- ASSISTANT PROFESSOR Neuroscience
B.S., Fudan University
Department of Computer Science and Engineering
Ph.D., Nanyang Technological University
School of Computer Engineering
Postdoc, University of California
Department of Biochemistry
Dr. Shen joined the Department of Neuroscience at the Mount Sinai School of Medicine in Oct. 2009 as an assistant professor. His group focuses on the analysis of Nextgen sequencing data for epigenetic changes in drug addiction and depression. He is also interested in developing novel computational tools for short read sequencing data analysis.
Visit Li Shen's Laboratory of Bioinformatics for more information.
Burroughs Wellcome Funds for Interfaces in Science
IBM ViaVoice National Campus Application Contest Excellence Prize
Specific Projects: Epigenomic changes in mouse brain regions in chronic drug administration and depression; Identification of modified histone modification sites from ChIP-seq data; Genome-wide association of various Nextgen sequencing data, including RNA-seq, ChIP-seq and DNA methyl-seq.
Postdoctoral Fellows: Ying Jin
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).
Warren BL, Vialou VF, Iñiguez SD, Alcantara LF, Wright KN, Feng J, Kennedy PJ, Laplant Q, Shen L, Nestler EJ, Bolaños-Guzmán CA. Neurobiological sequelae of witnessing stressful events in adult mice. Biological psychiatry 2013 Jan; 73(1).
Shen L, Choi I, Nestler EJ, Won KJ. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective. Genomics & informatics 2013 Jun; 11(2).
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).
Kurita M, Holloway T, García-Bea A, Kozlenkov A, Friedman AK, Moreno JL, Heshmati M, Golden SA, Kennedy PJ, Takahashi N, Dietz DM, Mocci G, Gabilondo AM, Hanks J, Umali A, Callado LF, Gallitano AL, Neve RL, Shen L, Buxbaum JD, Han MH, Nestler EJ, Meana JJ, Russo SJ, González-Maeso J. HDAC2 regulates atypical antipsychotic responses through the modulation of mGlu2 promoter activity. Nature neuroscience 2012 Sep; 15(9).
Warren BL, Vialou VF, Iñiguez SD, Alcantara LF, Wright KN, Feng J, Kennedy PJ, Laplant Q, Shen L, Nestler EJ, Bolaños-Guzmán CA. Neurobiological Sequelae of Witnessing Stressful Events in Adult Mice. Biological psychiatry 2012 Jul;.
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.
Shen L, Chepelev I, Liu J, Wang W. Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation. BMC Systems Biology 2010; 4(1).
Won K, Agarwal S, Shen L, Shoemaker R, Ren B, Wang W. An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome. PLoS ONE 2009; 4(5).
Shen L, Liu J, Wang W. GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach. BMC Bioinformatics 2008; 9(1).
Hawkins D, Hon G, Lee L, Ngo Q, Lister R, Pelizzola M, Edsall L, Kuan S, Luu Y, Klugman S, Antosiewicz-Bourget J, Ye Z, Espinoza C, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson J, Ecker J, Ren B. Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells. Cell Stem Cell 2010; 6(5): 479-491.
Shen L, Tan E. Reducing multiclass cancer classification to binary by output coding and SVM. Computational Biology and Chemistry 2006; 30(1): 63-71.
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.
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 2012 and/or 2013: 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 at http://icahn.mssm.edu/about-us/services-and-resources/faculty-resources/handbooks-and-policies/faculty-handbook. Patients may wish to ask their physician about the activities they perform for companies.
Icahn Medical Institute Floor 10 Room 20D
1425 Madison Avenue
New York, NY 10029