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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
Phone508-856-8866
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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. 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
    2. Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, Emde AK, Shah M, Arora K, Reeves C, Socci ND, Perlman E, Antonescu CR, Roberts CWM, Steen H, Mullen E, Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A. PGBD5 promotes site-specific oncogenic mutations in human tumors. Nat Genet. 2017 May 15. PMID: 28504702.
      View in: PubMed
    3. 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
    4. Moal IH, Barradas-Bautista D, Jiménez-García B, Torchala M, van der Velde A, Vreven T, Weng Z, Bates PA, Fernández-Recio J. IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection. Bioinformatics. 2017 Feb 14. PMID: 28200016.
      View in: PubMed
    5. 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
    6. Hung JH, Weng Z. Motif Finding. Cold Spring Harb Protoc. 2017 Feb 01; 2017(2):pdb.top093195. PMID: 27574195.
      View in: PubMed
    7. Hung JH, Weng Z. Discovering cis-Regulatory Motifs. Cold Spring Harb Protoc. 2017 Feb 01; 2017(2):pdb.prot093203. PMID: 27574199.
      View in: PubMed
    8. Hung JH, Weng Z. Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding). Cold Spring Harb Protoc. 2017 Feb 01; 2017(2):pdb.prot093187. PMID: 27574193.
      View in: PubMed
    9. Hung JH, Weng Z. Mapping Short Sequence Reads to a Reference Genome. Cold Spring Harb Protoc. 2017 Feb 01; 2017(2):pdb.prot093161. PMID: 27574204.
      View in: PubMed
    10. Hung JH, Weng Z. Mapping Billions of Short Reads to a Reference Genome. Cold Spring Harb Protoc. 2017 Jan 03; 2017(1):pdb.top093153. PMID: 27574203.
      View in: PubMed
    11. 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
    12. Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins. 2017 Jan; 85(1):10-16. PMID: 27172383.
      View in: PubMed
    13. Hung JH, Weng Z. Sequence Alignment and Homology Search. Cold Spring Harb Protoc. 2016 Nov 01; 2016(11):pdb.top093070. PMID: 27574200.
      View in: PubMed
    14. Hung JH, Weng Z. Visualizing Genomic Annotations with the UCSC Genome Browser. Cold Spring Harb Protoc. 2016 Nov 01; 2016(11):pdb.prot093062. PMID: 27574198.
      View in: PubMed
    15. Hung JH, Weng Z. Sequence Alignment and Homology Search with BLAST and ClustalW. Cold Spring Harb Protoc. 2016 Nov 01; 2016(11):pdb.prot093088. PMID: 27574197.
      View in: PubMed
    16. 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
    17. 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
    18. Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng Des Sel. 2016 Dec; 29(12):595-606. PMID: 27624308.
      View in: PubMed
    19. Hung JH, Weng Z. Designing Polymerase Chain Reaction Primers Using Primer3Plus. Cold Spring Harb Protoc. 2016; 2016(9):pdb.prot093096. PMID: 27574202.
      View in: PubMed
    20. Hung JH, Weng Z. Analyzing Microarray Data. Cold Spring Harb Protoc. 2016 Aug 29. PMID: 27574201.
      View in: PubMed
    21. Hung JH, Weng Z. Peak-Finding Algorithms. Cold Spring Harb Protoc. 2016 Aug 29. PMID: 27574196.
      View in: PubMed
    22. Hung JH, Weng Z. Analysis of Microarray and RNA-seq Expression Profiling Data. Cold Spring Harb Protoc. 2016 Aug 29. PMID: 27574194.
      View in: PubMed
    23. Henssen AG, Jiang E, Zhuang J, Pinello L, Socci ND, Koche R, Gonen M, Villasante CM, Armstrong SA, Bauer DE, Weng Z, Kentsis A. Forward genetic screen of human transposase genomic rearrangements. BMC Genomics. 2016 Aug 04; 17:548. PMID: 27491780.
      View in: PubMed
    24. Hung JH, Weng Z. Data Formats in Bioinformatics. Cold Spring Harb Protoc. 2016; 2016(8):pdb.top093211. PMID: 27480726.
