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Zhiping Weng PhD

TitleProfessor
InstitutionUniversity of Massachusetts Medical School
DepartmentBiochemistry and Molecular Pharmacology
AddressUniversity of Massachusetts Medical School
364 Plantation Street, LRB
Worcester MA 01605
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentBioinformatics and Computational Biology

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentInterdisciplinary Graduate Program

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentMD/PhD Program

    InstitutionUMMS - Graduate School of Biomedical Sciences
    DepartmentTranslational Science

    InstitutionUMMS - Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology


    Collapse Biography 
    Collapse education and training
    University of Science and 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.
    List All   |   Timeline
    1. Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD. The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Mol Cell. 2019 Apr 26. PMID: 31076285.
      View in: PubMed
    2. Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Goltsov AY, Solovyev V, Brizgalov L, Filippova E, Weng Z, Akbarian S, Rogaev EI. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons. FASEB J. 2019 Apr 10; fj201802646R. PMID: 30970224.
      View in: PubMed
    3. Zhang G, Tu S, Yu T, Zhang XO, Parhad SS, Weng Z, Theurkauf WE. Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin. Cell Rep. 2018 Sep 25; 24(13):3413-3422.e4. PMID: 30257203.
      View in: PubMed
    4. Zhang XO, Fu Y, Mou H, Xue W, Weng Z. The temporal landscape of recursive splicing during Pol II transcription elongation in human cells. PLoS Genet. 2018 Aug; 14(8):e1007579. PMID: 30148885.
      View in: PubMed
    5. Song CQ, Wang D, Jiang T, O'Connor K, Tang Q, Cai L, Li X, Weng Z, Yin H, Gao G, Mueller C, Flotte TR, Xue W. In vivo Genome Editing Partially Restores Alpha1-Antitrypsin in a Murine Model of AAT Deficiency. Hum Gene Ther. 2018 May 14. PMID: 29597895.
      View in: PubMed
    6. Chen W, Moore J, Ozadam H, Shulha HP, Rhind N, Weng Z, Moore MJ. Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling. Cell. 2018 May 03; 173(4):1031-1044.e13. PMID: 29727662.
      View in: PubMed
    7. Vreven T, Schweppe DK, Chavez JD, Weisbrod CR, Shibata S, Zheng C, Bruce JE, Weng Z. Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking. J Mol Biol. 2018 Jun 08; 430(12):1814-1828. PMID: 29665372.
      View in: PubMed
    8. Tang W, Seth M, Tu S, Shen EZ, Li Q, Shirayama M, Weng Z, Mello CC. A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans. Dev Cell. 2018 03 26; 44(6):762-770.e3. PMID: 29456136.
      View in: PubMed
    9. Seth M, Shirayama M, Tang W, Shen EZ, Tu S, Lee HC, Weng Z, Mello CC. The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans. Cell Rep. 2018 Feb 27; 22(9):2254-2264. PMID: 29456100.
      View in: PubMed
    10. Shen EZ, Chen H, Ozturk AR, Tu S, Shirayama M, Tang W, Ding YH, Dai SY, Weng Z, Mello CC. Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. Cell. 2018 Feb 22; 172(5):937-951.e18. PMID: 29456082.
      View in: PubMed
    11. Pierce BG, Boucher EN, Piepenbrink KH, Ejemel M, Rapp CA, Thomas WD, Sundberg EJ, Weng Z, Wang Y. Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope. J Virol. 2017 10 15; 91(20). PMID: 28794021.
      View in: PubMed
    12. Parhad SS, Tu S, Weng Z, Theurkauf WE. Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery. Dev Cell. 2017 10 09; 43(1):60-70.e5. PMID: 28919205.
      View in: PubMed
    13. Mou H, Smith JL, Peng L, Yin H, Moore J, Zhang XO, Song CQ, Sheel A, Wu Q, Ozata DM, Li Y, Anderson DG, Emerson CP, Sontheimer EJ, Moore MJ, Weng Z, Xue W. CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biol. 2017 Jun 14; 18(1):108. PMID: 28615073.
