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Zhiping Weng PhD

TitleChair and Professor
Endowed TitleLi Weibo Chair in Biomedical Research
InstitutionUMass Chan Medical School
DepartmentGenomics and Computational Biology
AddressUMass Chan Medical School
55 Lake Avenue North, Albert Sherman Bldg, Rm AS5-1069
Worcester MA 01655
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionT.H. Chan School of Medicine
    DepartmentGenomics and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiophysical Chemical and Computational Biology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentPostbaccalaureate Research Education Program

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentSystems Computational and Quantitative Biology


    Collapse Biography 
    Collapse education and training
    University of Science Technology of China, Hefei, , ChinaBSElectrical Engineering
    Boston University, Boston, MA, United StatesPHDBiomedical Engineering

    Collapse Overview 
    Collapse overview

    Zhiping Weng graduated from the University 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/ ).

    Bioinformatics and Computational Genomics

    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 labhas 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.


    Collapse Rotation Projects

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


    Collapse Post Docs

    The project aims to develop computational algorithms and software programs for analyzing high-throughput sequence data such as ChIP-Seq RNA-Seq small RNA sequencing data. PhD required. A strong background in computational biology especially experience with analyzing high-throughput sequencing data is highly desirable. Excellent communication and writing skills and the ability to work with experimental and computational collaborators are essential.
     
    To apply please forward CV cover letter and three references to:  Zhiping.Weng@umassmed.edu



