Xianghong Jasmine Zhou

Xianghong Jasmine Zhou

 

Associate Professor

Program in Molecular and Computational Biology

University of Southern California

Office: DRB291   Phone: 213-740-7055   Fax: 213-740-2437

Email: xjzhou at usc.edu
 

Research Interests

My research interests include:

  • Study the structure, function, and evolution of cellular interaction/regulatory networks
  • Develop novel methods to integrate heterogenous genomics data
  • Develop graph algorithms for mining biological networks
  • Biological models: aging, cancer

Background Summary

 

2008-

Associate Professor, University of Southern California

2003-2008

Assistant Professor, University of Southern California

2001-2003

Post-doc, Harvard University

2000 Fall

Post-doc, UCLA

1997-2000

PhD, Swiss Federal Institute of Technology (ETH Zurich)

1991-1995

Diplom, University of Tuebingen, Germany 

 

Teaching
  • Fall 2008: Statistics for Life Sciences (BISC305)
  • Spring 2008: Computational Molecular Biology (Math578a), Computational Genome Analysis (BISC478), Computational Molecular Biology Lab (Math 577a)
  • Fall 2007: Seminar in Computational Biology (BISC542)
  • Spring 2007: Computational Molecular Biology (Math578a), Computational Genome Analysis (BISC478), Computational Molecular Biology Lab (Math 577a)
  • Spring 2006: Computational Molecular Biology (Math578a), Computational Genome Analysis (BISC478), Computational Molecular Biology Lab (Math 577a), Molecular Genetics and Biochemistry (BISC502b)
  • Fall 2005: Computational Molecular Biology Lab (Math 577b), Seminar in Computational Biology (BISC542)
  • Spring 2005: Computational Molecular Biology (Math578a), Computational Molecular Biology Lab (Math 577a), Molecular Genetics and Biochemistry (BISC502b)  
  • Fall 2004: Genomics and Molecular genetics (BISC505)  
  • Spring 2004: Computational Molecular Biology (Math578a), Computational Molecular Biology Lab (Math 577a), Molecular Genetics and Biochemistry (BISC502b)

Publications
  • Liu CC, Hu J, Kalakrishnan M, Huang H, Zhou XJ (2008)
    • Integrative Disease Classification Based on Cross-platform Microarray Data.
    BMC Bioinformatics, in press.

  • Jin R, Macallen S, Liu CC, Xiang Y, Almaas E, Zhou XJ (2008)
    • Identifying Dynamic Network Modules with Temporal And Spatial Constraints.
    Pacific Symposium of Biocomputing 2009, in press.

  • Mulkar-Mehta R, Hobbs J, Liu CC, Zhou XJ (2008)
    • Discovering Causal and Temporal Relations in Biomedical Texts.
    AAAI Spring Symposium on Learning by Reading and Learning to Read. in press.

  • Mehan MR, Nunez_Iglesias J, Kalakrishan M, Waterman MS, Zhou XJ (2008)
    • An Integrative Network Approach to Map the Transcriptome to the Phenome
    RECOMB 2008 (also in Lecture Notes in Computer Science, 4955, 232-245)

  • Xu M, Kao MJ, Nunez_Iglesias J, Nevins JR, West M, Zhou XJ (2008)
    • Chracterizing disease-specific pathways and their coordination by integrative microarray analysis with application to cancer.
    BMC Genomics, 2008;9 Suppl 1:S12.

  • Teng S, Zhou XJ, Huang H (2008)
    • A statistical framework to infer functional gene associations across multiple biologically related microarray experiments.
    Journal of American Statistical Association, to appear

  • Huang Y, Li H, Hu H, Yan X, Waterman MS, Huang H, Zhou XJ (2007)
    • Systematic Discovery of Functional Modules and Context-Specific Functional Annotation of Human Genome.
    Bioinformatics (ISMB 2007), 23(13):i222-i229.    [pdf] [Supplementary Software]

  • Yan X, Mehan M, Huang Y, Waterman MS, Yu PS, Zhou XJ (2007)
    • A Graph-based Approach to Systematically Reconstruct Human Transcriptional Regulatory Modules.
    Bioinformatics (ISMB 2007), 23(13):i577-i586.[pdf] [Supplementary Software]

