Shen Lab

Laboratory of Bioinformatics

Research

Shen LiTo study the molecular mechanisms of drug addiction and depression, a lot of high throughput experimental data have been generated. Our lab focuses on the statistical and integrated analysis of these data and generates biological insights. We are especially interested in the next-generation sequencing data which provides a comprehensive and high-resolution view of the biological systems under study. We also develop bioinformatic tools employing Bayesian inference and machine learning to aid our data analysis.

Contact Us

Shen Laboratory
Li Shen, PhD
Professor, Neuroscience
Location
Lab: ICAHN 10-26
Office: ICAHN 10
Phone
Office: 212.659.8622
Email

Publications

2016

Sun, H., Martin, J.A., Werner, C.T., Wang, Z.-J., Damez-Werno, D.M., Scobie, K.N., Shao, N.-Y., Dias, C., Rabkin, J., Koo, J.W., Gancarz, A.M., Mouzon, E.A., Neve, R.L., Shen, L., Dietz, D.M. and Nestler, E.J. (2016) BAZ1B in Nucleus Accumbens Regulates Reward-Related Behaviors in Response to Distinct Emotional Stimuli, The Journal of Neuroscience, 36, 3954-3961.


Loh, Y.-H.E. and Shen, L. (2016) Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot. In Carugo, O. and Eisenhaber, F. (eds), Data Mining Techniques for the Life Sciences. Springer New York, New York, NY, pp. 371-383.


Bagot, R.C., Cates, H.M., Purushothaman, I., Lorsch, Z.S., Walker, D.M., Wang, J., Huang, X., Schluter, O.M., Maze, I., Pena, C.J., Heller, E.A., Issler, O., Wang, M., Song, W.M., Stein, J.L., Liu, X., Doyle, M.A., Scobie, K.N., Sun, H.S., Neve, R.L., Geschwind, D., Dong, Y., Shen, L., Zhang, B. and Nestler, E.J. (2016) Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility, Neuron.

2015

Shen, L. (2015) Automatic genome segmentation with HMM-ANN hybrid models. Workshops on Machine Learning in Computational Biology at the Annual Conference on Neural Information Processing Systems (NIPS). bioRxiv, http://dx.doi.org/10.1101/034579.


Sun, H., Damez-Werno, D.M., Scobie, K.N., Shao, N.Y., Dias, C., Rabkin, J., Koo, J.W., Korb, E., Bagot, R.C., Ahn, F.H., Cahill, M.E., Labonte, B., Mouzon, E., Heller, E.A., Cates, H., Golden, S.A., Gleason, K., Russo, S.J., Andrews, S., Neve, R., Kennedy, P.J., Maze, I., Dietz, D.M., Allis, C.D., Turecki, G., Varga-Weisz, P., Tamminga, C., Shen, L. and Nestler, E.J. (2015) ACF chromatin-remodeling complex mediates stress-induced depressive-like behavior, Nat Med, 21, 1146-1153.


Mitsi, V., Terzi, D., Purushothaman, I., Manouras, L., Gaspari, S., Neve, R.L., Stratinaki, M., Feng, J., Shen, L. and Zachariou, V. (2015) RGS9-2–controlled adaptations in the striatum determine the onset of action and efficacy of antidepressants in neuropathic pain states, Proceedings of the National Academy of Sciences, 112, E5088-E5097.


Ferguson, D., Shao, N., Heller, E., Feng, J., Neve, R., Kim, H.-D., Call, T., Magazu, S., Shen, L. and Nestler, E.J. (2015) SIRT1-FOXO3a Regulate Cocaine Actions in the Nucleus Accumbens, The Journal of Neuroscience, 35, 3100-3111.


Ding, J., Huang, X., Shao, N., Zhou, H., Lee, D.F., Faiola, F., Fidalgo, M., Guallar, D., Saunders, A., Shliaha, P.V., Wang, H., Waghray, A., Papatsenko, D., Sanchez-Priego, C., Li, D., Yuan, Y., Lemischka, I.R., Shen, L., Kelley, K., Deng, H., Shen, X. and Wang, J. (2015) Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming, Cell Stem Cell, 16, 653-668.