      View in: PubMed
    14. Mou H, Moore J, Malonia SK, Li Y, Ozata DM, Hough S, Song CQ, Smith JL, Fischer A, Weng Z, Green MR, Xue W. Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis. Proc Natl Acad Sci U S A. 2017 Mar 20. PMID: 28320962.
      View in: PubMed
    15. Borrman T, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, Weng Z. ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. Proteins. 2017 Feb 03. PMID: 28160322.
      View in: PubMed
    16. Song CQ, Li Y, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte D, Zender L, Wang XW, Thorgeirsson S, Weng Z, Xue W. Genome-wide CRISPR Screen Identifies Regulators of MAPK as Suppressors of Liver Tumors in Mice. Gastroenterology. 2016 Dec 09. PMID: 27956228.
      View in: PubMed
    17. Tsuji J, Weng Z. DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data. PLoS One. 2016; 11(10):e0164228. PMID: 27736901.
      View in: PubMed
    18. Vreven T, Pierce BG, Borrman TM, Weng Z. Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins. 2016 Oct 7. PMID: 27718275.
      View in: PubMed
    19. Tang W, Tu S, Lee HC, Weng Z, Mello CC. The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans. Cell. 2016 Feb 25; 164(5):974-84. PMID: 26919432.
      View in: PubMed
    20. Dong X, Tsuji J, Labadorf A, Roussos P, Chen JF, Myers RH, Akbarian S, Weng Z. The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. PLoS One. 2015; 10(12):e0144398. PMID: 26636336.
      View in: PubMed
    21. Tran H, Almeida S, Moore J, Gendron TF, Chalasani U, Lu Y, Du X, Nickerson JA, Petrucelli L, Weng Z, Gao FB. Differential Toxicity of Nuclear RNA Foci versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS. Neuron. 2015 Sep 23; 87(6):1207-14. PMID: 26402604.
      View in: PubMed
    22. Wang W, Han BW, Tipping C, Ge DT, Zhang Z, Weng Z, Zamore PD. Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. Mol Cell. 2015 Sep 3; 59(5):819-30. PMID: 26340424.
      View in: PubMed
    23. Zhuang J, Weng Z. Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes. Nucleic Acids Res. 2015 Sep 30; 43(17):8146-56. PMID: 26283183.
      View in: PubMed
    24. Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. J Mol Biol. 2015 Sep 25; 427(19):3031-41. PMID: 26231283.
      View in: PubMed
    25. Wang D, Mou H, Li S, Li Y, Hough S, Tran K, Li J, Yin H, Anderson DG, Sontheimer EJ, Weng Z, Gao G, Xue W. Adenovirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses. Hum Gene Ther. 2015 Jul; 26(7):432-42. PMID: 26086867.
      View in: PubMed
    26. Han BW, Wang W, Li C, Weng Z, Zamore PD. Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science. 2015 May 15; 348(6236):817-21. PMID: 25977554.
      View in: PubMed
    27. 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.
      View in: PubMed
    28. Tu S, Wu MZ, Wang J, Cutter AD, Weng Z, Claycomb JM. Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes. Nucleic Acids Res. 2015 Jan; 43(1):208-24. PMID: 25510497.
      View in: PubMed
    29. 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 1; 24(5):1441-56. PMID: 25480889.
      View in: PubMed
    30. Wang W, Yoshikawa M, Han BW, Izumi N, Tomari Y, Weng Z, Zamore PD. The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs. Mol Cell. 2014 Dec 4; 56(5):708-16. PMID: 25453759.
      View in: PubMed
    31. Han BW, Wang W, Zamore PD, Weng Z. piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. Bioinformatics. 2015 Feb 15; 31(4):593-5. PMID: 25342065.
      View in: PubMed
    32. Pierce BG, Vreven T, Weng Z. Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. BMC Bioinformatics. 2014 Sep 26; 15:319. PMID: 25260513.
      View in: PubMed
    33. Yildirim O, Hung JH, Cedeno RJ, Weng Z, Lengner CJ, Rando OJ. A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters. PLoS Genet. 2014 Aug; 10(8):e1004515. PMID: 25102063.
      View in: PubMed
    34. Carone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng Z, Fazzio TG, Rando OJ. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Dev Cell. 2014 Jul 14; 30(1):11-22. PMID: 24998598.