  • Pan F, Chiu C, Pulapura S, Mehan MR, Nunez-Iglesias J, Zhang K, Waterman MS, Finch CE, Zhou XJ (2007)
    • Gene Aging Nexus: A Web Database and Data Mining Platform for Microarray Data on Aging.
    Nucleic Acids Res. 2007 35:D756-9 [pdf] [Software]

  • Hu J, Li H, Waterman M, Zhou XJ (2006)
    • Integrative Missing Value Estimation for Microarray Data.
    BMC Bioinformatics. 2006 Oct 12;7:449.[pdf] [Software]

  • Pan F, Kamath K, Zhang K, Pulapura S, Achar A, Nunez-Iglesias J, Huang Y, Yan X, Han J, Hu H, Xu M, Zhou XJ. (2006)
    • Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.
    Bioinformatics. 22(13):1665-7.[pdf] [Software]

  • Tu Z, Wang L, Xu M, Zhou X, Chen T, Sun F (2006).
    • Further understanding human disease genes by comparing with housekeeping genes and other genes.
    BMC Genomics 7:31.

  • Hu H, Yan X, Huang Y, Han J, Zhou XJ (2005)
    • Mining coherent dense subgraphs across massive biological networks for functional discovery.
    Bioinformatics (ISMB 2005), Vol. 21 Suppl. 1 2005, pages i213-i221.[pdf] [Slides] Supplementary Material/Software

  • Zhou XJ, Kao MJ, Huang H, Wong A, Nunez-Iglesias J, Primig M, Aparicio OM, Finch CE, Morgan TE, Wong WH (2005)
    • Functional annotation and network reconstruction through cross-platform integration of microarray data.
    Nature Biotechnology. 2005 Feb;23(2):238-43.[pdf]  *This paper was highlighted in Nature Review Genetics 6, 164(2005).

  • Yan X, Zhou XJ, Han J (2005)
    • Mining Closed Relational Graphs with Connectivity Constraints.
    The Eleventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2005): 324-333

  • Zhou XJ, Gibson G. (2004)
    • Cross-species Comparison of Genome-wide Expression Patterns.
    Genome Biology 5(7):232.[pdf] 

  • Huang H, Kao MJ, Zhou X, Liu JS, Wong WH (2004)
    • Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification.
    Journal of Computational Biology 11(1):1-14.

  • Zhou X , Krueger JG, Kao MJ,Lee E, Du F, Menter A, Wong WH, Bowcock AM (2003)
    • Novel Mechanisms of T-cell and dendritic cell activation revealed by profiling of psoriasis on the 63,100-element oligonucleotide array.
    Physiological Genomics 13:69-78.    [pdf] [Abstract]

  • Zhou X, Kao MJ, Wong WH (2002)
    • From the Cover: Transitive Functional Annotation By Shortest Path Analysis of Gene Expression Data.
    Proc Natl Acad Sci USA. 99(20):12783-12788.     [pdf] [Abstract] [Website]
    *This paper was highlighted in PNAS: 99(20):12509-12511| BioMedNet | The Faculty of 1000.

  • Block-Alper L, Webster P, Zhou X, Supekov, Wong WH, Schultz P, and Meyer DI. (2002)
    • IN02, a Positive Regulator of Lipid Biosynthesis, is Essential for the Formation of Inducible Membranes in Yeast. Molecular Biology of the Cell. (13) 40-51. [pdf] [Abstract]

  • Zhou X, Gonnet GH, Hallett M, Folkers G, James P. (2001)
    • Cell Fingerprinting: An approach to classify cells using their protein extracts with mass spectrometric analysis.
    Proteomics. (1) 675-682.    [pdf] [Abstract]

  • Zhou X, Gonnet GH, Hallett M, Chelvanayagam G. Folkers G. (2001)
    • Identifying the most influential residues for alpha-helix formation: The subset selection problem using least squares optimization.
    Proceeding of the 16th ACM symposium on Applied Computing. 51-56. 2001.    [pdf]

  • Zhou X, Alber F, Folkers G, Gonnet GH, Chelvanayagam G. (2000)
    • An analysis of the helix-to-strand transition between peptides with identical sequence.
    Proteins: Struc. Func. Gen. 2000 (41):248-256.     [pdf] [Abstract] [Website]

  • Cannarozzi G, Hallett M, Norberg J, Zhou X. (2000)
    • A Cross-Comparison of a Large Dataset of Genes.
    Bioinformatics 2000. 16(7):654-655    [pdf] [Abstract]  [Website]