Difference between pages "Publications" and "Recent News"

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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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'''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on "The Dark Side of the Human Genome"]'''
  
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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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'''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''
  
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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.bme.jhu.edu/about/awards-achievements.php?id=201612 BME Associate Professors Beer and Karchin named top performers at CAGI4]'''
  
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* '''[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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'''[https://genomeinterpretation.org/content/4-eQTL-causal_SNPs gkmSVM among top-scoring methods for CAGI eQTL prediction challenge] '''
  
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* '''[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.
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'''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''
  
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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.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News & Views article on our deltaSVM paper]'''
  
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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.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''
  
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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.
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'''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''
  
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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.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''
  
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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.
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'''[http://www.bme.jhu.edu/news-events/news-highlights.php?id=412  Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''
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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/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.bme.jhu.edu/news-events/news-highlights.php?id=360  kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''
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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.
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'''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html  Dongwon Lee awarded Young Investigator Day Award.] '''

Revision as of 21:16, 27 October 2016

Our computational work featured in Nature news article on "The Dark Side of the Human Genome"

New R package for gkmSVM and deltaSVM released

BME Associate Professors Beer and Karchin named top performers at CAGI4

gkmSVM among top-scoring methods for CAGI eQTL prediction challenge

deltaSVM paper voted Top 10 in Regulatory Genomics 2015

Nature Genetics News & Views article on our deltaSVM paper

Nature Genetics paper on impact of regulatory variants

Newsweek article on Mouse ENCODE paper

Mouse ENCODE Consortium paper in Nature

Beer Lab awarded NIH grant for regulatory contributions to disease.

kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.

Dongwon Lee awarded Young Investigator Day Award.

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