Postdoctoral Position Available

Lab Page Link

Zhiping Weng, Ph.D.

Academic Role: Professor

Faculty Appointment(s) In:
   Biochemistry and Molecular Pharmacology
   Program in Bioinformatics & Integrative Biology

Other Affiliation(s):
   Interdisciplinary Graduate Program

Bioinformatics and Computational Genomics

We focus our research on regulatory molecules and their interactions, such as regulatory proteins and their DNA/RNA target sites, small silencing RNAs and their RNA targets, and protein-protein interaction. Our lab has three main projects:

• Gene Regulation

We aim to develop computational methods for understanding the molecular mechanism of gene regulation. We develop novel ways to discover transcription factor binding sites in genomic DNA. Because the sequences of these sites are of low information content, we pursue multiple approaches, including better characterizing transcriptional start sites and alternative proximal promoters, detecting clusters of transcription factor binding sites using probabilistic models, and identifying genes that are co-regulated and taking advantage of the enrichment of the sequence motifs in their promoters. We take an integrative approach using extensive high-throughput genomic and epigenomic data, such as chromatin-immunoprecipitation of transcription factors, nucleosome positioning, histone modifications, DNA methylation, and DNA replication.

• Protein Docking

We develop methods to compute binding affinities between protein molecules. Combining this ability with a fast Fourier transform-based search algorithm, we develop computational methods for predicting protein-complex structures. We take a multiple-stage approach, i.e., we develop an initial stage algorithm ZDOCK to perform an exhaustive search in the translational and rotational space, and subsequent refinement algorithms such as ZRANK for structure refinement and reranking. We participate in the community-wide blind test of protein docking algorithms CAPRI.

• Small Silencing RNAs

We develop computational methods to understand the biogenesis and regulatory mechanisms of small silencing RNAs (microRNAs or miRNAs, small silencing RNAs or siRNAs, and PIWI-interacting RNAs or piRNAs). We build computational pipelines to analyze high-throughput sequencing data of small silencing RNAs. We map tens of millions of sequence reads to the genome, quantify their length and nucleotide properties, genomic localization, relative abundance in different cell types and/or genotypes, evolutionary conservation, and discover any other features that can uncover the biogenesis and target recognition of the small silencing RNAs.

 For a complete list of publications with the PDF files of the articles, please see  http://zlab.umassmed.edu/zlab/publications.shtml

Recent Publications

• Klattenhoff C., Xi H., Li C., Lee S., Xu J., Khurana JS, Zhang F., Schultz N., Koppetsch BS., Nowosielska A., Seitz H., *Zamore PD., *Weng Z., *Theurkauf WE.(2009) *Co-corresponding authors. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell, Sep 18;138(6):1137-49. Epub 2009 Sep 3.
• Yu L, Coelho JE, Zhang X, Fu Y, Tillman A, Karaoz U, Fredholm BB, Weng Z, Chen JF. (2009)Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling. Physiol Genomics. May 13;37(3):199-210.
• Li, C., Vagin, V.V., Lee, S., Xu, J., Ma. S., Xi, H., Seitz, H., Horwich, M., Syrzycka, M., Honda, B., Kittler, E., Zapp, M., Klattenhoff, C., Schulz, N., Theurkauf, W., Weng, Z.,* Zamore, PD.* (2009) *Co-corresponding Authors. Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies. Cell. May 1;137(3):509-21. Epub 2009 Apr 23.
• Haidar, J.N.*, Pierce, B.*, Yu, Y., Tong, W., Li M., and Weng, Z. (2009) *Joint First Authors. Structure-Based Design of a T-Cell Receptor Leads to Nearly 100-Fold Improvement in Binding Affinity for pepMHC. Proteins: Structure, Function, and Bioinformatics, 74(4):948-960.
• Hwang, H., Pierce, B., Mintseris, J., Janin, J., and Weng, Z. (2008) Protein-protein docking benchmark version 3.0. Proteins: Structure, Function, and Bioinformatics, 73(3):705-709.
• Fu, Y., Sinha, M., Peterson, C. L., and Weng, Z. (2008) The Insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.   PLoS Genet., July; 4(7): e1000138.
• Ghildiya, M., Seitz, H., Horwich, M. D., Li, C., Du, T., Lee, S., Xu, J., Kittler, E. L., Zapp, M. L., Weng, Z., Zamore P.D. (2008) Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells. Science, May 23;320(5879):1077-81.
• Pierce B. & Weng Z. (2008) A combination of rescoring and refinement significantly improves protein docking performance. Proteins: Structure, Function, and Bioinformatics, 72(1):270-279
• Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z (2007)
  Nucleosome Positioning Signals in Genomic DNA. Genome Research, 17, 1170-1177.
• Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, and Weng Z (2007) Integrating Statistical Pair Potentials into Protein Complex Prediction. Proteins, 69(3), 511-520.
• Xi H., Shulha H.P., Lin J.M., Vales T.R., Fu Y., Bodine D.M., McKay R.D.J, Chenoweth J.G., Tesar P.J., Furey T.S., Ren B., Weng Z.⁺, Crawford G.E.⁺ (2007) +Co-corresponding authors  Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genetics, 8, 8-20.
• The ENCODE Consortium (2007)  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.  Nature 447, 799-816.  Weng Z. was as a co-chair for the ENCODE Transcriptional Regulation analysis group and a co-corresponding author of this Nature article.
• Trinklein ND*, Karaoz U*, Wu J*, Halees A*, Aldred SF, Collin PJ, Zheng D, Zhang ZD, Gerstein M, Snyder M, Myers RM⁺, Weng Z⁺ (2007) *Authors contributed equally. +Co-corresponding authors.  Integrated analysis of experimental datasets reveals many novel promoters in 1% of the human genome. Genome Research 17, 720-731.
• Xi H, Yu Y, Foley J, Halees A, Weng Z (2007) Analysis of Overrepresented Motifs in Human Core Promoters Reveals Dual Regulatory Roles of YY1.  Genome Research 17, 798-806.
• Lin J, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z (2007)
  Transcription Factor Binding and Modified Histones in Human Bidirectional Promoters.
  Genome Research 17, 818-827.