      View in: PubMed
    25. Filiano AJ, Xu Y, Tustison NJ, Marsh RL, Baker W, Smirnov I, Overall CC, Gadani SP, Turner SD, Weng Z, Peerzade SN, Chen H, Lee KS, Scott MM, Beenhakker MP, Litvak V, Kipnis J. Unexpected role of interferon-? in regulating neuronal connectivity and social behaviour. Nature. 2016 Jul 21; 535(7612):425-9. PMID: 27409813.
      View in: PubMed
    26. Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. 2016 Sep; 84 Suppl 1:323-48. PMID: 27122118.
      View in: PubMed
    27. 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
    28. Blevins SJ, Pierce BG, Singh NK, Riley TP, Wang Y, Spear TT, Nishimura MI, Weng Z, Baker BM. How structural adaptability exists alongside HLA-A2 bias in the human aß TCR repertoire. Proc Natl Acad Sci U S A. 2016 Mar 1; 113(9):E1276-85. PMID: 26884163.
      View in: PubMed
    29. Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi MF, Walsh S, Bogorad RL, Gao G, Weng Z, Dong Y, Koteliansky V, Wolfe SA, Langer R, Xue W, Anderson DG. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat Biotechnol. 2016 Mar; 34(3):328-33. PMID: 26829318.
      View in: PubMed
    30. Riley TP, Singh NK, Pierce BG, Weng Z, Baker BM. Computational Modeling of T Cell Receptor Complexes. Methods Mol Biol. 2016; 1414:319-40. PMID: 27094300.
      View in: PubMed
    31. Riley TP, Singh NK, Pierce BG, Baker BM, Weng Z. Computational Reprogramming of T Cell Antigen Receptor Binding Properties. Methods Mol Biol. 2016; 1414:305-18. PMID: 27094299.
      View in: PubMed
    32. Labadorf A, Hoss AG, Lagomarsino V, Latourelle JC, Hadzi TC, Bregu J, MacDonald ME, Gusella JF, Chen JF, Akbarian S, Weng Z, Myers RH. RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. PLoS One. 2015; 10(12):e0143563. PMID: 26636579.
      View in: PubMed
    33. 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
    34. The PsychENCODE project. Nat Neurosci. 2015 Dec; 18(12):1707-12. PMID: 26605881.
      View in: PubMed
    35. Tsuji J, Weng Z. Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. Brief Bioinform. 2016 Nov; 17(6):938-952. PMID: 26628557.
      View in: PubMed
    36. 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
    37. 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
    38. 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
    39. 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
    40. 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
    41. Li Y, Park AI, Mou H, Colpan C, Bizhanova A, Akama-Garren E, Joshi N, Hendrickson EA, Feldser D, Yin H, Anderson DG, Jacks T, Weng Z, Xue W. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol. 2015 May 28; 16:111. PMID: 26018130.
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    42. Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Res. 2015 Sep 30; 43(17):e109. PMID: 26007652.
      View in: PubMed
    43. 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
    44. Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF. Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. Dev Cell. 2015 Mar 23; 32(6):765-71. PMID: 25805138.
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    45. 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
    46. Gao M, Thomson TC, Creed TM, Tu S, Loganathan SN, Jackson CA, McCluskey P, Lin Y, Collier SE, Weng Z, Lasko P, Ohi MD, Arkov AL. Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements. EMBO Rep. 2015 Mar; 16(3):379-86. PMID: 25600116.
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    47. 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
    48. 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
    49. 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
    50. Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20; 515(7527):371-5. PMID: 25409826.
      View in: PubMed
    51. 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
    52. Shen E, Shulha H, Weng Z, Akbarian S. Regulation of histone H3K4 methylation in brain development and disease. Philos Trans R Soc Lond B Biol Sci. 2014 Sep 26; 369(1652). PMID: 25135975.
      View in: PubMed
    53. 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
    54. Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):E3366. PMID: 25275169.
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    55. 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
    56. 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
    57. 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
    58. 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
    59. Zhuang J, Wang J, Theurkauf W, Weng Z. TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res. 2014 Jun; 42(11):6826-38. PMID: 24753423.
      View in: PubMed
    60. Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. PMID: 24753594.
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    61. Trastoy B, Lomino JV, Pierce BG, Carter LG, Günther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang LX, Sundberg EJ. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Proc Natl Acad Sci U S A. 2014 May 6; 111(18):6714-9. PMID: 24753590.
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    62. 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.
