neuro
SHEN lab
laboratory of BIOINFORMATICS

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 Nestler, E.J. (2014) G9a influences neuronal subtype specification in striatum, Nat Neurosci, 17, 533-539.

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.

2011

 

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.

2010

 

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).

 

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.

2009

  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).

2008

 

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).

2006

 

Shen L, Tan E. Reducing multiclass cancer classification to binary by output coding and SVM. Computational Biology and Chemistry 2006; 30(1): 63-71.

2005

 

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.

   
Shen Laboratory
Lab Location: ICAHN 10th Floor
Office Location: ICAHN 10-20D
Office: (212) 659 - 8622
Lab Address:
Mount Sinai School of Medicine
1425 Madison Avenue, ICAHN 10-20D
New York, NY 10029

Admin Phone: (212) 659 - 5993
Admin Fax: (212) 849 - 2611
Mount Sinai School of Medicine
One Gustave L. Levy Place
Box 1065
New York, NY 10029

Courier Address:
Mount Sinai School of Medicine
New York, NY 10029