Difference between revisions of "Publications"

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* [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038695 Group Normalization for Genomic Data. Ghandi M, Beer MA, PLoS ONE 7(8): e38695. (2012) doi:10.1371/journal.pone.0038695]  
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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]  
  
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* [http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence. Lee D, Karchin R, Beer MA. Genome Res. 2011 21: 2167-2180]
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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]
  
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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, Pandey A. Proteomics. 2009 Mar;9(5):1374-84]
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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]
  
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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 TC, Zeitels LR, Hwang HW, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, Mendell JT. Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3384-9. Epub 2009 Feb 11.]
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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]
  
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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, McCallion AS. Genome Res. 2008 Feb;18(2):252-60. Epub 2007 Dec 10]
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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 Res 18: 252 –260. [http://www.ncbi.nlm.nih.gov/pubmed/18071029]
  
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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 TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, Mendell JT. Mol Cell. 2007 Jun 8;26(5):745-52. Epub 2007 May 31]
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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]
  
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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. D. J. Katz, M. A. Beer, J. M. Levorse and S. M. Tilghman, Mol Cell Biol 25, p3855-3863 (2005).]
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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]
  
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* [http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-genome discovery of transcription factor finding sites by network-level conservation. M. Pritsker, Y. C. Liu, M. A. Beer, and S. Tavazoie, Genome Res. 2004 Jan;14(1):99-108. Epub 2003 Dec 12.]
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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 Res. 14: 99–108. [http://www.ncbi.nlm.nih.gov/pubmed/14672978]
  
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* [http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence. M. A. Beer and S. Tavazoie, Cell 117, p185-198 (2004)]
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* Beer MA, Tavazoie S. 2004. Predicting Gene Expression from Sequence. Cell 117: 185–198. [http://www.ncbi.nlm.nih.gov/pubmed/15084257]

Revision as of 13:21, 21 August 2012

  • Ghandi M, and Beer MA. 2012. Group Normalization for Genomic Data. PLoS ONE 7: e38695. [1]
  • Lee D, Karchin R, and Beer MA. 2011. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Research 21: 2167 –2180. [2]
  • 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. [3]
  • 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. [4]
  • 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 Res 18: 252 –260. [5]
  • 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. [6]
  • 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. [7]
  • Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation. Genome Res. 14: 99–108. [8]
  • Beer MA, Tavazoie S. 2004. Predicting Gene Expression from Sequence. Cell 117: 185–198. [9]
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