Lee D, Beer MA. 2013. Genome Analysis: Current Procedures and Applications (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 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)
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