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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 Docking unbound proteins using shape complementarity, desolvation, and electrostatics.
Academic Article Atomic contact vectors in protein-protein recognition.
Academic Article RDOCK: refinement of rigid-body protein docking predictions.
Academic Article CisML: an XML-based format for sequence motif detection software.
Academic Article M-ZDOCK: a grid-based approach for Cn symmetric multimer docking.
Academic Article Assessing computational tools for the discovery of transcription factor binding sites.
Academic Article Optimizing protein representations with information theory.
Academic Article ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
Academic Article Protein-Protein Docking Benchmark 2.0: an update.
Academic Article Structure, function, and evolution of transient and obligate protein-protein interactions.
Academic Article Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum.
Academic Article A global map of p53 transcription-factor binding sites in the human genome.
Academic Article The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.
Academic Article A combination of rescoring and refinement significantly improves protein docking performance.
Academic Article The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome.
Academic Article Protein therapeutics: promises and challenges for the 21st century.
Academic Article Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins.
Academic Article Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins.
Academic Article Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals.
Academic Article Prediction of protein-protein binding free energies.
Academic Article Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.
Academic Article A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes.
Academic Article Exploring angular distance in protein-protein docking algorithms.
Academic Article A novel shape complementarity scoring function for protein-protein docking.
Academic Article Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Academic Article Performance of ZDOCK in CAPRI rounds 20-26.
Academic Article Blind prediction of interfacial water positions in CAPRI.
Academic Article ZDOCK predictions for the CAPRI challenge.
Academic Article ZDOCK: an initial-stage protein-docking algorithm.
Academic Article A protein-protein docking benchmark.
Academic Article FAST: a novel protein structure alignment algorithm.
Academic Article An avidin-like domain that does not bind biotin is adopted for oligomerization by the extracellular mosaic protein fibropellin.
Academic Article Main-chain conformational tendencies of amino acids.
Academic Article Identification of conserved structural features at sequentially degenerate locations in transcription factor binding sites.
Academic Article ZRANK: reranking protein docking predictions with an optimized energy function.
Academic Article The landscape of histone modifications across 1% of the human genome in five human cell lines.
Academic Article Transcription factor binding and modified histones in human bidirectional promoters.
Academic Article Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Academic Article Integrating statistical pair potentials into protein complex prediction.
Academic Article Protein-protein docking: overview and performance analysis.
Academic Article Protein-protein docking benchmark version 3.0.
Academic Article Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway.
Academic Article Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells.
Academic Article Sequence features that drive human promoter function and tissue specificity.
Academic Article Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains.
Academic Article Protein-protein docking benchmark version 4.0.
Academic Article Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.
Academic Article A structure-based benchmark for protein-protein binding affinity.
Academic Article A machine learning approach for the prediction of protein surface loop flexibility.
Academic Article Molecular basis of a million-fold affinity maturation process in a protein-protein interaction.
Academic Article Integrating atom-based and residue-based scoring functions for protein-protein docking.
Academic Article Accelerating protein docking in ZDOCK using an advanced 3D convolution library.
Academic Article Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
Academic Article Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains.
Academic Article Exploring the DNA-recognition potential of homeodomains.
Academic Article Cutting edge: Evidence for a dynamically driven T cell signaling mechanism.
Academic Article Understanding transcriptional regulation by integrative analysis of transcription factor binding data.
Academic Article The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus.
Academic Article Evaluating template-based and template-free protein-protein complex structure prediction.
Concept Protein Binding
Concept Early Growth Response Protein 2
Concept Amyloid beta-Protein Precursor
Concept Protein Folding
Concept Protein Processing, Post-Translational
Concept Ubiquitin-Protein Ligases
Concept Tumor Suppressor Protein p53
Concept Protein Interaction Mapping
Concept CDC2 Protein Kinase
Concept HIV Envelope Protein gp160
Concept Protein Interaction Domains and Motifs
Concept Protein-Serine-Threonine Kinases
Concept Protein Denaturation
Concept GA-Binding Protein Transcription Factor
Concept Protein Structure, Secondary
Concept Protein Structure, Tertiary
Concept Protein Multimerization
Concept Protein Structure, Quaternary
Concept Structural Homology, Protein
Concept ran GTP-Binding Protein
Concept TATA-Binding Protein Associated Factors
Concept Diet, Protein-Restricted
Concept Protein Conformation
Concept Databases, Protein
Concept Sequence Analysis, Protein
Concept Protein Engineering
Academic Article Computational design of the affinity and specificity of a therapeutic T cell receptor.
Academic Article ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers.
Academic Article Backbone flexibility of CDR3 and immune recognition of antigens.
Academic Article Binding interface prediction by combining protein-protein docking results.
Academic Article Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin.
Academic Article Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies.
Academic Article Systematic detection of statistically overrepresented DNA motif association rules.
Academic Article Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin.
Academic Article Managing biological sequence and protein structure data.
Academic Article Less is more: towards an optimal universal description of protein folds.
Academic Article A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules.
Academic Article Protein structure alignment using a genetic algorithm.
Academic Article VRDD: applying virtual reality visualization to protein docking and design.
Academic Article Computational determination of the structure of rat Fc bound to the neonatal Fc receptor.
Academic Article Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments.
Academic Article Effect of conformational flexibility and solvation on receptor-ligand binding free energies.
Academic Article Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules.
Academic Article Prediction of protein complexes using empirical free energy functions.
Academic Article Empirical free energy calculation: comparison to calorimetric data.
Academic Article 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.
Academic Article Free energy landscapes of encounter complexes in protein-protein association.
Academic Article Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms.
Academic Article Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Academic Article Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins.
Academic Article The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease.
Academic Article How structural adaptability exists alongside HLA-A2 bias in the human aß TCR repertoire.
Academic Article Computational Reprogramming of T Cell Antigen Receptor Binding Properties.
Academic Article Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Academic Article A benchmark testing ground for integrating homology modeling and protein docking.
Academic Article A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces.
Academic Article IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection.
Academic Article Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes.
Academic Article The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases.
Academic Article FXR1 regulates transcription and is required for growth of human cancer cells with TP53/FXR2 homozygous deletion.
Academic Article The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes.
Academic Article Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.
Academic Article The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans.
Academic Article Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.

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