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    63. 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
    64. 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.
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    65. 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.
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    66. Chen W, Shulha HP, Ashar-Patel A, Yan J, Green KM, Query CC, Rhind N, Weng Z, Moore MJ. Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes. RNA. 2014 Mar; 20(3):308-20. PMID: 24442611.
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    67. Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. Backbone flexibility of CDR3 and immune recognition of antigens. J Mol Biol. 2014 Apr 3; 426(7):1583-99. PMID: 24380763.
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    68. 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.
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    69. 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.
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    70. Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ. Blind prediction of interfacial water positions in CAPRI. Proteins. 2014 Apr; 82(4):620-32. PMID: 24155158.
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    156. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007 Mar; 39(3):311-8. PMID: 17277777.
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    157. Kothe DL, Decker JM, Li Y, Weng Z, Bibollet-Ruche F, Zammit KP, Salazar MG, Chen Y, Salazar-Gonzalez JF, Moldoveanu Z, Mestecky J, Gao F, Haynes BF, Shaw GM, Muldoon M, Korber BT, Hahn BH. Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins. Virology. 2007 Mar 30; 360(1):218-34. PMID: 17097711.
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    158. Zeller KI, Zhao X, Lee CW, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, Dang CV, Wei CL. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17834-9. PMID: 17093053.
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    159. Kothe DL, Li Y, Decker JM, Bibollet-Ruche F, Zammit KP, Salazar MG, Chen Y, Weng Z, Weaver EA, Gao F, Haynes BF, Shaw GM, Korber BT, Hahn BH. Ancestral and consensus envelope immunogens for HIV-1 subtype C. Virology. 2006 Sep 1; 352(2):438-49. PMID: 16780913.
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    160. Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y. A global map of p53 transcription-factor binding sites in the human genome. Cell. 2006 Jan 13; 124(1):207-19. PMID: 16413492.
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    161. 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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    162. Szustakowski JD, Kasif S, Weng Z. Less is more: towards an optimal universal description of protein folds. Bioinformatics. 2005 Sep 1; 21 Suppl 2:ii66-71. PMID: 16204127.
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    163. Anderson RJ, Weng Z, Campbell RK, Jiang X. Main-chain conformational tendencies of amino acids. Proteins. 2005 Sep 1; 60(4):679-89. PMID: 16021632.
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    164. Leyfer D, Weng Z. Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. Bioinformatics. 2005 Sep 1; 21 Suppl 2:ii197-203. PMID: 16204103.
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    165. 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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    166. Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins. 2005 Aug 1; 60(2):214-6. PMID: 15981264.
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    167. Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins. 2005 Aug 1; 60(2):207-13. PMID: 15981263.
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    168. 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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    169. Mintseris J, Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A. 2005 Aug 2; 102(31):10930-5. PMID: 16043700.
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    170. Zhu J, Weng Z. FAST: a novel protein structure alignment algorithm. Proteins. 2005 Feb 15; 58(3):618-27. PMID: 15609341.
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    171. Yanai I, Yu Y, Zhu X, Cantor CR, Weng Z. An avidin-like domain that does not bind biotin is adopted for oligomerization by the extracellular mosaic protein fibropellin. Protein Sci. 2005 Feb; 14(2):417-23. PMID: 15659374.
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    172. Burden HE, Weng Z. Identification of conserved structural features at sequentially degenerate locations in transcription factor binding sites. Genome Inform. 2005; 16(1):49-58. PMID: 16362906.
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    173. 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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    174. Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, Régnier M, Simonis N, Sinha S, Thijs G, van Helden J, Vandenbogaert M, Weng Z, Workman C, Ye C, Zhu Z. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005 Jan; 23(1):137-44. PMID: 15637633.
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    175. Pierce B, Tong W, Weng Z. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics. 2005 Apr 15; 21(8):1472-8. PMID: 15613396.
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    176. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22; 306(5696):636-40. PMID: 15499007.
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    177. 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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    178. Haverty PM, Hsiao LL, Gullans SR, Hansen U, Weng Z. Limited agreement among three global gene expression methods highlights the requirement for non-global validation. Bioinformatics. 2004 Dec 12; 20(18):3431-41. PMID: 15256402.
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    179. Fu Y, Frith MC, Haverty PM, Weng Z. MotifViz: an analysis and visualization tool for motif discovery. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W420-3. PMID: 15215422.