Feng, J., Shao, N., Szulwach, K.E., Vialou, V., Huynh, J., Zhong, C., Le, T., Ferguson, D., Cahill, M.E., Li, Y., Koo, J.W., Ribeiro, E., Labonte, B., Laitman, B.M., Estey, D., Stockman, V., Kennedy, P., Courousse, T., Mensah, I., Turecki, G., Faull, K.F., Ming, G.-l., Song, H., Fan, G., Casaccia, P., Shen, L., Jin, P. and Nestler, E.J. (2015) Role of Tet1 and 5-hydroxymethylcytosine in cocaine action, Nat Neurosci, 18, 536-544.


Hodes, G.E., Pfau, M.L., Purushothaman, I., Ahn, H.F., Golden, S.A., Christoffel, D.J., Magida, J., Brancato, A., Takahashi, A., Flanigan, M.E., Ménard, C., Aleyasin, H., Koo, J.W., Lorsch, Z.S., Feng, J., Heshmati, M., Wang, M., Turecki, G., Neve, R., Zhang, B., Shen, L., Nestler, E.J. and Russo, S.J. (2015) Sex Differences in Nucleus Accumbens Transcriptome Profiles Associated with Susceptibility versus Resilience to Subchronic Variable Stress, The Journal of Neuroscience, 35, 16362-16376.


Maze, I., Wenderski, W., Noh, K.-M., Bagot, Rosemary C., Tzavaras, N., Purushothaman, I., Elsässer, Simon J., Guo, Y., Ionete, C., Hurd, Yasmin L., Tamminga, Carol A., Halene, T., Farrelly, L., Soshnev, Alexey A., Wen, D., Rafii, S., Birtwistle, Marc R., Akbarian, S., Buchholz, Bruce A., Blitzer, Robert D., Nestler, Eric J., Yuan, Z.-F., Garcia, Benjamin A., Shen, L., Molina, H. and Allis, C.D. (2015) Critical Role of Histone Turnover in Neuronal Transcription and Plasticity, Neuron, 87, 77-94.


Noh, K.M., Maze, I., Zhao, D., Xiang, B., Wenderski, W., Lewis, P.W., Shen, L., Li, H. and Allis, C.D. (2015) ATRX tolerates activity-dependent histone H3 methyl/phos switching to maintain repetitive element silencing in neurons, Proc Natl Acad Sci U S A, 112, 6820-6827.


Roadmap Epigenomics, Consortium (2015) Integrative analysis of 111 reference human epigenomes, Nature, 518, 317-330.

2014

Dias, C., Feng, J., Sun, H., Shao, N.y., Mazei-Robison, M.S., Damez-Werno, D., Scobie, K., Bagot, R., LaBonte, B., Ribeiro, E., Liu, X., Kennedy, P., Vialou, V., Ferguson, D., Pena, C., Calipari, E.S., Koo, J.W., Mouzon, E., Ghose, S., Tamminga, C., Neve, R., Shen, L. and Nestler, E.J. (2014) [bgr]-catenin mediates stress resilience through Dicer1/microRNA regulation, Nature, advance online publication.


Heller, E.A., Cates, H.M., Pena, C.J., Sun, H., Shao, N., Feng, J., Golden, S.A., Herman, J.P., Walsh, J.J., Mazei-Robison, M., Ferguson, D., Knight, S., Gerber, M.A., Nievera, C., Han, M.H., Russo, S.J., Tamminga, C.S., Neve, R.L., Shen, L., Zhang, H.S., Zhang, F. and Nestler, E.J. (2014) Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors, Nat Neurosci, 17, 1720-1727.


