CURRICULUM VITAE     (PDF)

Zhenjun Hu

WORK ADDRESS

Center for Advanced Genomic Technology

Bioinformatics, Boston University

24 Cummington Street, Boston, MA 02215

Phone: (617) 358-3121      email: zhenjun.hu

Mobile: (617) 9663608

EDUCATION

1996-2000    PhD in Bio-Mechanical Engineering, Northeastern University, Boston, MA, USA

PhD Thesis: "IN-VIVO CHARACTERIZATION OF HUMAN CORONARY ARTERY FLOW".

1991-1994    MS in Mechanical Engineering. Institute of Engineering Thermophysics, Chinese Academy of Sciences (CAS), Beijing, China

1987-1991     BS in Mechanical Engineering. Huazhong University of Science and Technology, Wuhan, China

RESEARCH AND PROFESSIONAL EXPERIENCE

 

2011-                    Research Associate Professor,

2007-2011             Research Assistant Professor,

2002-2007             Research Associate, Center for Advanced Genomic Technology, Bioinformatics Program, Boston University, MA, USA. My research is focused on biological networks and their application in Systems Biology, Systems Pharmacology and Translational Science. There are two major component: i) Network integration, reconstruction and visualization: we developed VisANT--- one of the most popular integrative platforms for visual analysis of biological networks [6,7,9,12,16]. In particular, we initiated a new graph type-metagraph to visually integrate context information into the network, and to achieve the large-scale network visualization with improved system performance and network readability [6,7,8,9]; ii) Network-based analysis and inference: we develop methods to predict new disease genes and disease-disease correlations using functional linkage network [5] inferred by integrating many different types of interaction --- PPI, genetic interaction etc. We develop network-based GO (Gene Ontology) enrichment methods to predict the function of network modules [6]. We also develop network-based expression enrichment algorithms to detect the disturbed network modules/pathways for a given phenotype that can be used as functional signatures [4]. The positive correlation between functional signatures of different diseases represents their similarity, while the negative correlations between drug responses and disease perturbations are used to find potential drugs [1]. My long term goal is to design, implement and apply a system that is able to manipulate genome-wide networks to model and simulate cellular behavior, and therefore to help decode disease mechanisms and aid drug development

1999-2002             Software Engineer. KANA Software Inc., Natick, MA, USA. Architecture design and implementation of the knowledge database for KANA's enterprise CRM (Customer Relationship Management) system using J2EE (Java 2 Platform, Enterprise Edition) technology. Development of an integration solution to integrate other enterprise CRM system with KANA's knowledge database.

1996-1999             Research Assistant. Department of Mechanical, Industrial and Manufacturing Engineering, Northeastern University, Boston, MA, USA. Three-dimensional reconstruction of human coronary artery based on biplane angiograph and intra-coronary ultrasound images. In vivo research of blood flow in human coronary artery and relationships between local hemodynamic factors and atherogenesis and restenosis. The highly irregular geometry of the segment of coronary artery is represented in curvilinear coordinates and a CFD (computational fluid dynamics) technique is used to investigate the detailed, phasic intravascular velocity profile and shear stress distribution.

1994-1996             Assistant Professor. Institute of Thermal Physics, Chinese Academy of Science, Beijing, China. Fundamental research of heat-transfer augmentation and flow visualization for blade cooling of the turbine machine. Designed and directed the manufacture of three key components of the thermal control system for the Chinese first spacecraft "ShenZhou" that is successfully launched in 1999.

PUBLICATIONS

Reported in News

  1. Software Watch | Annotation Illustration, The Scientists, Volume 17 | Issue 7 | 41 | Apr. 7, 2003
  2. Visualizing genetic interactions | Visualization and analysis platforms are revolutionizing systems biology and disease research, BioTechniques, Volume 67 | No. 6 | Dec. 10, 2009

