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Zhiping Weng PhD

TitleProfessor
Endowed TitleLi Weibo Chair in Biomedical Research
InstitutionUMass Chan Medical School
DepartmentBiochemistry and Molecular Biotechnology
AddressUMass Chan Medical School
364 Plantation Street LRB
Worcester MA 01605
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    Other Positions
    InstitutionT.H. Chan School of Medicine
    DepartmentBiochemistry and Molecular Biotechnology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBiochemistry and Molecular Pharmacology

    InstitutionMorningside Graduate School of Biomedical Sciences
    DepartmentBioinformatics 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

    InstitutionUMass Chan Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative 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.
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    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. Morrill K, Hekman J, Li X, McClure J, Logan B, Goodman L, Gao M, Dong Y, Alonso M, Carmichael E, Snyder-Mackler N, Alonso J, Noh HJ, Johnson J, Koltookian M, Lieu C, Megquier K, Swofford R, Turner-Maier J, White ME, Weng Z, Colubri A, Genereux DP, Lord KA, Karlsson EK. Ancestry-inclusive dog genomics challenges popular breed stereotypes. Science. 2022 04 29; 376(6592):eabk0639. PMID: 35482869.
      Citations:    Fields:    
    2. Wang IH, Murray E, Andrews G, Jiang HC, Park SJ, Donnard E, Durán-Laforet V, Bear DM, Faust TE, Garber M, Baer CE, Schafer DP, Weng Z, Chen F, Macosko EZ, Greer PL. Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing. Nat Neurosci. 2022 Apr; 25(4):484-492. PMID: 35314823.
      Citations:    Fields:    Translation:AnimalsCells
    3. Pratt HE, Andrews GR, Phalke N, Purcaro MJ, van der Velde A, Moore JE, Weng Z. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Res. 2022 01 07; 50(D1):D141-D149. PMID: 34755879.
      Citations: 1     Fields:    Translation:HumansCells
    4. Moore JE, Zhang XO, Elhajjajy SI, Fan K, Pratt HE, Reese F, Mortazavi A, Weng Z. Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome Res. 2022 02; 32(2):389-402. PMID: 34949670.
      Citations:    Fields:    Translation:HumansCells
    5. Tsuji J, Thomson T, Brown C, Ghosh S, Theurkauf WE, Weng Z, Schwartz LM. Somatic piRNAs and Transposons are Differentially Expressed Coincident with Skeletal Muscle Atrophy and Programmed Cell Death. Front Genet. 2021; 12:775369. PMID: 35003216.
      Citations:    
    6. Jiang T, Zhang XO, Weng Z, Xue W. Deletion and replacement of long genomic sequences using prime editing. Nat Biotechnol. 2022 02; 40(2):227-234. PMID: 34650270.
      Citations: 2     Fields:    Translation:Animals
    7. Zhang G, Yu T, Parhad SS, Ho S, Weng Z, Theurkauf WE. piRNA-independent transposon silencing by the Drosophila THO complex. Dev Cell. 2021 09 27; 56(18):2623-2635.e5. PMID: 34547226.
      Citations: 1     Fields:    Translation:AnimalsCells
    8. Fan K, Moore JE, Zhang XO, Weng Z. Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes. Nucleic Acids Res. 2021 06 04; 49(10):5705-5725. PMID: 33978759.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    9. Zhang XO, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annu Rev Genomics Hum Genet. 2021 08 31; 22:199-218. PMID: 33792357.
      Citations: 1     Fields:    Translation:HumansCells
    10. van der Velde A, Fan K, Tsuji J, Moore JE, Purcaro MJ, Pratt HE, Weng Z. Annotation of chromatin states in 66 complete mouse epigenomes during development. Commun Biol. 2021 02 22; 4(1):239. PMID: 33619351.
      Citations:    
    11. Belaghzal H, Borrman T, Stephens AD, Lafontaine DL, Venev SV, Weng Z, Marko JF, Dekker J. Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nat Genet. 2021 03; 53(3):367-378. PMID: 33574602.
      Citations: 15     Fields:    Translation:HumansCells
    12. Smith JL, Rodríguez TC, Mou H, Kwan SY, Pratt H, Zhang XO, Cao Y, Liang S, Ozata DM, Yu T, Yin Q, Hazeltine M, Weng Z, Sontheimer EJ, Xue W. YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte-Like Cells. Hepatology. 2021 03; 73(3):1011-1027. PMID: 32452550.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    13. Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics. 2020 Dec 23. PMID: 33355667.
      Citations: 1     Fields:    
    14. Tsuji J, Thomson T, Chan E, Brown CK, Oppenheimer J, Bigelow C, Dong X, Theurkauf WE, Weng Z, Schwartz LM. High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death. Physiol Genomics. 2020 10 01; 52(10):492-511. PMID: 32926651.