Please contact Dr. Weng for information on rotations that are available in her lab.

Zhiping Weng graduated from theUniversity of Science and Technology of China in 1992 with B.S. in Electrical Engineering. In 1993, she entered the graduate program in Biomedical Engineering at Boston University, and received her Ph.D. in 1997. The focus of her thesis research was in computational biology, specifically on calculating binding free energies of protein-protein interactions. In January 1997 Dr. Weng was appointed Instructor of Biomedical Engineering at Boston University. In that capacity she taught and conducted research, and had primary responsibility for the development of the Bioinformatics program and the core curriculum in Bioinformatics.  In January 1999 the Biomedical Engineering Department at Boston University decided to grow in the area of Bioinformatics.  After a national search, the department appointed Dr. Weng a tenure-track assistant professor. In September 2003, Dr. Weng was promoted to Associate Professor with tenure. Until December 2007, Dr. Weng’s research had been focused on developing computational methods to obtain a predictive understanding of transcriptional regulation and protein-protein interaction. She had published 90 articles, including 75 peer-reviewed journal articles.

On 1 January 2008, Dr. Weng moved to University of Massachusetts Medical School to build and direct a new Program in Bioinformatics and Integrative Biology. She is a full professor, with tenure in Department of Biochemistry and Molecular Pharmacology. She continues research on computational analysis of transcriptional regulation. She has started to study epigenomics and nucleosome positioning, which play important roles in transcriptional regulation. In addition, she is investigating the function and regulation of small RNAs in metazoan. For more information, please visit Dr. Weng's lab Website (http://zlab.umassmed.edu/ ).

Office: LRB 1010
Phone: 508-856-8866
Fax: 508-856-2392
E-mail: Zhiping.Weng@umassmed.edu
Keywords: Systems Biology, Genomics, Bioinformatics, Gene Expression, Gene Regulation

More on Zhiping Weng's Research Research | Publications | Rotations | Biography View All Sections on One Page

Postdoctoral Position Available Please contact Dr. Weng directly for more information regarding this post-doctoral position. Postdoc Position in Comparative Genomics The laboratories of Profs. Zhiping Weng (Bioinformatics) and Bob Brown (Neurology) at University of Massachusetts Medical School (UMMS) invite applications for a postdoc position in comparative genomics. In an NIH-funded project undertaken jointly with Dr. David Goldstein (Director, Center for Human Genome Variation, Institute for Genome Sciences & Policy, Duke University), the Brown lab will perform whole genome sequencing with the Solexa platform on 40 amyotrophic lateral sclerosis (ALS) patients. The postdoc will develop and apply computational tools to analyze this wealth of sequence data and identify genetic variations among the individuals and prioritize them with other functional data, such as those generated with the HapMap and ENCODE projects. Subsequently, the Brown lab will genotype the prioritized variations in cohorts of 1,000 cases and 1,000 controls, and the postdoc will participate in the analysis of the resulting data to discover determinants of susceptibility and phenotype. An ideal candidate would have a PhD in computational biology, bioinformatics, computer science, or another quantitative field and have substantial experience in analyzing high-throughput genomics data. Excellent programming skills and statistics knowledge are essential. UMMS is a highly collaborative research environment and Profs. Weng and Brown have recently been recruited to UMMS to establish the Program in Bioinformatics and Integrative Biology and neurogenetics research in the Neurology Department. The collaboration between the two labs will lead to many future projects in comparative genomics and its application to human diseases.