Maze, I., Shen, L., Zhang, B., Garcia, B.A., Shao, N., Mitchell, A., Sun, H., Akbarian, S., Allis, C.D. and Nestler, E.J. (2014) Analytical tools and current challenges in the modern era of neuroepigenomics, Nat Neurosci, 17, 1476-1490.


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, E. and Shen, L. (2014) Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens, Genome Biology, 15, R65.


Shen, L., Shao, N., Liu, X. and Nestler, E. (2014) ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases, BMC Genomics, 15, 284.


Scobie, K.N., Damez-Werno, D., Sun, H., Shao, N., Gancarz, A., Panganiban, C.H., Dias, C., Koo, J., Caiafa, P., Kaufman, L., Neve, R.L., Dietz, D.M., Shen, L. and Nestler, E.J. (2014) Essential role of poly(ADP-ribosyl)ation in cocaine action, Proceedings of the National Academy of Sciences, 111, 2005-2010.


Maze, I., Chaudhury, D., Dietz, D.M., Von Schimmelmann, M., Kennedy, P.J., Lobo, M.K., Sillivan, S.E., Miller, M.L., Bagot, R.C., Sun, H., Turecki, G., Neve, R.L., Hurd, Y.L., Shen, L., Han, M.H., Schaefer, A. and N

2013

Shen, L., Choi, I., Nestler, E.J. and Won, K.-J. (2013) Human Transcriptome and Chromatin Modifications: An ENCODE Perspective, Genomics Inform, 11, 60-67.


Shen, L., Shao, N.-Y., Liu, X., Maze, I., Feng, J. and Nestler, E.J. (2013) diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates, PLoS ONE, 8, e65598.


Warren, B.L., Vialou, V.F., Iñiguez, S.D., Alcantara, L.F., Wright, K.N., Feng, J., Kennedy, P.J., LaPlant, Q., Shen, L., Nestler, E.J. and Bolanos – Guzman, C.A. (2013) Neurobiological Sequelae of Witnessing Stressful Events in Adult Mice, Biological Psychiatry, 73, 7-14.

2012

Kurita, M., Holloway, T., Garcia – Bea, A., Kozlenkov, A., Friedman, A.K., Moreno, J.L., Heshmati, M., Golden, S.A., Kennedy, P.J., Takahashi, N., Dietz, D.M., Mocci, G., Gabilondo, A.M., Hanks, J., Umali, A., Callado, L.F., Gallitano, A.L., Neve, R.L., Shen, L., Buxbaum, J.D., Han, M.-H., Nestler, E.J., Meana, J.J., Russo, S.J. and Gonzalez-Maeso, J. (2012) HDAC2 regulates atypical antipsychotic responses through the modulation of mGlu2 promoter activity, Nat Neurosci, 15, 1245-1254.


Sun, H., Maze, I., Dietz, D.M., Scobie, K.N., Kennedy, P.J., Damez – Werno, D., Neve, R.L., Zachariou, V., Shen, L.* and Nestler, E.J.* (2012) Morphine Epigenomically Regulates Behavior through Alterations in Histone H3 Lysine 9 Dimethylation in the Nucleus Accumbens, The Journal of Neuroscience, 32, 17454-17464.


Warren, B.L., Vialou, V.F., Iñiguez, S.D., Alcantara, L.F., Wright, K.N., Feng, J., Kennedy, P.J., LaPlant, Q., Shen, L., Nestler, E.J. and Bolaños – Guzmán, C.A. (in press) Neurobiological Sequelae of Witnessing Stressful Events in Adult Mice, Biological Psychiatry.

Meet the Team

noimageprofileEddie Loh
Bioinformatician

Data & Software

Data

Cocaine Epigenome Paper – Supplemental Information

Password-protected files. Please obtain the password from Dr. Shen

Software

  • Detecting differential chromatin modification sites from ChIP-seq data with biological replicates – diffReps
  • An easy-to-use visualization tool for global enrichment of next-generation sequencing data – ngs.plot