      Citations: 2     Fields:    Translation:AnimalsCells
    15. Wu PH, Fu Y, Cecchini K, Özata DM, Arif A, Yu T, Colpan C, Gainetdinov I, Weng Z, Zamore PD. The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility. Nat Genet. 2020 07; 52(7):728-739. PMID: 32601478.
      Citations: 25     Fields:    Translation:AnimalsCells
    16. Pratt H, Weng Z. LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. Bioinformatics. 2020 06 01; 36(11):3573-3575. PMID: 32181813.
      Citations: 1     Fields:    Translation:HumansCells
    17. Jiang T, Henderson JM, Coote K, Cheng Y, Valley HC, Zhang XO, Wang Q, Rhym LH, Cao Y, Newby GA, Bihler H, Mense M, Weng Z, Anderson DG, McCaffrey AP, Liu DR, Xue W. Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope. Nat Commun. 2020 04 24; 11(1):1979. PMID: 32332735.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    18. Parhad SS, Yu T, Zhang G, Rice NP, Weng Z, Theurkauf WE. Adaptive Evolution Targets a piRNA Precursor Transcription Network. Cell Rep. 2020 02 25; 30(8):2672-2685.e5. PMID: 32101744.
      Citations: 5     Fields:    Translation:AnimalsCells
    19. Vreven T, Vangaveti S, Borrman TM, Gaines JC, Weng Z. Performance of ZDOCK and IRAD in CAPRI rounds 39-45. Proteins. 2020 08; 88(8):1050-1054. PMID: 31994784.
      Citations:    Fields:    Translation:HumansCells
    20. Vangaveti S, Vreven T, Zhang Y, Weng Z. Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinformatics. 2020 02 01; 36(3):751-757. PMID: 31393558.
      Citations: 2     Fields:    
    21. Moore JE, Pratt HE, Purcaro MJ, Weng Z. A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. Genome Biol. 2020 01 22; 21(1):17. PMID: 31969180.
      Citations: 22     Fields:    Translation:Cells
    22. Casserly AP, Tsuji J, Zhao-Shea R, Smith CB, Molas S, Tapper AR, Weng Z, Gardner PD. Integrated miRNA-/mRNA-Seq of the Habenulo-Interpeduncular Circuit During Acute Nicotine Withdrawal. Sci Rep. 2020 01 21; 10(1):813. PMID: 31965003.
      Citations: 3     Fields:    Translation:Animals
    23. Özata DM, Yu T, Mou H, Gainetdinov I, Colpan C, Cecchini K, Kaymaz Y, Wu PH, Fan K, Kucukural A, Weng Z, Zamore PD. Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans. Nat Ecol Evol. 2020 01; 4(1):156-168. PMID: 31900453.
      Citations: 19     Fields:    Translation:HumansAnimals
    24. Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Filippova E, Weng Z, Akbarian S, Rogaev EI. Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Transl Psychiatry. 2019 10 17; 9(1):256. PMID: 31624234.
      Citations: 6     Fields:    Translation:HumansCells
    25. Yu T, Koppetsch BS, Pagliarani S, Johnston S, Silverstein NJ, Luban J, Chappell K, Weng Z, Theurkauf WE. The piRNA Response to Retroviral Invasion of the Koala Genome. Cell. 2019 10 17; 179(3):632-643.e12. PMID: 31607510.
      Citations: 22     Fields:    Translation:AnimalsCells
    26. Zhang XO, Gingeras TR, Weng Z. Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function. Genome Res. 2019 09; 29(9):1402-1414. PMID: 31413151.
      Citations: 26     Fields:    Translation:HumansCells
    27. Kwan SY, Sheel A, Song CQ, Zhang XO, Jiang T, Dang H, Cao Y, Ozata DM, Mou H, Yin H, Weng Z, Wang XW, Xue W. Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes. Hepatology. 2020 01; 71(1):275-290. PMID: 31188495.
      Citations: 12     Fields:    Translation:HumansCells
    28. 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 06 06; 74(5):982-995.e6. PMID: 31076285.
      Citations: 22     Fields:    Translation:AnimalsCells
    29. 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 07; 33(7):8161-8173. PMID: 30970224.
      Citations: 4     Fields:    Translation:HumansCells
    30. 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 09 25; 24(13):3413-3422.e4. PMID: 30257203.
      Citations: 9     Fields:    Translation:AnimalsCells
    31. 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 08; 14(8):e1007579. PMID: 30148885.
      Citations: 5     Fields:    Translation:HumansCells
    32. 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 08; 29(8):853-860. PMID: 29597895.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    33. 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 05 03; 173(4):1031-1044.e13. PMID: 29727662.
