Shenlab-sinai

Shenlab's unofficial (but most updated) website

Shen Lab@Mount Sinai

Our lab is located on the Mount Sinai campus in the New York City. We are on the Madison Avenue that is only one block away from the central park. Our lab is about bioinformatics and currently there are two focuses:

  1. Large-scale next-generation sequencing (NGS) analysis
  2. Novel software development for NGS analytics

This is our webpage on Github. For our official webpages (yes, there are two), please visit Mount Sinai Profile and Neuroscience Department Website.

Members

We are actively looking for a postdoc in bioinformatics with emphasis on NGS analysis and software. Interested? Send your CV to li.shen@mssm.edu.

Li Shen, Principal Investigator, @shenlab-sinai, @lishen

Ningyi Shao, postdoc, @ny-shao

Immanuel Purushothaman, bioinformatician, @ipurusho

Past Members

Ying Jin, postdoc ==> scientist@Cold Spring Harbor Laboratory

Xiaochuan Liu, postdoc ==> postdoc@Rutgers University

Software Projects

These are the software we are currently working on:

We have participated in:

STAR genome browser: An Integrated Solution to Management and Visualization of Sequencing Data. STAR website

Publications (See citations on Google Scholar)

2014

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. Paper on BMC genomics

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.

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.

2013

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. Paper on PLoS ONE

Wang, T., Liu, J., Shen, L., Tonti-Filippini, J., Zhu, Y., Jia, H., Lister, R., Whitaker, J.W., Ecker, J.R., Millar, A.H., Ren, B. and Wang, W. (2013) STAR: an integrated solution to management and visualization of sequencing data, Bioinformatics, 29, 3204-3210.

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.

Ferguson, D., Koo, J.W., Feng, J., Heller, E., Rabkin, J., Heshmati, M., Renthal, W., Neve, R., Liu, X., Shao, N., Sartorelli, V., Shen, L. and Nestler, E.J. (2013) Essential Role of SIRT1 Signaling in the Nucleus Accumbens in Cocaine and Morphine Action, The Journal of Neuroscience, 33, 16088-16098.

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. (2013) Neurobiological Sequelae of Witnessing Stressful Events in Adult Mice, Biological Psychiatry, 73, 7-14.

2012

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.

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.

2010-2011

Maze, I., Feng, J., Wilkinson, M.B., Sun, H., Shen, L. and Nestler, E.J. (2011) Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens, Proceedings of the National Academy of Sciences, 108, 3035-3040.

Hawkins, R.D., Hon, G.C., Lee, L.K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L.E., 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.A., Ecker, J.R. and Ren, B. (2010) Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells, Cell Stem Cell, 6, 479-491.

Shen, L., Chepelev, I., Liu, J. and Wang, W. (2010) Prediction of quantitative phenotypes based on genetic networks: a case study in yeast sporulation, BMC Systems Biology, 4, 128.

2005-2009

Won, K.-J., Agarwal, S., Shen, L., Shoemaker, R., Ren, B. and Wang, W. (2009) An Integrated Approach to Identifying Cis-Regulatory Modules in the Human Genome, PLoS ONE, 4, e5501.

Shen, L., Liu, J. and Wang, W. (2008) GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach, BMC Bioinformatics, 9, 395.

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

Shen, L. and Tan, E.C. (2006) A Generalized Output-Coding Scheme with SVM for Multiclass Microarray Classification. Fourth Asia-Pacific Bioinformatics Conference. Imperial College Press, Taipei, Taiwan, pp. 179-186.

Shen, L. and Tan, E.C. (2005) Dimension Reduction-Based Penalized Logistic Regression for Cancer Classification Using Microarray Data, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 02, 166-175.

Shen, L. and Tan, E.C. (2005) Combining Kernel Dimension-Reduction with Regularized Classifiers for Tissue Categorization, Online Journal of Bioinformatics, 6, 91-98.


*Correspondence Author