About me:
About my research:
My research interests are in the general areas of Bioinformatics, Computational Biology, and Data Mining.
I have worked and continue to work on the following projects:
- Protein-Protein Interaction Complex Prediction and Evaluation: Proteins usually interact with other proteins either in pairs or as components of larger complexes to perform some common biological functions. While many protein complexes have been identified by large-scale experimental studies, due to a large number of false-positive interactions existing in current protein complexes, it is still difficult to obtain an accurate understanding of functional modules, which encompass groups of proteins involved in common elementary biological function.
Furthermore, there is no "gold standard" to evaluate the goodness of a Protein-Protein Interaction Complex. Collaborate with Chris Ding (Computer Scientist at LBNL), Stephen Holbrook (Biophysics Scientist at LBNL), and Giri Narasimhan (Computer Scientist at FIU).
- Enhancing Motif Discovery Using Comparative Genomics Data: Understanding gene regulation is a key step to investigating gene functions and their relationships. Many algorithms have been developed
to discover transcription factor binding sites (TFBS); they are predominantly located in upstream regions of genes and contribute
to transcription regulation if they are bound by a specific transcription factor. However, traditional methods focusing on finding
motifs have shortcomings, which can be overcome by using comparative genomics data that is now increasingly available. Collaborate with Giri Narasimhan and Kalai Mathee (Biologist at FIU).
- Data Mining on Heterogeneous Biological Data: Many sources of data are available to better understand of genes function and their roles in cellular activities. Such sources include gene expression data, text literature data, protein-protein interaction data, transcription factor and regulatory elements data, comparative genomics data, protein expression data and much more. These data provide us with a means to begin
elucidating the large-scale modular organization of the cell. Conclusions drawn from more than one data source is likely to lead to new insights. However, dealing with multiple heterogeneous data is a big challenge. Collaborate with Chengyong Yang (Algorithm Developer at Applied Biosystems Inc., ), Tao Li (Computer Scientist at FIU) and Giri Narasimhan.
- Mining Regulatory Elements Using Gene Expression Data: A primary goal of this project is to investigate the design and use of a variety of computational tools to identify regulatory elements in DNA sequences using a combination of gene expression data and DNA sequence data.
One of the difficulties with the motif discovery programs is that they produce a large number of predicted TFBS along with associated scores representing the statistical significance of the predictions. However, drawing biologically useful inferences or conjectures remains a difficult problem.
we present a new approach that will facilitate the process of drawing meaningful conclusions that are likely to be useful to a biologist. This is achieved by constructing a comprehensive
relational database and an intelligent, user-friendly query system. Collaborate with Chengyong Yang, Kalai Mathee and Giri Narasimhan.
- Summer work at Centocor (A Subsidiary of Johnson & Johnson):
Implemented a web-based program for target explorer for research groups at Centocor, develop a web application of codon usage for research groups at Centocor, analyzed flow cytometry data for Department of Experimental Pathology, and microarray data analysis and promoter sequence data analysis. Collaborate with Jin Lu (Bioinformatician at Centocor) and other biologists at Centocor.
For more details about my research, please refer to my publications.
About my teaching:
Teaching is an important part of academic life. I met so many excellent teachers who opened my eyes and sparked
my interest during different periods of my life. I learned a lot from them. I hope I can become one member of this group one day. My previous teaching experience at FIU is one of the steps to fulfill my dream.
About my hobby:
Personal link:
ND E-mail
SCS E-mail
RNA Related Links
NCBI HomePage
R project
|
|
|
nd.edu