Peer-reviewed Journal Articles

  1. Hu, Z.* Y. Chang, Wang, Y, Huang, C., Liu,Y., Tian, F., Granger, B. & DeLisi, C. (2013).   VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.  Nucleic Acids Res. vol. 41 (Web Server issue), pp. W225-31 PDF
  2. Shigemizu, D., Hu, Z., Hung, J., Huang, C Delisi, C. (2012).  Using Dynamic Gene Signature Sets to Identify Repositioned Drugs for Breast, Leukemia and Prostate Cancer. PLoS Computational Biology, vol. 8, p. e1002347
  3. Hung, J. H., Yang, T. H., Hu, Z., Weng, Z., DeLisi, C.. Gene set enrichment analysis: performance evaluation and usage guidelines. Brief Bioinform, 2012. 13(3): p. 281-91. PDF
  4. Roberts, R. J., Chang, Y. C. Hu, Z., et al. (2011).  COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res, vol. 39, pp. D11-4, Jan 2011.
  5. Demir, E., et al. (2010). The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28(9): p. 935-42.
  6. Hung, J.H., Whitfield, T.W., Yang, T.H., Hu, Z., Weng, Z. and DeLisi, C. (2009). Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biology, 11, R23. PDF
  7. Linghu, B. Snitkin, E. S. Hu, Z. Xia, Y. & DeLisi, C. (2009).  Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biology, vol. 10, pp. R91
  8. Hu, Z. Hung, J. Wang, Y. Chang, Y. Huang, C. Huyck, M. & DeLisi, C. (2009).  VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res. 37(Web Server issue): p. W115-W121. PDF
  9. Hu, Z. Mellor, Snitkin, S. E.,  & DeLisi, C. (2008).  VisANT: an integrative framework for networks in systems biology,. Briefings in Bioinformatics, 2008;9:317-325. PDF
  10. Hu, Z. Mellor, J. Wu, J. Kanehisa, M. Stuart, J. & DeLisi, C. (2007). Toward Scalable Multidimensional Maps of the Cell. Nature Biotechnology, 25(5): p. 547-54. PDF, Highlighted as a Special Section in the corresponding issue of NBT
  11. Hu, Z. Ng, D. Yamada, T. Chen, C. Kawashima, S. Mellor, J. Linghu, B. Kanehisa, M. & DeLisi, C. (2007).   VisANT 3.0: New Modules for Pathway Visualization, Editing, Prediction and Construction. Nucleic Acids Res. 33(Web Server issue): p. W625-32. PDF
  12. Lamesch, P. Li, N. Milstein, S. Fan. C. Hao, T. Szabo, G. Hu, Z. Venkatesan, K. Bethel G, Vidal M.  (2007). h0RFeome v3.1: A resource of human open reading frames representing over 10,000 human genes. GENOMICS. 89(3): p. 307-315.
  13. Wu, J., Hu, Z. and C. DeLisi, Gene annotation and network inference by phylogenetic profiling. BMC Bioinformatics, 2006. 7: p. 80
  14. Hu, Z. Mellor, J. Wu, J. Yamada, T., Holloway, D. & DeLisi, C. (2005).  VisANT: Data-Integrating Visual Framework for Biological Networks and Modules. Nucleic Acids Res. 33(Web Server issue): p. W352-7. PDF
  15. Niu T*, Hu Z*. (2005) Dynamic Visual Data Mining: Biological Sequence Analysis and Annotation Using SeqVISTA. International Journal of Bioinformatics Research and Application. Vol. 1, No.1  pp. 18 - 30
  16. Hu, Z. Fu, Y. Halees, A. S. Kielbasa, S. M. & Weng, Z. (2004).  SeqVISTA: a New Module of Integrated Computational Tools for Studying Transcriptional Regulation, Nucleic Acids Res, 32(suppl_2): p. W235-241.
  17. Niu T, Hu Z. (2004) SNPicker: A Graphical Tool for Primer Picking in Designing Mutagenic Endonuclease Restriction Assays, Bioinformatics. Vol. 20, No. 17, pp. 3263-3265.
  18. Hu Z, Joseph M, Wu J, DeLisi C, (2004). VisANT: an online visualization and analysis tool for biological interaction data, BMC Bioinformatics, 2004, 5:17. PDF
  19. Hu Z, Frith M, Niu T, Weng Z, (2003). SeqVISTA: a graphical tool for sequence feature visualization and comparison, BMC Bioinformatics, 4(1): 1
  20. Feldman CL, Ilegbusi OJ, Hu Z, Nesto R, Waxman S, Stone PH. (2002). Determination of in Vivo Velocity and Endothelial Shear Stress Patterns with Phasic Flow in Human Coronary Arteries:  A Methodology to Predict Progression of Coronary Atherosclerosis. American Heart Journal. Vol. 143, No. 6, pp. 931-939.
  21. Ilegbusi OJ, Hu Z, Nesto R, Waxman S, Cyganski D, Kilian J, Stone PH, Feldman CL. (1999).  Determination of Blood Flow and Endothelial Shear Stress in Human Coronary Artery in Vivo. The Journal of Invasive Cardiology, Vol. 11, No. 11.
  22. Hu Z., and Shen J. (1996). Heat Transfer Enhancement in A Converging Passage with Discrete Ribs, Int. J. of Heat&Mass Transfer, Vol. 39, No 8, pp. 1719-1727.
  23. Hu Z., and Shen J., Heat Transfer Enhancement and Flow Characteristics of A Surface with Discrete Ribs. Journal of Engineering Thermophysics (in Chinese), Vol.16, No.3, Aug. 1995.

Book Chapters

  1. Hu Z. (2010). Advanced Visualization, Analysis, and Inference of Biological Networks Using VisANT, In Cancer Systems Biology. Edited by Edwin Wang. CRC Press.
  2. Hu Z, Joseph M, DeLisi C (2004). Analyzing Networks with VisANT, In Current Protocols in Bioinformatics. Edited by Andreas Baxevanis, Daniel Davision, Roderic Page, Gregory Petsko, Lincon Stein and Gary Stormo. John Wiley & Sons, Inc.