    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen JF, Akbarian S, Weng Z, Vonsattel JP, Myers RH. miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. BMC Med Genomics. 2015 Mar 01; 8:10. PMID: 25889241.
      Citations: 73     Fields:    Translation:Humans
    2. Bai G, Cheung I, Shulha HP, Coelho JE, Li P, Dong X, Jakovcevski M, Wang Y, Grigorenko A, Jiang Y, Hoss A, Patel K, Zheng M, Rogaev E, Myers RH, Weng Z, Akbarian S, Chen JF. Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. Hum Mol Genet. 2015 Mar 01; 24(5):1441-56. PMID: 25480889.
      Citations: 34     Fields:    Translation:HumansCells
    3. Zhang L, Zhang Z, Weng Z, Shi W. Substitution rates of the internal genes in the novel avian H7N9 influenza virus. Clin Infect Dis. 2013 Oct; 57(8):1213-5. PMID: 23821733.
      Citations: 6     Fields:    Translation:HumansCells
    4. Zhang L, Zhang Z, Weng Z. Rapid reassortment of internal genes in avian influenza A(H7N9) virus. Clin Infect Dis. 2013 Oct; 57(7):1059-61. PMID: 23788242.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    5. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      Citations: 8471     Fields:    Translation:HumansAnimalsCells
    6. Shulha H*, Cheung I*, Whittle C, Wang J, Virgil D, Lin C, Guo Y, Lessard A, Akbarian S+ and Weng+. (2011) . . Epigenetic Signatures of Autism: Histone Methylation H3K4me3 Landscapes in Prefrontal Neurons *Joint First Authors +Co-corresponding authors 2011 Nov 7. 2011; (Arch Gen P).
    7. McNally B, Singer A, Yu Z, Sun Y, Weng Z, Meller A. Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett. 2010 Jun 09; 10(6):2237-44. PMID: 20459065.
      Citations: 61     Fields:    Translation:Cells
    8. Lin JM, Weng Z. Systematic detection of statistically overrepresented DNA motif association rules. Genome Inform. 2006; 17(1):124-33. PMID: 17503362.
      Citations: 1     Fields:    Translation:HumansCells
    9. Peters B, Bui HH, Sidney J, Weng Z, Loffredo JT, Watkins DI, Moth? BR, Sette A. A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules. Vaccine. 2005 Nov 01; 23(45):5212-24. PMID: 16137805.
      Citations: 15     Fields:    Translation:AnimalsCells
    10. Fu Y, Weng Z. Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences. Genome Inform. 2005; 16(1):68-72. PMID: 16362908.
      Citations: 5     Fields:    Translation:Cells
    11. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22; 306(5696):636-40. PMID: 15499007.
      Citations: 1105     Fields:    Translation:HumansAnimalsCells
    12. Leyfer D, Bond A, Tworog E, Perron D, Maska S, Brito A, Kamens J, Weng Z, Voss J. cis-Element clustering correlates with dose-dependent pro- and antisignaling effects of IL18. Genes Immun. 2004 Aug; 5(5):354-62. PMID: 15190265.
      Citations: 1     Fields:    Translation:HumansCells
    13. Frith MC, Halees AS, Hansen U, Weng Z. Site2genome: locating short DNA sequences in whole genomes. Bioinformatics. 2004 Jun 12; 20(9):1468-9. PMID: 14962939.
      Citations: 1     Fields:    
    14. Mintseris J, Weng Z. Optimizing protein representations with information theory. Genome Inform. 2004; 15(1):160-9. PMID: 15712119.
      Citations: 8     Fields:    Translation:Cells
    15. Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins. 2003 Nov 15; 53(3):629-39. PMID: 14579354.
      Citations: 40     Fields:    Translation:Cells
    16. Weng Z. Managing biological sequence and protein structure data. OMICS. 2003; 7(1):25-6. PMID: 12831551.
      Citations:    Fields:    Translation:Cells
    17. Wong JY, Weng Z, Moll S, Kim S, Brown CT. Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin. Biomaterials. 2002 Sep; 23(18):3865-70. PMID: 12164191.
      Citations: 7     Fields:    Translation:AnimalsCells
    18. Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, Clark KE, Haverty P, Weng Z, Mutter GL, Frosch MP, MacDonald ME, Milford EL, Crum CP, Bueno R, Pratt RE, Mahadevappa M, Warrington JA, Stephanopoulos G, Stephanopoulos G, Gullans SR. A compendium of gene expression in normal human tissues. Physiol Genomics. 2001 Dec 21; 7(2):97-104. PMID: 11773596.
      Citations: 181     Fields:    Translation:Humans
    19. Frith MC, Hansen U, Weng Z. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics. 2001 Oct; 17(10):878-89. PMID: 11673232.
      Citations: 107     Fields:    Translation:HumansAnimalsCells
    20. Szustakowski JD, Weng Z. Protein structure alignment using a genetic algorithm. Proteins. 2000 Mar 01; 38(4):428-40. PMID: 10707029.
      Citations: 26     Fields:    Translation:HumansCells
    21. Esposito M, Venkatesh V, Otvos L, Weng Z, Vajda S, Banki K, Perl A. Human transaldolase and cross-reactive viral epitopes identified by autoantibodies of multiple sclerosis patients. J Immunol. 1999 Oct 01; 163(7):4027-32. PMID: 10491006.
      Citations: 10     Fields:    Translation:HumansCells
    22. Anderson A, Weng Z. VRDD: applying virtual reality visualization to protein docking and design. J Mol Graph Model. 1999 Jun-Aug; 17(3-4):180-6, 217. PMID: 10736775.
      Citations: 3     Fields:    Translation:Cells
    23. Khanna R, Silins SL, Weng Z, Gatchell D, Burrows SR, Cooper L. Cytotoxic T cell recognition of allelic variants of HLA B35 bound to an Epstein-Barr virus epitope: influence of peptide conformation and TCR-peptide interaction. Eur J Immunol. 1999 05; 29(5):1587-97. PMID: 10359113.
      Citations: 6     Fields:    Translation:HumansCells
    24. Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophys J. 1999 Mar; 76(3):1166-78. PMID: 10049302.
      Citations: 50     Fields:    Translation:HumansAnimalsCells
    25. Skvorak AB, Weng Z, Yee AJ, Robertson NG, Morton CC. Human cochlear expressed sequence tags provide insight into cochlear gene expression and identify candidate genes for deafness. Hum Mol Genet. 1999 Mar; 8(3):439-52. PMID: 9949203.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    26. Weng Z, Gulukota K, Vaughn DE, Bjorkman PJ, DeLisi C. Computational determination of the structure of rat Fc bound to the neonatal Fc receptor. J Mol Biol. 1998 Sep 18; 282(2):217-25. PMID: 9735282.
      Citations: 5     Fields:    Translation:AnimalsCells
    27. Weng Z, DeLisi C. Toward a predictive understanding of molecular recognition. Immunol Rev. 1998 Jun; 163:251-66. PMID: 9700515.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    28. DeLisi C, Cantor C, Weng Z. Hedgehogs, foxes, and a new science. Nat Biotechnol. 1997 Sep; 15(9):819. PMID: 9306387.
      Citations:    Fields:    Translation:HumansCells
    29. Weng Z, Delisi C, Vajda S. Empirical free energy calculation: comparison to calorimetric data. Protein Sci. 1997 Sep; 6(9):1976-84. PMID: 9300497.
      Citations: 11     Fields:    Translation:Cells
    30. Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions. Protein Sci. 1996 Apr; 5(4):614-26. PMID: 8845751.
      Citations: 19     Fields:    Translation:Cells
    31. Vajda S, Weng Z, DeLisi C. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments. Protein Eng. 1995 Nov; 8(11):1081-92. PMID: 8819974.
      Citations: 11     Fields:    Translation:Cells
    32. Vajda S, Weng Z, Rosenfeld R, DeLisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry. 1994 Nov 29; 33(47):13977-88. PMID: 7947806.
      Citations: 42     Fields:    Translation:Cells
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