Section: Publications

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

 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.

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.