People in Bioengineering
Sheng Zhong
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Assistant Professor
Bioengineering
3215 Digital Computer Lab, MC-278
1304 W. Springfield
Urbana, Illinois 61801
(217) 265-6589
Ph.D., Department of Biostatistics with Ph.D. minor in Molecular Biology, Harvard University, 2005
Research Interests:
- We use computational and experimental approaches to study cellular differentiation and evolution. We aim to address two scientific questions: 1) how gene expression evolves as a consequence of genome sequence evolution; and 2) how genetic network regulate early cell fate decision. We study two biological processes: 1) differentiation of embryonic stem cells, and 2) mammalian preimplantation development. We generate genomic data, develop probabilistic models, use computational inference and experimental validation to understand how gene expression is regulated and how such regulatory mechanisms evolve.
- Identification of transcriptional network in high eukaryote organisms. The control of gene transcription is a crucial component in regulating many important biological processes. For example, in the early stages of development, cell fate decisions and differentiation programs are often controlled by the expression of key transcription factor and receptor molecules whose presence or absence help to specify the cell fate, or to activate or suppress a particular differentiation pathway. We are interested in identifying the active transcription factors and their DNA binding sites in certain biological processes. Especially we are developing computational methodologies that (1) identify long range enhancers; (2) model the cooperation of multiple transcription factors; (3) model phylogenetic distance and improve DNA motif finding accuracy.
- Inferring gene functions and protein networks through the use of gene expression data, ChIP-chip data, epigenetic modification data together with prior knowledge on singling pathways, Gene Ontology and protein domains. We work on statistical models and machine learning methods that jointly utilize genomics data and prior functional knowledge to infer gene functions, protein-DNA and protein-protein interactions.
- Software and database developments for functional genomics research. We work on providing software and databases for the management, analysis, and visualization of genome sequences, microarray data, Gene Ontology, and signaling pathways.
Undergraduate Research Opportunities:
We seek highly motivated undergraduate research fellows from both biology and computer science backgrounds to assist systems biology research. Available projects include but do not limit to:
1) develop a luciferase reporter assay for testing conserved cis-regulatory elements in vertebrates.
1) develop computational tools, especially cloud computing tools (http://en.wikipedia.org/wiki/Cloud_computing), for analysis of the next generation sequencing data.
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