Genomes and Genes
Affiliation: University of Massachusetts Medical School
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..