Li Shen, PhD

• 2006
  Burroughs Wellcome Funds for Interfaces in Science
  

• 2000
  IBM ViaVoice National Campus Application Contest Excellence Prize
  

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.

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.

Machine learning

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.

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 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, 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).

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).

Shen L. Automatic genome segmentation with HMM-ANN hybrid models. bioRxiv 2015;.

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).