Bai 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:       (703)387-6049



I am a Ph.D. candidate in the Bradley Department of Electrical and Computer Engineering at Virginia Tech. My research interests are in the fields of machine learning, data mining, and bioinformatics, with an emphasis on their applications in biomedical research.





Aug. 2006 - present

Ph.D. candidate, Bradley Department of Electrical and Computer Engineering, Virginia Tech


Aug. 2004 - Jul. 2006

M.S., Department of Automation, Tsinghua University


Aug. 2000 - Jul. 2004

B.S., Department of Automation, Tsinghua University




  Research Interests

Machine Learning and Data Mining

- Graphical model learning

- High dimensional data analysis and sparse modeling

- Classification, clustering and data visualization

- Neural networks and dynamical system modeling

- Message passing algorithms

- Sequential Monte Carlo methods (particle filtering)

Bioinformatics and Computational Biology

- Biological network inference and modeling

- DNA copy number data analysis

- Next-generation sequence data analysis

- Biomarker identification

- Normal tissue contamination correction

- Tumor progression

- Computational epigenetics

- Integrative analysis of biological data





Journal Publications


G. Yu*, B. Zhang*, J. Xu, G. S. Bova, I.-M. Shih, and Y. Wang, "BACOM: In silico detection of genomic deletion types and correction of normal cell contamination in copy number data", in press (doi: 10.1093/bioinformatics/btr183), Bioinformatics. (* Joint first author)

B. Zhang, Y. Tian, L. Jin, H. Li, I.-M. Shih, S. Madhavan, R. Clarke, E. P. Hoffman, J. Xuan, L. Hilakivi-Clarke, and Y. Wang, "DDN: A caBIG® analytical tool for differential network analysis", Bioinformatics, 27(7):1036-1038, 2011.

B. Zhang, H. Li, R. B. Riggins, M. Zhan, J. Xuan, Z. Zhang, E. P. Hoffman, R. Clarke, and Y. Wang, "Differential dependency network analysis to identify condition-specific topological changes in biological networks," Bioinformatics, 25(4):526-532, 2009.


Book Chapters

B. Zhang, H. Li, R. Clarke, L. Hilakivi-Clarke, and Y. Wang, “Differential dependency network analysis to identify topological changes in biological networks”, in F. Emmert-Streib and M. Dehmer (Eds.) Medical Biostatistics for Complex Diseases, pp. 185-204, Wiley-VCH, Weinheim, 2010.


Conference Publications

Y. Tian, B. Zhang, I.-M. Shih, Y. Wang, “Knowledge-guided differential dependency network learning for detecting structural changes in biological networks”, to appear in Proc. of ACM Conference on Bioinformatics and Computational Biology (ACM BCB 2011), Aug. 2011.

B. Zhang and Y. Wang, “Learning structural changes of Gaussian graphical models in controlled experiments”, in Proc. of the 26th Conference on Uncertainty in Artificial Intelligence (UAI 2010), Avalon, CA: 701-708, July 2010.

G. Yu, B. Zhang, J. Xu, I.-M. Shih, and Y. Wang, "Accurate estimation of genomic deletions and normal cell contamination by Bayesian analysis of mixtures," in Proc. IEEE Intl Conf. on Bioinformatics & Biomedicine, Washington D.C., USA, Nov. 2009. (Best student paper award)

B. Zhang, Y. Wang, "Echo state networks with decoupled reservoir states," in Proc. IEEE Machine Learning for Signal Processing, Cancun, Mexico, 2008.

B. Zhang, M. Chen, D.H. Zhou, "A variance-adaptive particle filter with application to time-varying parameter estimation," in Proc. of 16th IFAC World Congress 2005, Prague, Czech Republic.





For more information about me, please visit here.



Last Updated: May 1, 2011