Deyou Zheng PI: Deyou Zheng, Ph.D.
Email: deyou.zheng aT
Phone: 718-678-1217
Office: Price 320

Our lab is in the Department of Neurology at Albert Einstein College of Medicine. We are located in Rose F. Kennedy Center for Intellectual and Developmental Disabilities Research. Our lab is also affiliated with the Institute for Brain Disorders and Neural Regeneration, and member of the Department of Genetics and the Department of Neuroscience. The research areas of the lab are computational genomics and bioinformatics, with a strong focus on mining and interpreting large-scale genomic data. We develop and apply computational techniques for integrating data from comparative genomics and functional (epi)genomics to understand the structure, function and evolution of the human genome, and to investigate its functional importances in developments and diseases.

+ Research

Decoding the human genome and other mammalian genomes is our primary research interest, and comparative genomics and integrated analysis of functional genomics data are our major research approaches. In general, we are interested in developing and applying computational methods for exploiting patterns in high-throughput genomic data and for extracting information from experimental and computational bigdata. We are highly interested in studying the expression, regulation, and evolution of human nervous systems genes (coding or noncoding), especially those implicated in neuropsychiatric disorders, using big experimental data from next-generation sequencing (e.g., ChIP-Seq and RNA-Seq). One fundamental question of our research is how a single human genome is used for establishing and maintaining distinct cell lineages and how this important process is disrupted during disease development. Our research group focuses on these areas:

+ iPSC system for studying the genetic basis of psychiatric disorders, to use iPSC technology for studying neural development and abnormal gene regulation in neuropsychiatric disorders, like schizophrenia and autism spectrum disorders.

In collaboration with experimentalist experts, we grow human neurons in dish by induced pluripotent stem cell (iPSC) technology in order to model human neuronal development and differentiation. We begin by developing iPSC lines from both patients and healthy subjects, differentiate them to neural progenitors and neurons, then use RNA-seq and other deep sequencing technology to identify differentially regulate genes by comparing the transcriptomes between patient-derived neurons and controls. Using this systems biology approach, we have identified many novel long non-coding RNA genes that are involved in embryonic neurogenesis and potentially neuropsychiatric disorders. We also find that many genes show allele-biased gene expression in different brain regions, including some that have been implicated in major psychiatric disorders, which may help explain some aspects of parent-of-origin effects, twin discordance and reduced penetrance. Our studies have also continously to uncover molecular pathways that are affected by critical genes that are major risk factors for schizophrenia and autisms.

+ Integrated analysis of functional genomics data, to explore computational techniques for combining experimental and computational genomics data in order to achieve a global understanding of the function of the human genome.

We are interested in developing bioinformatics algorithms to mine big genomics data and to conduct cross-genome sequence comparisons (e.g., syntenic assignment) with a focus on deciphering the gene regultory networks underlying normal development and development disorders. As large amount of functional genomic data from diverse sources (microarray, high-throughput sequencing, protein-protein interaction, etc.) are combined and used in our studies, our group develop and apply effective computational methods for data integration and at the same time for addressing common concerns of data quality in genome-scale experiments. A rigorous statistical framework needs to be built in order to extract biologically meaningful signals from noises or stochastic background.

+ Gene duplication, to investigate how gene duplication has shaped the human genome and how novel genes or regulatory elements emerge in humans and other primates.

Gene expansion (through either duplication or retrotransposition) is a major driving force for the emergence of novel functions during evolution. Inter- and intra-genome sequence comparison can reveal DNA elements that are either uniquely present or specifically selected in certain species. Tracking the evolutionary history of such sequences can lead to the discovery of genes or regulatory elements (including non-coding RNAs) that function specifically in humans. Thus, the long-term goal is to search for functional genomic components that set us apart from other animals. To this end, our research will compare the human genome with other mammalian (e.g., chimp, macaque, dog, and mouse) genomes to exploit the role of gene duplication in generating novel protein-protein interactions and novel biochemical pathways. We are interested in both the birth and the death (pseudogenization or loss) of such lineage-specific functional DNA sequences, especially for those involved in the development of nervous system and brains.

