Center for Biomedical Research Informatics
Research Scientist I

Contact Information
224.364.7437
847.570.8033 fax
yzhu@northshore.org and yitanzhu@uchicago.edu

Education

  • Undergraduate: BE, Automatic Control, Shanghai Jiao Tong University, Shanghai, China
  • Post Graduate: MS, Pattern Recognition and Intelligent Systems, Shanghai Jiao Tong University, Shanghai, China
    PhD, Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA

Research Interests

Bioinformatics, systems biology, and drug development:

  • Biomarker discovery, genomic regulation network, integrative genomic data analysis, tumor heterogeneity, drug target identification, drug toxicity/efficacy prediction.

Machine learning, statistical pattern recognition, signal/image processing, and data visualization:

  • Clustering, classification, feature selection/extraction, optimization, blind source separation, data projection.

Scholarly Work

Publications in Peer-Review Journals:

  1. J. Lee, P. Müller, Y. Zhu, Y. Ji, A Nonparametric Bayesian Model for Local Clustering with Application to Proteomics, Journal of the American Statistical Association, in press.
  2. Y. Zhu, H. Li, D.J. Miller, Z. Wang, J. Xuan, R. Clarke, E.P. Hoffman, and Y. Wang, caBIG® VISDA: modeling, visualization, and discovery for cluster analysis of genomic data, BMC Bioinformatics, vol. 9, 383, 2008.
  3. Y. Zhu, Z. Wang, D.J. Miller, R. Clarke, J. Xuan, E.P. Hoffman, and Y. Wang, A ground truth based comparative study on clustering of gene expression data, Frontiers in Bioscience, vol. 13, pp. 3839-3849, 2008.
  4. J. Yang, X. Ling, Y. Zhu, and Z. Zheng, A face detection and recognition system in color image series, Mathematics and Computers in Simulation, vol. 77, no. 5-6, pp. 531-539, 2008.
  5. J. Wang, H. Li, Y. Zhu, M. Yousef, M. Nebozhyn, M. Showe, L. Showe, J. Xuan, R. Clarke, and Y. Wang, VISDA: An open-source caBIG® analytical tool for data clustering and beyond, Bioinformatics, vol. 23, no. 15, pp. 2024-2027, 2007.
  6. Z. Zheng, J. Yang, and Y. Zhu, Initialization enhancer for non-negative matrix factorization, Engineering Applications of Artificial Intelligence, vol. 20, no. 1, pp. 101-110, 2007.
  7. M. Bakay, Z. Wang, G. Melcon, L. Schiltz, J. Xuan, P. Zhao, V. Sartorelli, J. Seo, E. Pegoraro, C. Angelini, B. Shneiderman, D. Escolar, Y. Chen, S.T. Winokur, L.M. Pachman, C. Fan, R. Mandler, Y. Nevo, E. Gordon, Y. Zhu, Y. Dong, Y. Wang, and E.P. Hoffman, Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb–MyoD pathways in muscle regeneration, Brain, vol. 129, no. 4, pp. 996-1013, 2006.
  8. Z. Zheng, J. Yang, and Y. Zhu, Face detection and recognition using color sequential images, Journal of Research and Practice in Information Technology, vol. 38, no. 2, 2006.

Peer-Review Conference Publications:

  1. Y. Zhu, T. Chan, E.P. Hoffman, Y. Wang, Gene expression dissection by non-negative well-grounded source separation, Proc. IEEE Intl. Workshop on Machine Learning for Signal Processing, Cancún, Mexico, October 2008.
  2. J. Molineaux, J. Xuan, T. Gong, Y. Zhu, E.P. Hoffman, R. Clarke and Y. Wang, ModVis: an information visualization tool for gene module discovery, Proc. 19th Intl. Conf. Computer Applications in Industry and Engineering, pp. 24-31, Las Vegas, NV, November 2006.
  3. Y. Feng, Z. Wang, Y. Zhu, J. Xuan, D.J. Miller, R. Clarke, E.P. Hoffman, and Y. Wang, Learning the tree of phenotypes using genomic data and VISDA, Proc. Sixth IEEE Symposium on Bioinformatics and Bioengineering, pp. 165-170, Washington DC, October 2006.
  4. Y. Zhu, Z. Wang, J. Xuan, E.P. Hoffman, and Y. Wang, Phenotypic-specific gene module discovery using diagnostic tree and VISDA, Proc. IEEE Intl. Conf. Engineering in Medicine and Biology Society, pp. 5767-5770, New York City, NY, August 2006.
  5. T. Gong, Y. Zhu, J. Xuan, H. Li, R. Clarke, E.P. Hoffman, and Y. Wang, Latent variable and nICA modeling of pathway gene module composite, Proc. IEEE Intl. Conf. Engineering in Medicine and Biology Society, pp. 5872-5875, New York City, NY, August 2006.
  6. T. Gong, J. Xuan, Y. Zhu, H. Li, R. Clarke, E.P. Hoffman, and Y. Wang, Composite gene module discovery using non-negative independent component analysis, Proc. IEEE/NLM Life Science Systems and Applications Workshop, pp. 1-2, Bethesda, MD, July 2006.

Peer Review Service:

  1. BMC Genomics, 2013
  2. International Journal of Biomedical Imaging, 2013
  3. BMC Bioinformatics, 2009
  4. EURASIP Journal on Bioinformatics and Systems Biology, 2009
  5. Current Bioinformatics, 2009
  6. Personalized Medicine, 2009
  7. Cancer Informatics, 2009

Software:

  1. VIsual Statistical Data Analyzer (VISDA)
    Link: https://cabig.nci.nih.gov/community/tools/VISDA
    Supporting Paper 1
    : Y. Zhu, H. Li, D.J. Miller, Z. Wang, J. Xuan, R. Clarke, E.P. Hoffman, and Y. Wang, caBIG® VISDA: modeling, visualization, and discovery for cluster analysis of genomic data, BMC Bioinformatics, vol. 9, 383, 2008.
    Supporting Paper 2: J. Wang, H. Li, Y. Zhu, M. Yousef, M. Nebozhyn, M. Showe, L. Showe, J. Xuan, R. Clarke, and Y. Wang, VISDA: An open-source caBIG® analytical tool for data clustering and beyond, Bioinformatics, vol. 23, no. 15, pp. 2024-2027, 2007.
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