      View in: PubMed
    35. Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody. PLoS One. 2014; 9(6):e100325. PMID: 24956119.
      View in: PubMed
    36. Zhang Z, Wang J, Schultz N, Zhang F, Parhad SS, Tu S, Vreven T, Zamore PD, Weng Z, Theurkauf WE. The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing. Cell. 2014 Jun 5; 157(6):1353-63. PMID: 24906152.
      View in: PubMed
    37. Zhang Z, Koppetsch BS, Wang J, Tipping C, Weng Z, Theurkauf WE, Zamore PD. Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin. EMBO J. 2014 Mar 18; 33(6):536-9. PMID: 24652836.
      View in: PubMed
    38. Hoss AG, Kartha VK, Dong X, Latourelle JC, Dumitriu A, Hadzi TC, Macdonald ME, Gusella JF, Akbarian S, Chen JF, Weng Z, Myers RH. MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis. PLoS Genet. 2014 Feb; 10(2):e1004188. PMID: 24586208.
      View in: PubMed
    39. Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics. 2014 Jun 15; 30(12):1771-3. PMID: 24532726.
      View in: PubMed
    40. Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. PLoS Comput Biol. 2014 Feb; 10(2):e1003478. PMID: 24550723.
      View in: PubMed
    41. Chen PB, Hung JH, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG. Hdac6 regulates Tip60-p400 function in stem cells. Elife. 2013 Dec 03; 2:e01557. PMID: 24302573.
      View in: PubMed
    42. Vreven T, Pierce BG, Hwang H, Weng Z. Performance of ZDOCK in CAPRI rounds 20-26. Proteins. 2013 Dec; 81(12):2175-82. PMID: 24123140.
      View in: PubMed
    43. Hwang H, Vreven T, Weng Z. Binding interface prediction by combining protein-protein docking results. Proteins. 2014 Jan; 82(1):57-66. PMID: 23836482.
      View in: PubMed
    44. 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.
      View in: PubMed
    45. Vreven T, Hwang H, Pierce BG, Weng Z. Evaluating template-based and template-free protein-protein complex structure prediction. Brief Bioinform. 2014 Mar; 15(2):169-76. PMID: 23818491.
      View in: PubMed
    46. 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.
      View in: PubMed
    47. Shulha HP, Cheung I, Guo Y, Akbarian S, Weng Z. Coordinated cell type-specific epigenetic remodeling in prefrontal cortex begins before birth and continues into early adulthood. PLoS Genet. 2013 Apr; 9(4):e1003433. PMID: 23593028.
      View in: PubMed
    48. Perrat PN, DasGupta S, Wang J, Theurkauf W, Weng Z, Rosbash M, Waddell S. Transposition-driven genomic heterogeneity in the Drosophila brain. Science. 2013 Apr 5; 340(6128):91-5. PMID: 23559253.
      View in: PubMed
    49. Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell. 2013 Apr 11; 50(1):67-81. PMID: 23523368.
      View in: PubMed
    50. Pierce BG, Eberwine R, Noble JA, Habib M, Shulha HP, Weng Z, Blankenhorn EP, Mordes JP. The Missing Heritability in T1D and Potential New Targets for Prevention. J Diabetes Res. 2013; 2013:737485. PMID: 23691517.
      View in: PubMed
    51. Vreven T, Hwang H, Weng Z. Exploring angular distance in protein-protein docking algorithms. PLoS One. 2013; 8(2):e56645. PMID: 23437194.
      View in: PubMed
    52. Tu S, Pederson T, Weng Z. Networking development by Boolean logic. Nucleus. 2013 Mar-Apr; 4(2):89-91. PMID: 23412653.
      View in: PubMed
    53. Pierce BG, Weng Z. A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. Protein Sci. 2013 Jan; 22(1):35-46. PMID: 23109003.
      View in: PubMed
    54. Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012 Dec 28; 3(1):9. PMID: 23273270.
      View in: PubMed
    55. Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan; 41(Database issue):D171-6. PMID: 23203885.
