Bioinformatics, Computational Biology, Epigenetics, Genomics, Mathematical Modeling of Biomedical Systems, Mathematical and Computational Biology, Neural Networks
BS, Fudan University
PhD, Nanyang Technological University
Postdoc, University of California San Diego
Burroughs Wellcome Funds for Interfaces in Science
IBM ViaVoice National Campus Application Contest Excellence Prize
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.
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.
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.
Shen L, Tan E. Dimension Reduction-Based Penalized Logistic Regression for Cancer Classification Using Microarray Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2005; 2(2): 166-175.
Maze I, Feng J, Wilkinson M, Sun H, Shen L, Nestler E. Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens. Proceedings of the National Academy of Sciences 2011 February; 108(7): 3035-3040.
Sun H, Maze I, Dietz DM, Scobie KN, Kennedy PJ, Damez-Werno D, Neve RL, Zachariou V, Shen L, Nestler EJ. Morphine Epigenomically Regulates Behavior through Alterations in Histone H3 Lysine 9 Dimethylation in the Nucleus Accumbens. The Journal of neuroscience : the official journal of the Society for Neuroscience 2012 Nov; 32(48).
Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PloS one 2013; 8(6).
Wang T, Liu J, Shen L, Tonti-Filippini J, Zhu Y, Jia H, Lister R, Whitaker JW, Ecker JR, Millar AH, Ren B, Wang W. STAR: an integrated solution to management and visualization of sequencing data. Bioinformatics (Oxford, England) 2013 Dec; 29(24).
Feng J, Wilkinson M, Liu X, Purushothaman I, Ferguson D, Vialou V, Maze I, Shao N, Kennedy P, Koo J, Dias C, Laitman B, Stockman V, Laplant Q, Cahill M, Nestler EJ, Shen L. Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome biology 2014 Apr; 15(4).
Shen L, Shao N, Liu X, Nestler E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC genomics 2014; 15.
Dias C, Feng J, Sun H, Shao NY, Mazei-Robison MS, Damez-Werno D, Scobie K, Bagot R, LaBonté B, Ribeiro E, Liu X, Kennedy P, Vialou V, Ferguson D, Peña C, Calipari ES, Koo JW, Mouzon E, Ghose S, Tamminga C, Neve R, Shen L, Nestler EJ. β-catenin mediates stress resilience through Dicer1/microRNA regulation. Nature 2014 Nov;.
Maze I, Shen L, Zhang B, Garcia BA, Shao N, Mitchell A, Sun H, Akbarian S, Allis CD, Nestler EJ. Analytical tools and current challenges in the modern era of neuroepigenomics. Nature neuroscience 2014 Nov; 17(11).
Feng J, Shao N, Szulwach KE, Vialou V, Huynh J, Zhong C, Le T, Ferguson D, Cahill ME, Li Y, Koo JW, Ribeiro E, Labonte B, Laitman BM, Estey D, Stockman V, Kennedy P, Couroussé T, Mensah I, Turecki G, Faull KF, Ming GL, Song H, Fan G, Casaccia P, Shen L, Jin P, Nestler EJ. Role of Tet1 and 5-hydroxymethylcytosine in cocaine action. Nature neuroscience 2015 Apr; 18(4).
Bagot RC, Cates HM, Purushothaman I, Lorsch ZS, Walker DM, Wang J, Huang X, Schlüter OM, Maze I, Peña CJ, Heller EA, Issler O, Wang M, Song WM, Stein JL, Liu X, Doyle MA, Scobie KN, Sun HS, Neve RL, Geschwind D, Dong Y, Shen L, Zhang B, Nestler EJ. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility. Neuron 2016 Jun; 90(5).
Physicians and scientists on the faculty of the Icahn School of Medicine at Mount Sinai often interact with pharmaceutical, device and biotechnology companies to improve patient care, develop new therapies and achieve scientific breakthroughs. In order to promote an ethical and transparent environment for conducting research, providing clinical care and teaching, Mount Sinai requires that salaried faculty inform the School of their relationships with such companies.
Dr.Shen did not report having any of the following types of financial relationships with industry during 2017 and/or 2018: 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.
Mount Sinai's faculty policies relating to faculty collaboration with industry are posted on our website. Patients may wish to ask their physician about the activities they perform for companies.
Physicians who provide services at hospitals and facilities in the Mount Sinai Health System might not participate in the same health plans as those Mount Sinai hospitals and facilities (even if the physicians are employed or contracted by those hospitals or facilities).
Information regarding insurance participation and billing by this physician may be found on this page, and can also be obtained by contacting this provider directly. Because physicians insurance participation can change, the insurance information on this page may not always be up-to-date. Please contact this physician directly to obtain the most up-to-date insurance information.
Insurance and health plan networks that the various Mount Sinai Health System hospitals and facilities participate in can be found on the Mount Sinai Health System website.