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    180. Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z. SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W235-41. PMID: 15215387.
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    181. Halees AS, Weng Z. PromoSer: improvements to the algorithm, visualization and accessibility. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W191-4. PMID: 15215378.
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    182. Haverty PM, Frith MC, Weng Z. CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W213-6. PMID: 15215383.
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    183. Yu L, Frith MC, Suzuki Y, Peterfreund RA, Gearan T, Sugano S, Schwarzschild MA, Weng Z, Fink JS, Chen JF. Characterization of genomic organization of the adenosine A2A receptor gene by molecular and bioinformatics analyses. Brain Res. 2004 Mar 12; 1000(1-2):156-73. PMID: 15053963.
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    184. Haverty PM, Weng Z. CisML: an XML-based format for sequence motif detection software. Bioinformatics. 2004 Jul 22; 20(11):1815-7. PMID: 15001475.
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    185. Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z. Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res. 2004; 32(4):1372-81. PMID: 14988425.
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    186. 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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    187. Frith MC, Hansen U, Spouge JL, Weng Z. Finding functional sequence elements by multiple local alignment. Nucleic Acids Res. 2004; 32(1):189-200. PMID: 14704356.
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    188. Haverty PM, Hansen U, Weng Z. Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res. 2004; 32(1):179-88. PMID: 14704355.
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    189. Mintseris J, Weng Z. Optimizing protein representations with information theory. Genome Inform. 2004; 15(1):160-9. PMID: 15712119.
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    190. Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins. 2003 Nov 15; 53(3):693-707. PMID: 14579360.
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    191. 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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    192. Peters B, Tong W, Sidney J, Sette A, Weng Z. Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics. 2003 Sep 22; 19(14):1765-72. PMID: 14512347.
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    193. Halees AS, Leyfer D, Weng Z. PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res. 2003 Jul 1; 31(13):3554-9. PMID: 12824364.
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    194. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins. 2003 Jul 1; 52(1):80-7. PMID: 12784371.
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    195. Frith MC, Li MC, Weng Z. Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 2003 Jul 1; 31(13):3666-8. PMID: 12824389.
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    196. Chen R, Tong W, Mintseris J, Li L, Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins. 2003 Jul 1; 52(1):68-73. PMID: 12784369.
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    197. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins. 2003 Jul 1; 52(1):88-91. PMID: 12784372.
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    198. Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins. 2003 May 15; 51(3):397-408. PMID: 12696051.
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    199. Hu Z, Frith M, Niu T, Weng Z. SeqVISTA: a graphical tool for sequence feature visualization and comparison. BMC Bioinformatics. 2003 Jan 4; 4:1. PMID: 12513700.
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    200. Weng Z. Managing biological sequence and protein structure data. OMICS. 2003; 7(1):25-6. PMID: 12831551.
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    201. Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Res. 2002 Oct 15; 30(20):e106. PMID: 12384608.
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    202. 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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    203. Frith MC, Spouge JL, Hansen U, Weng Z. Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res. 2002 Jul 15; 30(14):3214-24. PMID: 12136103.
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    204. Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins. 2002 May 15; 47(3):281-94. PMID: 11948782.
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    205. Resendes BL, Robertson NG, Szustakowski JD, Resendes RJ, Weng Z, Morton CC. Gene discovery in the auditory system: characterization of additional cochlear-expressed sequences. J Assoc Res Otolaryngol. 2002 Mar; 3(1):45-53. PMID: 12083723.
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    206. Weng Z, DeLisi C. Protein therapeutics: promises and challenges for the 21st century. Trends Biotechnol. 2002 Jan; 20(1):29-35. PMID: 11742675.
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    207. Haverty PM, Weng Z, Best NL, Auerbach KR, Hsiao LL, Jensen RV, Gullans SR. HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Res. 2002 Jan 1; 30(1):214-7. PMID: 11752297.
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    208. 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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    209. 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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    210. 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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    211. 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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    212. 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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    213. 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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    214. 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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    215. 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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    216. 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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    217. Weng Z, DeLisi C. Toward a predictive understanding of molecular recognition. Immunol Rev. 1998 Jun; 163:251-66. PMID: 9700515.
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    218. 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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    219. 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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    220. 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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    221. 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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    222. 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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