|
|
| Line 1: |
Line 1: |
| − | __NOTOC__
| + | '''[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"]''' |
| − | <head>
| |
| − | <meta name="description" content="Computational Regulatory Genomics at Johns Hopkins University for graduate PhD and postdoctoral research in the Department of Biomedical Engineering and Human Genetics, top ranking programs in quantitative modeling of regulatory DNA using machine learning. ">
| |
| − | </head>
| |
| − | <h1>Beer Lab: Computational Regulatory Genomics</h1>
| |
| | | | |
| − | [[File:Beer_Michael_small.jpg]] [[File:EncodeNatureGraphic_small.png]] [[File:Beer_lab_plate_art_small.jpg]] | + | '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]''' |
| | | | |
| − | We are in the '''[http://www.bme.jhu.edu/people/primary.php?id=384 Department of Biomedical Engineering]''' and the '''[https://igm.jhmi.edu/faculty/mike-beer McKusick-Nathans Institute of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/primary.php?id=384 BME]''' or the Ph.D. program in '''[http://humangenetics.jhmi.edu/index.php/faculty/michael-beer.html Human Genetics.]'''
| + | '''[http://www.bme.jhu.edu/about/awards-achievements.php?id=201612 BME Associate Professors Beer and Karchin named top performers at CAGI4]''' |
| − |
| |
| − | <h3>Research Interests: </h3> The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.
| |
| − | We have recently made significant progress in understanding how DNA sequence features specify cell-type specific mammalian enhancer activity by using kmer-based SVM machine learning approaches. For details, see:
| |
| | | | |
| − | * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.
| + | '''[https://genomeinterpretation.org/content/4-eQTL-causal_SNPs gkmSVM among top-scoring methods for CAGI eQTL prediction challenge] ''' |
| | | | |
| − | * '''[http://scholar.google.com/citations?view_op=view_citation&hl=en&user=9aH8_eEAAAAJ&sortby=pubdate&citation_for_view=9aH8_eEAAAAJ:1sJd4Hv_s6UC Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press
| + | '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] ''' |
| | | | |
| − | * '''[http://scholar.google.com/citations?view_op=view_citation&hl=en&user=9aH8_eEAAAAJ&sortby=pubdate&citation_for_view=9aH8_eEAAAAJ:NhqRSupF_l8C Robust k-mer Frequency Estimation Using Gapped k-mers.]''' Ghandi M, Mohammad-Noori M, and Beer MA. 2013. Journal of Mathematical Biology 69:469-500.
| + | '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News & Views article on our deltaSVM paper]''' |
| | | | |
| − | * '''[http://www.ncbi.nlm.nih.gov/pubmed/23771147 kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.]''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2013. Nucleic Acids Research 41: W544–W556.
| + | '''[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]''' |
| | | | |
| − | * '''[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.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]''' |
| | | | |
| − | * '''[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.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]''' |
| | | | |
| − | Our work uses functional genomics DNase-seq, ChIP-seq, RNA-seq, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers. We are currently focused on:
| + | '''[http://www.bme.jhu.edu/news-events/news-highlights.php?id=412 Beer Lab awarded NIH grant for regulatory contributions to disease. ]''' |
| | | | |
| − | * improving SVM methodology by including more general sequence features and constraints
| + | '''[http://www.bme.jhu.edu/news-events/news-highlights.php?id=360 kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] ''' |
| − | * predicting the impact of SNPs on enhancer activity (delta-SVM) and GWAS association for specific diseases
| |
| − | * experimentally assessing the predicted impact of regulatory element mutation in mammalian cells
| |
| − | * systematically determining regulatory element logic from ENCODE human and mouse data
| |
| − | * using this sequence based regulatory code to assess common modes of regulatory element evolution and variation
| |
| | | | |
| − | We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins, including research in Genomics, Systems Biology, Machine Learning, and Network Modeling.
| + | '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] ''' |
| − | | |
| − | <h3>[[Recent News]]</h3>
| |
| − | <h3>[[Lab Members]]</h3>
| |
| − | <h3>[[Publications]]</h3>
| |
| − | <h3>[[Postdoctoral Positions Available]]</h3>
| |
| − | <h3>About Computational Biology in JHU Biomedical Engineering:</h3>
| |
| − | The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.
| |
| − | | |
| − | <h3>[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]</h3>
| |
| − | | |
| − | <h3>[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]</h3>
| |
| − | | |
| − | [[File:bmesmall.png]]
| |