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| + | ==PI== |
| − | <metadesc>Computational Regulatory Genomics for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.</metadesc>
| + | [[Users:Mbeer|Mike Beer (with short hair)]] |
| − | <!-- <h2>Computational Regulatory Genomics</h2> -->
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| − | <h3>[[Recent News ]] [[Lab Members ]] [[Publications]] [[Postdoctoral Positions Available]] [[Resources]]</h3>
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| − | [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/primary]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]] | + | [[File:Beer_m.gif]] [[File:group_pic.jpg|350px]] |
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| − | We are in the '''[http://www.bme.jhu.edu/people/primary.php?id=384 Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department 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 '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer Human Genetics.]'''
| + | ==Postdocs== |
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| + | * Ayoti Patra |
| − | <h3>Research Interests: </h3> The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.
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| − | We have recently made significant progress in understanding how DNA sequence features specify cell-type specific mammalian enhancer activity using machine learning, and how enhancer-gene networks control cell-fate decisions and contribute to human disease. For details, see:
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| − | * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020. | + | ==Graduate students== |
| | + | * Justin Shigaki |
| | + | * Wang Xi |
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| − | * '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation. ]''' Li Q, et al. Nature Genetics 2019. | + | ==Current Undergraduates== |
| | + | * Nico Eng |
| | + | * Jin-woo Oh |
| | + | * Michael Mudgett |
| | + | * Felix Yu |
| | + | * Amy Xiao |
| | + | * Ganesh Avrapalli |
| | + | * Sunny Thodupunuri |
| | + | * Richard Liu |
| | + | * Gianluca Silva Croso |
| | + | * Zachary Heiman |
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| − | * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA. Human Mutation 2017. | + | ==Former graduate students== |
| | + | * Paul Michel (summer MD genomics rotation) |
| | + | * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&hl=en Dongwon Lee] |
| | + | * Kipper Fletez-Brant (Hansen Lab, JHU) |
| | + | * Mahmoud Ghandi (now at Broad Institute) |
| | + | * [http://www.genebrew.com Rahul Karnik] (now at Broad Institute) |
| | + | * Jun Kyu Rhee (now at Korea Institute of Science and Technology) |
| | + | * Donavan Cheng (now Director of Oncology Bioinformatics and Data Sciences at Illumina) |
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| − | * '''[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3331.html A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015. | + | ==Former Undergraduates== |
| − | | + | * Kendrick Hougen |
| − | * '''[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. | + | * Nole Lin |
| − | | + | * Ashutosh Jindal |
| − | and other [[Publications]].
| + | * Kyle Xiong |
| − | | + | * Ben Strober |
| − | Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, MPRA, Hi-C, 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:
| + | * Alessandro Asoni |
| − | | + | * Billy Kang |
| − | * improving on the SVM methodology by including more general sequence features and constraints | + | * John Lee |
| − | * predicting the impact of SNPs on enhancer activity (delta-SVM) and GWAS association for specific diseases | + | * Andrew Pao |
| − | * experimentally assessing the predicted impact of regulatory element mutation in mammalian cells | + | * Tuo Li |
| − | * systematically determining regulatory element logic from ENCODE human and mouse data | + | * Peter Li |
| − | * using this sequence based regulatory code to assess common modes of regulatory element evolution and variation | + | * Juinting Chiang |
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| − | 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.
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| − | <h3>About Computational Biology in JHU Biomedical Engineering:</h3>
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| − | 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.
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| − | <h3>[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]</h3>
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| − | <h3>[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]</h3>
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| − | [[File:bmesmall.png]]
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