      Citations: 10     Fields:    Translation:AnimalsCells
    34. 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 06 08; 430(12):1814-1828. PMID: 29665372.
      Citations: 7     Fields:    Translation:Cells
    35. 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.
      Citations: 17     Fields:    Translation:AnimalsCells
    36. 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 02 27; 22(9):2254-2264. PMID: 29456100.
      Citations: 20     Fields:    Translation:AnimalsCells
    37. 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 02 22; 172(5):937-951.e18. PMID: 29456082.
      Citations: 73     Fields:    Translation:AnimalsCells
    38. 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.
      Citations: 37     Fields:    Translation:AnimalsCells
    39. 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.
      Citations: 27     Fields:    Translation:AnimalsCells
    40. 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 06 14; 18(1):108. PMID: 28615073.
      Citations: 69     Fields:    Translation:HumansCells
    41. 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 04 04; 114(14):3648-3653. PMID: 28320962.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    42. 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 05; 85(5):908-916. PMID: 28160322.
      Citations: 25     Fields:    Translation:HumansCells
    43. 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 Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice. Gastroenterology. 2017 04; 152(5):1161-1173.e1. PMID: 27956228.
      Citations: 35     Fields:    Translation:HumansAnimalsCells
    44. Vreven T, Pierce BG, Borrman TM, Weng Z. Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins. 2017 03; 85(3):408-416. PMID: 27718275.
      Citations: 2     Fields:    Translation:Cells
    45. Tsuji J, Weng Z. DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data. PLoS One. 2016; 11(10):e0164228. PMID: 27736901.
      Citations: 11     Fields:    Translation:Humans
    46. 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.
      Citations: 60     Fields:    Translation:AnimalsCells
    47. 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.
      Citations: 20     Fields:    Translation:HumansCells
    48. 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):1207-1214. PMID: 26402604.
      Citations: 106     Fields:    Translation:HumansAnimals
    49. 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 03; 59(5):819-30. PMID: 26340424.
      Citations: 52     Fields:    Translation:AnimalsCells
    50. 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.
      Citations: 11     Fields:    Translation:HumansCells
    51. 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.
      Citations: 92     Fields:    Translation:HumansAnimalsCells
    52. 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.
      Citations: 131     Fields:    Translation:HumansAnimalsCells
    53. 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.
      Citations: 165     Fields:    Translation:AnimalsCells
    54. 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: 55     Fields:    Translation:Humans
    55. 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.
      Citations: 13     Fields:    Translation:AnimalsCells
    56. 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: 25     Fields:    Translation:HumansCells
    57. 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 04; 56(5):708-16. PMID: 25453759.
      Citations: 47     Fields:    Translation:Animals
    58. 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.
      Citations: 63     Fields:    Translation:AnimalsCells
    59. 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.
      Citations: 3     Fields:    Translation:HumansAnimals
    60. 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.
      Citations: 14     Fields:    Translation:AnimalsCells
    61. 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.
      Citations: 99     Fields:    Translation:AnimalsCells
    62. 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.
      Citations: 16     Fields:    Translation:HumansCellsCTClinical Trials
    63. 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 05; 157(6):1353-1363. PMID: 24906152.
      Citations: 98     Fields:    Translation:AnimalsCells
    64. 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.
      Citations: 11     Fields:    Translation:AnimalsCells
    65. 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.
      Citations: 50     Fields:    Translation:HumansAnimalsCells
    66. 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.
      Citations: 453     Fields:    Translation:Cells
    67. 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.
      Citations: 45     Fields:    Translation:Humans
    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.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    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.
      Citations: 7     Fields:    Translation:Cells
    70. Hwang H, Vreven T, Weng Z. Binding interface prediction by combining protein-protein docking results. Proteins. 2014 Jan; 82(1):57-66. PMID: 23836482.
      Citations: 16     Fields:    Translation:Cells
    71. 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: 5     Fields:    Translation:HumansCells
    72. 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.
      Citations: 14     Fields:    Translation:Cells
    73. 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: 15     Fields:    Translation:HumansAnimalsCells
    74. 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.
      Citations: 42     Fields:    Translation:HumansCells
    75. 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 05; 340(6128):91-5. PMID: 23559253.
      Citations: 111     Fields:    Translation:AnimalsCells
    76. 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.
      Citations: 155     Fields:    Translation:AnimalsCells
    77. 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.
      Citations: 4     Fields:    
    78. Vreven T, Hwang H, Weng Z. Exploring angular distance in protein-protein docking algorithms. PLoS One. 2013; 8(2):e56645. PMID: 23437194.