      View in: PubMed
    56. Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, Akbarian S. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol. 2012; 10(11):e1001427. PMID: 23185133.
      View in: PubMed
    57. Zhang F, Wang J, Xu J, Zhang Z, Koppetsch BS, Schultz N, Vreven T, Meignin C, Davis I, Zamore PD, Weng Z, Theurkauf WE. UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell. 2012 Nov 9; 151(4):871-84. PMID: 23141543.
      View in: PubMed
    58. Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell. 2012 Nov 9; 151(4):750-64. PMID: 23084401.
      View in: PubMed
    59. Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell. 2012 Oct 26; 151(3):533-46. PMID: 23063653.
      View in: PubMed
    60. Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng Z. Functional analysis of transcription factor binding sites in human promoters. Genome Biol. 2012 Sep 26; 13(9):R50. PMID: 22951020.
      View in: PubMed
    61. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      View in: PubMed
    62. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep; 22(9):1798-812. PMID: 22955990.
      View in: PubMed
    63. Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Jun 13; 13(9):R53. PMID: 22950368.
      View in: PubMed
    64. Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Res. 2012 Oct; 22(10):1889-98. PMID: 22539651.
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    65. Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol. 2012; 13(4):R27. PMID: 22531001.
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    66. Xie J, Ameres SL, Friedline R, Hung JH, Zhang Y, Xie Q, Zhong L, Su Q, He R, Li M, Li H, Mu X, Zhang H, Broderick JA, Kim JK, Weng Z, Flotte TR, Zamore PD, Gao G. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nat Methods. 2012 Mar 04; 9(4):403-9. PMID: 22388288.
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    67. Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Sci. 2012 Mar; 21(3):396-404. PMID: 22238219.
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    68. Khurana JS, Wang J, Xu J, Koppetsch BS, Thomson TC, Nowosielska A, Li C, Zamore PD, Weng Z, Theurkauf WE. Adaptation to P element transposon invasion in Drosophila melanogaster. Cell. 2011 Dec 23; 147(7):1551-63. PMID: 22196730.
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    69. Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell. 2011 Dec 23; 147(7):1498-510. PMID: 22196727.
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    70. Zhang Z, Xu J, Koppetsch BS, Wang J, Tipping C, Ma S, Weng Z, Theurkauf WE, Zamore PD. Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains. Mol Cell. 2011 Nov 18; 44(4):572-84. PMID: 22099305.
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    71. 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).
    72. Han BW, Hung JH, Weng Z, Zamore PD, Ameres SL. The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1. Curr Biol. 2011 Nov 22; 21(22):1878-87. PMID: 22055293.
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    73. Pierce BG, Hourai Y, Weng Z. Accelerating protein docking in ZDOCK using an advanced 3D convolution library. PLoS One. 2011; 6(9):e24657. PMID: 21949741.
      View in: PubMed
    74. Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C. Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform. 2012 May; 13(3):281-91. PMID: 21900207.
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    75. Vreven T, Hwang H, Weng Z. Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Sci. 2011 Sep; 20(9):1576-86. PMID: 21739500.
      View in: PubMed
    76. Hwang H, Vreven T, Whitfield TW, Wiehe K, Weng Z. A machine learning approach for the prediction of protein surface loop flexibility. Proteins. 2011 Aug; 79(8):2467-74. PMID: 21633973.
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    77. Carone BR, Fauquier L, Habib N, Shea JM, Hart CE, Li R, Bock C, Li C, Gu H, Zamore PD, Meissner A, Weng Z, Hofmann HA, Friedman N, Rando OJ. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell. 2010 Dec 23; 143(7):1084-96. PMID: 21183072.
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    78. Xie J, Xie Q, Zhang H, Ameres SL, Hung JH, Su Q, He R, Mu X, Seher Ahmed S, Park S, Kato H, Li C, Mueller C, Mello CC, Weng Z, Flotte TR, Zamore PD, Gao G. MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression. Mol Ther. 2011 Mar; 19(3):526-35. PMID: 21179009.
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    79. Khurana JS, Xu J, Weng Z, Theurkauf WE. Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. PLoS Genet. 2010 Dec 16; 6(12):e1001246. PMID: 21179579.
