Zheng Wang

Asst. Professor

Locator Code:
4245
 
About
Home Page : http://www.cs.miami.edu/~zwang/
Career

Education

2008 Ph.D. Computer Science, University of Missouri-Columbia

Professional Experience

2017 - Assistant Professor, University of Miami
2015 - 2017Nina Bell Suggs Professor, The University of Southern Mississippi
2013 - 2015Assistant Professor, The University of Southern Mississippi
2012 - 2013"Mizzou Advantage - Preparing Future Faculty" Postdoctoral Fellow, University of Missouri-Columbia

Honors & Acknowledgements

Academic research enhancement award (R15)
National Institutes of Health (NIH), sole PI, 2016
Nina Bell Suggs endowed professorship
University of Southern Mississippi, 2015
First place award for postdoctoral oral presentation
MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference, 2013
"Mizzou Advantage - Preparing Future Faculty" postdoctoral fellowship
  • (40% research, 40% teaching, and 20% service), Chancellor's Fund for Excellence, University of Missouri, 2012
  • Shumaker fellowship, University of Missouri, 201
Research

LIST OF SPECIALTIES: Bioinformatics, particularly, in the topics of three-dimensional structure of chromosomes, protein structure prediction, protein function prediction, protein domain co-occurrence network, and species phylogeny inference

Research Projects

scHiCNorm

scHiCNorm is a software package for eliminating systematic biases in single-cell Hi-C data. Considering that single-cell Hi-C data are zero-inflated, here we use zero-inflated (Poisson and Negative Binomial) and hurdle (Poisson and Negative Binomial) models to remove biases, including cutting sites, GC content, and mappability.

SOV_refine

SOV_refine is a refined definition of segment overlap score based on the previous definitons of SOV scores (SOV'99) (Zemla, A. et al., 1999, proteins) and (SOV'94) (Rost, B. et al., 1994, J. Mol. Biol.), which were initially designed to evaluate the quality of protein secondary structure predictions. SOV_refine redefined the assignment of allowance in SOV'99, which can ensure that the amount of allowance is incremental when one more element in the predicted sequence is further predicted accurately.

SOV scores (SOV'99 and SOV_refine) can be used in all sequence similarity comparison especially for those sequences with multiple overlapping segments

PANDA

Protein Function Prediction Using Domain Architecture and Affinity Propagation on the Gene Ontology Graph

Wang, Z., Zhao, C., Wang, Y., Sun, Z., and Wang, N. (2018) PANDA: Protein Function Prediction using Domain Architecture and Affinity PropagationScientific Reports, 8, doi:10.1038/s41598-018-21849-1.

DeepMethyl

Predicting DNA methylation state of CpG dinucleotide using genome topological features and deep networks

Reference


If you use DeepMethyl, please cite: Yiheng Wang, Tong Liu, Dong Xu, Huidong Shi, Chaoyang Zhang, Yin-Yuan Mo and Zheng Wang. Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks. Sci. Rep. 6, 19598, doi:10.1038/srep19598. [PDF]

Publications

Liu, T. and Wang, Z. "SOV_refine: A further refined definition of segment overlap score and its significance for protein structure similarity" Source Code for Biology and Medicine 13:1 (2018). [Link]


Wang, Z., Zhao, C., Wang, Y., Sun, Z., and Wang, N. "PANDA: Protein function prediction using domain architecture and affinity propagation" Scientific Reports (2018). [Link]