      Citations: 7     Fields:    Translation:Cells
    79. Tu S, Pederson T, Weng Z. Networking development by Boolean logic. Nucleus. 2013 Mar-Apr; 4(2):89-91. PMID: 23412653.
      Citations: 1     Fields:    Translation:AnimalsCells
    80. 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.
      Citations: 34     Fields:    Translation:Cells
    81. 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.
      Citations:    
    82. 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.
      Citations: 166     Fields:    Translation:HumansCells
    83. 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.
      Citations: 65     Fields:    Translation:HumansAnimalsCells
    84. 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 09; 151(4):871-884. PMID: 23141543.
      Citations: 109     Fields:    Translation:AnimalsCells
    85. 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 09; 151(4):750-764. PMID: 23084401.
      Citations: 166     Fields:    Translation:HumansCells
    86. 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.
      Citations: 95     Fields:    Translation:HumansAnimalsCells
    87. 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.
      Citations: 79     Fields:    Translation:HumansCells
    88. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
      Citations: 6978     Fields:    Translation:HumansAnimalsCells
    89. 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.
      Citations: 458     Fields:    Translation:HumansCells
    90. 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.
      Citations: 115     Fields:    Translation:HumansCells
    91. 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.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    92. 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 Apr 24; 13(4):R27. PMID: 22531001.
      Citations: 50     Fields:    Translation:AnimalsCells
    93. 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.
      Citations: 115     Fields:    Translation:AnimalsCells
    94. 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.
      Citations: 30     Fields:    Translation:Cells
    95. 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.
      Citations: 112     Fields:    Translation:AnimalsCells
    96. 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.
      Citations: 249     Fields:    Translation:HumansAnimalsCells
    97. 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.
      Citations: 96     Fields:    Translation:AnimalsCells
    98. 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).
    99. 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.
      Citations: 92     Fields:    Translation:AnimalsCells
    100. 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.
      Citations: 191     Fields:    Translation:Cells
    101. 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.
      Citations: 96     Fields:    Translation:Humans
    102. 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.
      Citations: 31     Fields:    Translation:Cells
    103. 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.
      Citations: 6     Fields:    Translation:Cells
    104. 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.
      Citations: 434     Fields:    Translation:HumansAnimalsCells
    105. 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.
      Citations: 66     Fields:    Translation:HumansAnimalsCells
    106. 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.
      Citations: 47     Fields:    Translation:AnimalsCells
    107. 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.
      Citations: 32     Fields:    Translation:AnimalsCells
    108. 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.
      Citations: 172     Fields:    Translation:Cells
    109. 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 01; 5(5):392-5. PMID: 20458167.
      Citations: 3     Fields:    Translation:Cells
    110. 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.
      Citations: 273     Fields:    Translation:HumansAnimalsCells
    111. 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: 57     Fields:    Translation:Cells
    112. 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.
      Citations: 120     Fields:    Translation:HumansCells
    113. 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.
      Citations: 166     Fields:    Translation:AnimalsCells
    114. 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.
      Citations: 206     Fields:    Translation:AnimalsCells
    115. 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 01; 137(3):509-21. PMID: 19395009.
      Citations: 290     Fields:    Translation:AnimalsCells
    116. 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.
      Citations: 340     Fields:    Translation:AnimalsCells
    117. 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
    118. 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 01; 23(45):5212-24. PMID: 16137805.
      Citations: 15     Fields:    Translation:AnimalsCells
    119. 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.
      Citations: 5     Fields:    Translation:AnimalsCells
    120. 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
    121. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22; 306(5696):636-40. PMID: 15499007.
      Citations: 989     Fields:    Translation:HumansAnimalsCells
    122. 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
    123. 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:    
    124. Mintseris J, Weng Z. Optimizing protein representations with information theory. Genome Inform. 2004; 15(1):160-9. PMID: 15712119.
      Citations: 8     Fields:    Translation:Cells
    125. Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins. 2003 Nov 15; 53(3):629-39. PMID: 14579354.
      Citations: 39     Fields:    Translation:Cells
    126. Weng Z. Managing biological sequence and protein structure data. OMICS. 2003; 7(1):25-6. PMID: 12831551.
      Citations:    Fields:    Translation:Cells
    127. 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: 6     Fields:    Translation:AnimalsCells
    128. 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: 168     Fields:    Translation:Humans
    129. 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: 105     Fields:    Translation:HumansAnimalsCells
    130. 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
    131. 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
    132. 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
    133. 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
    134. 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
    135. 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: 51     Fields:    Translation:HumansAnimalsCells
    136. 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
    137. 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
    138. 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
    139. 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
    140. 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: 20     Fields:    Translation:Cells
    141. 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: 10     Fields:    Translation:Cells
    142. 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: 43     Fields:    Translation:Cells
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