Difference between revisions of "Publications"

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* Ghandi M, and Beer MA. 2012. '''Group Normalization for Genomic Data.''' PLoS ONE 7: e38695. [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038695 Direct]
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* '''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)
  
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* Lee D, Karchin R, and Beer MA. 2011. '''Discriminative prediction of mammalian enhancers from DNA sequence.''' Genome Research 21: 2167 –2180. [http://www.ncbi.nlm.nih.gov/pubmed/21875935 Pubmed]
+
* '''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 (in press)
  
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* Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. '''Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.''' PROTEOMICS 9: 1374–1384. [http://www.ncbi.nlm.nih.gov/pubmed/19253296 Pubmed]
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* '''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 Direct]
  
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* 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. '''Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.''' PNAS 106: 3384–3389. [http://www.ncbi.nlm.nih.gov/pubmed/19211792 Pubmed]
+
* '''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 Pubmed]
  
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* McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. '''Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.''' Genome Research 18: 252 –260. [http://www.ncbi.nlm.nih.gov/pubmed/18071029 Pubmed]
+
* '''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/19253296 Pubmed]
  
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* Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, et al. 2007. '''Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.''' Molecular Cell 26: 745–752. [http://www.ncbi.nlm.nih.gov/pubmed/17540599 Pubmed]
+
* '''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/19211792 Pubmed]
  
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* Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. '''Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.''' Mol Cell Biol 25: 3855–3863. [http://www.ncbi.nlm.nih.gov/pubmed/15870260 Pubmed]
+
* '''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/18071029 Pubmed]
  
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* Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. '''Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.''' Genome Research 14: 99–108. [http://www.ncbi.nlm.nih.gov/pubmed/14672978 Pubmed]
+
* '''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/17540599 Pubmed]
  
−
* Beer MA, Tavazoie S. 2004. '''Predicting Gene Expression from Sequence.''' Cell 117: 185–198. [http://www.ncbi.nlm.nih.gov/pubmed/15084257 Pubmed]
+
* '''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/15870260 Pubmed]
 +
 
 +
* '''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. [http://www.ncbi.nlm.nih.gov/pubmed/14672978 Pubmed]
 +
 
 +
* '''Predicting Gene Expression from Sequence.''' Beer MA, Tavazoie S. 2004. Cell 117: 185–198. [http://www.ncbi.nlm.nih.gov/pubmed/15084257 Pubmed]

Revision as of 16:19, 21 August 2012

  • 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)
  • 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 (in press)
  • Group Normalization for Genomic Data. Ghandi M, and Beer MA. 2012. PLoS ONE 7: e38695. Direct
  • Discriminative prediction of mammalian enhancers from DNA sequence. Lee D, Karchin R, and Beer MA. 2011. Genome Research 21: 2167 –2180. Pubmed
  • 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. Pubmed
  • 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. Pubmed
  • 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. Pubmed
  • 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. Pubmed
  • 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. Pubmed
  • 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. Pubmed
  • Predicting Gene Expression from Sequence. Beer MA, Tavazoie S. 2004. Cell 117: 185–198. Pubmed
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