Zhiping Weng

Summary

Affiliation: University of Massachusetts Medical School
Country: USA

Publications

  1. Han B, Wang W, Li C, Weng Z, Zamore P. Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science. 2015;348:817-21 pubmed publisher
    ..The ping-pong pathway increases only the abundance of piRNAs, whereas production of phased primary piRNAs from cleaved transposon RNAs adds sequence diversity to the piRNA pool, allowing adaptation to changes in transposon sequence. ..
  2. Chang T, Mattei E, Gainetdinov I, Colpan C, Weng Z, Zamore P. Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster. Mol Cell. 2018;: pubmed publisher
    ..We propose that by repressing canonical transcription of individual transposon mRNAs, Mael helps Rhi drive non-canonical transcription of piRNA precursors without generating mRNAs encoding transposon proteins. ..
  3. Zhang F, Wang J, Xu J, Zhang Z, Koppetsch B, Schultz N, et al. UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell. 2012;151:871-884 pubmed publisher
    ..We therefore propose that UAP56 and Vasa function in a piRNA-processing compartment that spans the nuclear envelope. ..
  4. Zhang G, Tu S, Yu T, Zhang X, Parhad S, Weng Z, et al. Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin. Cell Rep. 2018;24:3413-3422.e4 pubmed publisher
    ..Rhino thus promotes assembly of piRNA precursor complexes, and these complexes restrict Rhino at cluster heterochromatin. ..
  5. Zhuang J, Wang J, Theurkauf W, Weng Z. TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res. 2014;42:6826-38 pubmed publisher
    ..TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git. ..
  6. Fu Y, Wu P, Beane T, Zamore P, Weng Z. Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers. BMC Genomics. 2018;19:531 pubmed publisher
    ..Finally, we show that computational removal of PCR duplicates based only on their mapping coordinates introduces substantial bias into data analysis. ..
  7. Zhuang J, Weng Z. Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes. Nucleic Acids Res. 2015;43:8146-56 pubmed publisher
    ..We further characterized how the gene structures of the oncogene JAK1 and the tumor suppressors KDM6A and RB1 are affected by somatic SVs and discussed the potential functional implications of intergenic SVs. ..
  8. Li Y, Park A, Mou H, Colpan C, Bizhanova A, Akama Garren E, et al. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biol. 2015;16:111 pubmed publisher
    ..Moreover, we detect Cas9 cleavage at the fourth nucleotide on the non-complementary strand, leading to staggered instead of blunt DNA breaks. These reporters allow mechanisms of chromosomal rearrangements to be investigated. ..
  9. Vreven T, Moal I, Vangone A, Pierce B, Kastritis P, Torchala M, et al. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. J Mol Biol. 2015;427:3031-41 pubmed publisher
    ..Predicted affinity scores are found to correlate with experimental binding energies up to r=0.52 overall and r=0.72 for the rigid complexes. ..

More Information

Publications19

  1. Vreven T, Schweppe D, Chavez J, Weisbrod C, Shibata S, Zheng C, et al. Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking. J Mol Biol. 2018;430:1814-1828 pubmed publisher
    ..Employing the symmetry information for these cases further improved the performance of complex structure prediction. ..
  2. Song C, Li Y, Mou H, Moore J, Park A, Pomyen Y, et al. Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice. Gastroenterology. 2017;152:1161-1173.e1 pubmed publisher
    ..We associated decreased levels of NF1 and increased levels of its downstream protein HMGA2 with survival times of patients with HCC. Strategies to inhibit or reduce HMGA2 might be developed to treat patients with liver cancer. ..
  3. Parhad S, Tu S, Weng Z, Theurkauf W. Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery. Dev Cell. 2017;43:60-70.e5 pubmed publisher
    ..Deadlock binding thus directs Rhino to piRNA clusters, and Rhino-Deadlock co-evolution has produced cross-species incompatibilities, which may contribute to reproductive isolation. ..
  4. Vreven T, Hwang H, Pierce B, Weng Z. Evaluating template-based and template-free protein-protein complex structure prediction. Brief Bioinform. 2014;15:169-76 pubmed publisher
    ..Finally, we show that the near-native (correct) predictions were generally not shared by the various approaches, suggesting that integrating their results could be the superior strategy. ..
  5. Hoss A, Labadorf A, Latourelle J, Kartha V, Hadzi T, Gusella J, et al. miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. BMC Med Genomics. 2015;8:10 pubmed publisher
  6. Wang W, Han B, Tipping C, Ge D, Zhang Z, Weng Z, et al. Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. Mol Cell. 2015;59:819-30 pubmed publisher
    ..This alternative pathway may help flies silence newly acquired transposons for which they lack extensively complementary piRNAs. ..
  7. Mou H, Smith J, Peng L, Yin H, Moore J, Zhang X, et al. CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biol. 2017;18:108 pubmed publisher
    ..Exon skipping adds to the unexpected outcomes that must be accounted for, and perhaps taken advantage of, in CRISPR experiments. ..
  8. Tu S, Wu M, Wang J, Cutter A, Weng Z, Claycomb J. Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes. Nucleic Acids Res. 2015;43:208-24 pubmed publisher
    ..This first comparative characterization of a small RNA pathway in Caenorhabditis establishes a conserved nuclear role for CSR-1 and highlights its key role in germline gene regulation across multiple animal species. ..
  9. Wang W, Yoshikawa M, Han B, Izumi N, Tomari Y, Weng Z, et al. The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs. Mol Cell. 2014;56:708-16 pubmed publisher
  10. Zhang W, Zhu X, Fu Y, Tsuji J, Weng Z. Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. BMC Bioinformatics. 2017;18:464 pubmed publisher
    ..In the computational experiments, two ensemble learning methods outperform benchmark branchpoint prediction methods, and can produce high-accuracy results on the benchmark dataset. ..