Research

Teaching

Resume

Funding

 

ZLAB

BME

Bioinformatics



 

Research Interests

Bioinformatics; DNA and protein sequence analysis; protein-protein interactions, protein structure analysis; optimization algorithms and their applications in molecular biology; drug and vaccine design.

Current Research

Dr. Weng's research is focused on molecular interactions: (1) interaction between regulatory proteins and their DNA/RNA target sites (2) protein-protein interaction (3) protein-peptide interaction (4) interaction between protein structure building blocks.   Her lab (ZLAB) has both computational and experimental components. The computational members of the lab develop a variety of algorithms, including transcriptional regulation (Cister, Comet, Cluster-buster, Glam, Clover, PromoSer, HugeIndex, Site2genome and CARRIE), protein-protein docking (ZDOCK and RDOCK), protein structure alignment (K2), predicting peptides bound by major-histocompatibility-complex (SMM) and sequence visualization (SeqVISTA).  The experimental members of the lab test computational predictions. Some of them design mutant proteins with enhanced binding affinity or solubility, and others perform high-throughput and accurate gene expression measurements using Mass Spectrometry.

Selected Publications

  1. Haverty, P. M., Hansen, U. & Weng, Z. (2004). Computational Inference of Transcriptional Regulatory Networks from Expression Profiling and Transcription Factor Binding Site Identification. Nucleic Acids Res. Jan 1;32(1):179-188.
  2. Frith, M. C., Hansen, U., Spouge, J. L. & Weng, Z. (2004). Finding Functional Sequence Elements by Multiple Local Alignment Nucleic Acids Res. Jan 1;32(1):189-200.
  3. Peters, B., Tong, W., Sidney, J., Sette, A. & Weng, Z. (2003). Examining the Independent Binding Assumption for Binding of Peptide Epitopes to MHC-I Molecules Bioinformatics 19:1765-1772.
  4. Halees, A.S., Leyfer, D. & Weng, Z. (2003). Promoser: A Larger-scale Mammalian Promoter and Transcription Start Site Identification Service. Nucleic Acids Research. 31:3554-9.
  5. Frith, M.C., Li, M.C. & Weng, Z. (2003). Cluster-Buster: Finding Dense Clusters of Motifs in DNA Sequences. Nucleic Acids Res. 31:3666-8.
  6. Chen, R., Tong, W., Mintseris, J., Li, L. & Weng, Z. (2003). ZDOCK Predictions for the CAPRI Chanllenge. Proteins. Structure, Function and Genetics. 52:68-73.
  7. Chen, R., Li, L. & Weng, Z. (2003). ZDOCK: An Initial-stage Protein Docking Algorithm. Proteins. Structure, Function and Genetics. 52:80-7.
  8. Hu, Z., Frith, M., Niu, T. and Weng, Z. (2003). SeqVISTA: a graphical tool for sequence feature visualization and comparison. BMC Bioinformatics. 4:1.
  9. Frith, M., Spouge, J., Hansen, U. & Weng, Z. (2002). Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res. 30:3214-3224.
  10. Szustakowski, J. & Weng, Z. (2000). Structural alignment using a genetic algorithm.  Proteins: Structure, Function and Genetics, 38:438-440.

For a complete list of publications, please visit ZLAB publication page.

A man who dares to waste one hour of time has not discovered the value of life.
– Charles Robert Darwin, naturalist (1809-82)