Yuji Zhang

 Ph.D. Candidate

  Computational Bioinformatics and Bio-imaging Laboratory(CBIL)
  Electrical and Computer Engineering, Virginia Tech

  Address:    4300 Wilson Blvd., Suite 750
                     Arlington, VA 22203
  Phone:       (202)687-6466
  Email:        yjzhang@vt.edu

 

 

I am a Ph.D. student in the Computational Bioinformatics and Bio-imaging Laboratory. The focus of my research is inferring transcriptional regulatory networks by combining high-throughput gene expression measurements with other biological data in publicly available databases. I am also interested in network-based identification of cancer biomarkers and their applications in diagnostic, prognostic and drug treatment prediction.  

 

 

 

 

  Education

Jan. 2005 - present

Ph.D. Student, Electrical and Computer Engineering, Virginia Tech

 

Sept. 2000 - Jun 2003

M.S., Biomedical Engineering, Southeast University

 

Sept. 1996 - Jun 2000

B.S., Biomedical Engineering, Southeast University

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  Research Interests

Computational Biology

- Gene Regulatory Network Inference

- Network Motif Analysis

- Molecular Interaction Network Analysis

- Biomarker Discovery

Pattern Recognition and Machine Learning

- Neural Networks

- Computational Intelligence

- Cluster Analysis

- Pattern Classification

 

 

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  Publications

Journal Publications

Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Reverse engineering module networks by PSO-RNN hybrid modeling," BMC Genomics,  vol. 10 (S1): S15, 2009. 

 

Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data," BMC Bioinformatics, vol. 9: 203, 2008.

 

Y. Zhang, J. Zhu, X. Sun and Z. Lu, ''A method of oligonucleotide synthesis optimization,'' Biotechnolgy, vol. 12, pp. 26-28, 2002. (in Chinese)

 

 

Conference Publications

Y. Zhang, J. Xuan, B. G. de Los Reyes, R. Clarke, and H. W. Ressom, "Network motif-based identification of breast cancer susceptibility genes," Proc. of Conf Proc IEEE Eng Med Biol Soc (EMBC), pp. 5696-5699, Vancouver, British Columbia, Canada, 2008.

 

Y. Zhang, J. Xuan, B. G. de los Reyes, R. Clarke, and H. W. Ressom, "Reverse engineering module networks by PSO-RNN hybrid modeling," Proc. of The 2008 International Conference on Bioinformatics & Computational Biology (BIOCOMP08), pp. 401-407, Las Vegas, NV, 2008.

 

H. W. Ressom, Y. Zhang, J. Xuan, Y. Wang, and R. Clarke, "Integrating Multi-Source Biological Data for Transcriptional Regulatory Module Discovery," Proc. of Third IEEE/NIH Life Science Systems and Applications (LISA) Workshop, Bethesda, MD, 2007.

 

H. W. Ressom, Y. Zhang, J. Xuan, Y. Wang, and R. Clarke, "Inferring network interactions using recurrent neural networks and swarm intelligence," in Proc. of Conf Proc IEEE Eng Med Biol Soc (EMBC), pp. 4241-4244, New York City, New York, USA, 2006.

 

H. W. Ressom, Y. Zhang, J. Xuan, J. Wang, and R. Clarke, "Inferring network interactions using recurrent neural networks and particle swarm optimization," Proc. of Proceedings of the First International Conference on Computational Systems Biology, pp. 387-392, Shanghai, China, 2006.

 

H. W. Ressom, Y. Zhang, J. Xuan, J. Wang, and R. Clarke, "Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence," Proc. of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB2006), pp. 435-442, Toronto, ON, Canada, 2006.

 

Y. Zhang, H. Wang, ''Comparative analysis of circadian clock genes in Zebrafish, Fugu and Tetraodon,'' The 6th International Meeting on Zebrafish Development and Genetics, Madison, Wisconsin, 2004.

 

 

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  Others

 

 

 

Last Updated: Sept. 20, 2009