Dr. Shen joined the Department of Neuroscience at the Icahn School of Medicine at Mount Sinai in 2009 with a Ph.D. in computer science. He is currently associate professor of bioinformatics. He has made contributions to epigenomics in brain diseases and bioinformatic tools development. His current research interests include the applications of machine learning in healthcare and genomics. He has more than 90 publications with >5,500 total citations. See his Google scholar page for a full list of his publications. Visit Li Shen's Laboratory of Bioinformatics for more information on his research activities.
Addiction, Bioinformatics, Biomedical Informatics, Breast Cancer, Chromatin, Computational Biology, Depression, Epigenomics, Genomics, Image Analysis, Mathematical Modeling of Biomedical Systems, Mathematical and Computational Biology, Neural Networks
BS, Fudan University
PhD, Nanyang Technological University
Postdoc, University of California San Diego
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Burroughs Wellcome Funds for Interfaces in Science
IBM ViaVoice National Campus Application Contest Excellence Prize
Large-scale next-generation sequencing data analysis
Our research scope includes but is not limited to: ChIP-seq, RNA-seq, small RNA-seq and DNA methyl-seq. From 2009-2016, my group analyzed more than 6,000 NGS samples with a total storage of more than 50TB. The results have generated numerous publications in top-tier journals, such as Nature, Neuron, Nature Neuroscience, Genome Biology and PNAS.
Dr. Shen has made several contributions to the open-source machine learning community: https://github.com/lishen/my-contributions-to-open-ml. He has also done some research in using machine learning for automated genome segmentation: http://dx.doi.org/10.1101/034579. Machine learning has and will always be an important tool for his research and a focus of research on its own.
Software for next-generation sequencing analysis
We have developed two popular programs: diffReps (https://github.com/shenlab-sinai/diffreps) for ChIP-seq differential analysis and ngs.plot (https://github.com/shenlab-sinai/ngsplot) for data mining and visualization of NGS data. Please visit our group Github page at: https://github.com/shenlab-sinai.
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Dr.Shen did not report having any of the following types of financial relationships with industry during 2018 and/or 2019: consulting, scientific advisory board, industry-sponsored lectures, service on Board of Directors, participation on industry-sponsored committees, equity ownership valued at greater than 5% of a publicly traded company or any value in a privately held company. Please note that this information may differ from information posted on corporate sites due to timing or classification differences.
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