+ Functional implication of alternative splicing, to investigate how higher eukaryotes (e.g., humans) achieve functional diversity through producing multiple RNA transcripts from one gene locus.

We are particularly interested in the generation of isoforms in different tissues / cells and how these special isoforms carry out their tissue-specific functions.

+ People

+ PI: Deyou Zheng, Associate Professor.

  • YALE UNIVERSITY, New Haven, CT. 2003-2007, Postdoctoral Fellow, Department of Molecular Biophysics and Biochemistry. Research Area: Bioinformatics & Human Genomics.
  • RUTGERS UNIVERSITY, Piscataway, NJ. Ph.D. in Biochemistry, 2003. Rsearch Area: Structural Genomics & Bioinformatics.
  • AUBURN UNIVERSITY, Auburn, AL. M.S. in Pathobiology, 1998. Research Area: Molecular Biology.
  • BEIJING¬†AGRICULTURAL UNIVERSITY, Beijing, China. B.S. in Microbiology, 1992

+ Mingyan Lin, Graduate Student.

+ Yilin Zhao, Graduate Student.

+ Dejian Zhao, Postdoctoral Fellow.

+ Ping Wang, Postdoctoral Fellow.

+ Shira Rockowitz, Graduate Student. 09/10-05/15

+ Xingyi Guo, Postdoctoral Fellow. 09/08-03/13

+ Positions

We are looking for enthusiastic undergraduate students, graduate students, and postdoctoral associates to join our group. Reasonable computer programming skills is a plus. Candidates are expected to work in a wide range of bioinformatics projects. Please contact the PI, Deyou Zheng, for details.

Selected Publications (*co-corresponding authors)

1. Wang P#, Lin M#, Pedrosa E, Hrabovsky A, Zhang Z, Guo W, Lachman HM*, Zheng D*. (2015). CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment. Molecular Autism 6:55. (*co-corresponding authors)
2. Adam RC, Yang H, Rockowitz S, Larsen SB, Nikolova M, Oristian DS, Polak L, Kadaja M, Asare A, Zheng D, Fuchs E. (2015). Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice. Nature 521:366-370
3. Rockowitz S, Lien WH, Pedrosa E, Wei G, Lin M, Zhao K, Lachman HM, Fuchs E, Zheng D. (2014). Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions. PLoS Comput Biol 10: e1003671
4. Chen Y, Chi P, Rockowitz S, Iaquinta PJ, Shamu T, Shukla S, Gao D, Sirota I, Carver BS, Wongvipat J, Scher HI, Zheng D, Sawyers CL. (2013) ETS Factors Reprogram the Androgen Receptor Cistrome and Prime Prostate Tumorigenesis in Response to PTEN Loss. Nat Med 19: 1023-1029.
5. Wontakal SN, Guo X, Smith C, Maccarthy T, Bresnick EH, Bergman A, Snyder MP, Weissman SM*, Zheng D*, Skoultchi AI*. (2012). A Core Erythroid Transcriptional Network is Repressed by a Master Regulator of Myelo-lymphoid Differentiation. Proc Natl Acad Sci USA 109: 3832-3837
6. Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, Wen D, Chapgier A, DeKelver RC, Miller JC, Lee YL, Boydston EA, Holmes MC, Gregory PD, Greally JM, Rafii S, Yang C, Scambler PJ, Garrick D, Gibbons R, Higgs DR, Cristea IM, Urnov FD, Zheng D*, Allis CD* (2010). Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions. Cell 140:678-691.
7. Guo X, Zhang Z, Gerstein M, Zheng D. (2009) Small RNAs Originated from Pseudogenes: cis- or trans-Acting? PLoS Comput Biol 5:e1000449.
8. Zheng D*, Zhao K, Mehler M. (2009) Profiling RE1/REST-mediated Histone Modifications in the Human Genome. Genome Biol 10:R9. (*corresponding author)
9. Zheng D. (2008) Asymmetric Histone Modifications between the Original and Derived Loci of Human Segmental Duplications. Genome Biol 9:R105.
10. Zheng D, Gerstein M. (2007) The Ambiguous Boundary between Genes and Pseudogenes: the dead rise up, or do they? Trends Genet 23: 219-24.