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Search Results to Zhiping Weng PhD

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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.


One or more keywords matched the following items that are connected to Weng, Zhiping

Item TypeName
Academic Article Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum.
Academic Article The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters.
Academic Article Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex.
Academic Article A simple method for improving the specificity of anti-methyl histone antibodies.
Academic Article MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression.
Academic Article Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals.
Academic Article An integrated encyclopedia of DNA elements in the human genome.
Academic Article Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Academic Article Human-specific histone methylation signatures at transcription start sites in prefrontal neurons.
Academic Article An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes.
Academic Article Transposition-driven genomic heterogeneity in the Drosophila brain.
Academic Article Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells.
Academic Article Modeling gene expression using chromatin features in various cellular contexts.
Academic Article Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Concept Down-Regulation
Concept Chromatin Immunoprecipitation
Concept Up-Regulation
Concept Chromatin
Concept Gene Expression Regulation, Developmental
Concept Gene Expression Regulation
Concept Chromatin Assembly and Disassembly
Academic Article MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis.
Academic Article High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm.
Academic Article A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters.
Academic Article 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.
Academic Article Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains.
Academic Article Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes.
Academic Article miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement.
Academic Article The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease.
Academic Article The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans.
Academic Article A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans.
Academic Article Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.
Academic Article Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia.

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  • Chromatin
  • Regulation