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    80. Ameres SL, Hung JH, Xu J, Weng Z, Zamore PD. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA. 2011 Jan; 17(1):54-63. PMID: 21106652.
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    81. Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins. 2010 Nov 15; 78(15):3111-4. PMID: 20806234.
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    82. Connor C, Cheung I, Simon A, Jakovcevski M, Weng Z, Akbarian S. A simple method for improving the specificity of anti-methyl histone antibodies. Epigenetics. 2010 Jul 1; 5(5):392-5. PMID: 20458167.
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    83. Ameres SL, Horwich MD, Hung JH, Xu J, Ghildiyal M, Weng Z, Zamore PD. Target RNA-directed trimming and tailing of small silencing RNAs. Science. 2010 Jun 18; 328(5985):1534-9. PMID: 20558712.
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    84. 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 9; 10(6):2237-44. PMID: 20459065.
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    85. Cheung I, Shulha HP, Jiang Y, Matevossian A, Wang J, Weng Z, Akbarian S. Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proc Natl Acad Sci U S A. 2010 May 11; 107(19):8824-9. PMID: 20421462.
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    86. Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA. 2010 Jan; 16(1):43-56. PMID: 19917635.
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    87. 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. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell. 2009 Sep 18; 138(6):1137-49. PMID: 19732946.
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    88. Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, Seitz H, Horwich MD, Syrzycka M, Honda BM, Kittler EL, Zapp ML, Klattenhoff C, Schulz N, Theurkauf WE, Weng Z, Zamore PD. Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell. 2009 May 1; 137(3):509-21. PMID: 19395009.
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    89. Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, Lee S, Xu J, Kittler EL, Zapp ML, Weng Z, Zamore PD. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science. 2008 May 23; 320(5879):1077-81. PMID: 18403677.
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    90. Lin JM, Weng Z. Systematic detection of statistically overrepresented DNA motif association rules. Genome Inform. 2006; 17(1):124-33. PMID: 17503362.
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    91. Peters B, Bui HH, Sidney J, Weng Z, Loffredo JT, Watkins DI, Mothé BR, Sette A. A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules. Vaccine. 2005 Nov 1; 23(45):5212-24. PMID: 16137805.
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    92. Yu L, Haverty PM, Mariani J, Wang Y, Shen HY, Schwarzschild MA, Weng Z, Chen JF. Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum. Physiol Genomics. 2005 Sep 21; 23(1):89-102. PMID: 16046619.
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    93. 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.
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    94. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22; 306(5696):636-40. PMID: 15499007.
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    95. 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.
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    96. 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.
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    97. Mintseris J, Weng Z. Optimizing protein representations with information theory. Genome Inform. 2004; 15(1):160-9. PMID: 15712119.
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    98. Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins. 2003 Nov 15; 53(3):629-39. PMID: 14579354.
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    99. Weng Z. Managing biological sequence and protein structure data. OMICS. 2003; 7(1):25-6. PMID: 12831551.
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    100. 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.
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    101. 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.
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    102. Frith MC, Hansen U, Weng Z. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics. 2001 Oct; 17(10):878-89. PMID: 11673232.
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    103. Szustakowski JD, Weng Z. Protein structure alignment using a genetic algorithm. Proteins. 2000 Mar 1; 38(4):428-40. PMID: 10707029.
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    104. 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 1; 163(7):4027-32. PMID: 10491006.
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    105. 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.
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    106. 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 May; 29(5):1587-97. PMID: 10359113.
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    107. 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.
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    108. 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.
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    109. 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.
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    110. Weng Z, DeLisi C. Toward a predictive understanding of molecular recognition. Immunol Rev. 1998 Jun; 163:251-66. PMID: 9700515.
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    111. DeLisi C, Cantor C, Weng Z. Hedgehogs, foxes, and a new science. Nat Biotechnol. 1997 Sep; 15(9):819. PMID: 9306387.
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    112. Weng Z, Delisi C, Vajda S. Empirical free energy calculation: comparison to calorimetric data. Protein Sci. 1997 Sep; 6(9):1976-84. PMID: 9300497.
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    113. 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.
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    114. 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.
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    115. 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.
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