Conference Presentations

  1. Zhenjun Hu, Technology Track at ISMB 2010 (Boston, MA): TT37, VisANT: multi-scale network visualization, analysis and inference based on the Gene Ontology, July 13, 2010
  2. Zhenjun Hu, Technology Track at ISMB 2008 (Toronto, Canada): TT08, VisANT: an integrative platform for multiple-scale visualization and modeling of biological networks/pathways, July 20, 2008
  3. Zhenjun Hu, Presentation at 9th BioPathways Meeting Satellite of ISMB 2008, "Metagraph: a new graph structure for multiple-scale visualization and modeling of biological networks/pathways", July 19, 2008
  4. Zhenjun Hu, et. al., Presentation at BioPathways Meeting Satellite of ISMB 2005 (Detroit, MI), "VisANT: Integrative Visual Analysis Tool for Biological Networks, Pathways and Modules  ", June 28, 2005
  5. Charles L. Feldman, Sergio Waxman, Olusegun J. Ilegbusi, Zhenjun Hu, David Cyganski, James Kilian, Richard W. Nesto, Peter H. Stone, "Determination of Flow Field Patterns and Shear Stress on Endothelium in Human Coronary Arteries in vivo," American Heart Association Meeting on Vascular and Myocardial Aspects of Ischemic Heart Disease. February 22-25, 1998. Hyatt Regency lake Tahoe Resort and Casino, Incline Village, Nevada.
  6. Hu, Z., and Shen, J. Secondary Flow and It's Contribution to Heat Transfer Enhancement in a Blade Cooling Passage with Discrete Ribs, Proceedings, International Gas Turbine and Aeroengine Congress & Exhibition Birmingham, UK, June 10-13, 1996, 96-GT-313.
  7. Jiarui Shen and Zhenjun Hu, 1996. Heat Transfer Enhancement in A Turbine Blade Cooling Passage with Discrete Ribs. The 9th Symposium on Transport Phenomena in Thermal-Fluids Eng.

Invited Lectures

  1. Zhenjun Hu, "Hierarchical Visualization and Modeling of Biological Networks/Pathways", Dec. 3, 2010. Pennsylvania State University
  2. Zhenjun Hu and Charles DeLisi, "Towards The Systematic Understanding Of Disease Genomics", Sept. 22, 2010. TianTan Hospital, Capital Medical University, China
  3. Zhenjun Hu, "Visualization and Modeling of Biological Networks/Pathways", June. 23, 2010. Zhejiang University, China.
  4. Zhenjun Hu, Lecture at Fall 2008 Talk Series on Networks and Complex Systems, "Multiple-Scale Visualization and Modeling of Biological Networks/Pathways", Oct. 06, 2008. Indiana University.
  5. Zhenjun Hu, lecture at Canadian Bioinformatics Workshops in Toronto University, "Databases and multi-scale visualization", June 28, 2008

SOFTWARE DEVELOPMENT

  1. VisANT: An integrative platform for visual analysis of biological networks (http://visant.bu.edu).
  2. COMBREX: Computational Bridge to Experiments (http://combrex.bu.edu/, in charge of the architecture design)
  3. SeqVISTA: An integrative platform for visual data mining of biological sequences (http://zlab.bu.edu/SeqVISTA).
  4. ScatterPlot: Scatter Plot for gene expression analysis (http://zlab.bu.edu/HugeSearch/nph-HugeSearch.cgi)

 

HONORS AND PROFESSIONAL SERVICES

Ongoing Research Support

R01 GM103502-05            C DeLisi, Z Hu, D. Segre (Multi-PI)   08/01/2011-07/31/2016

VisANT-Predictome: A System for Integration, Mining Visualization and Analysis, PI, C DeLisi, Z Hu, D. Segre,.NIH Overall supervision of the development and application of a widely used tool for mining, discovering and visualizing regulatory and other networks.

Role: PI

Completed Research Support

R01 RR02297-01A1                   C DeLisi (PI)                       08/01/2007-07/31/2010

VisANT-Predictome: A System for Integration, Mining Visualization and Analysis, PI, C DeLisi,  NIH Overall supervision of the development and application of a widely used tool for mining, discovering and visualizing regulatory and other networks

Role: Investigator

R21 CA135882-01             C DeLisi (PI)                       08/01/2008-07/31/2010

New Methods for Cancer Class Discovery And Prediction: Integration and Visualization. This project explores new computational methods for integrating, analyzing and visualizing the rapidly growing genomic and epigenetic information in The Cancer Genome Atlas (TCGA). The long term objective is to develop methods that will be widely disseminated and used to discover reliable biomarkers for cancer development and progression, and to gain a deeper understanding of the key alterations that occur during transformation.

Role: Investigator  

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   Reviewer for:

Nature Biotechnology, Bioinformatics, Nucleic Acids Research, BMC Bioinformatics, The BioTechniques, The Source Code for Biology and Medicine, Computer Methods and Programs in Biomedicine, Briefings in Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics

  • 2011- Editorial Board of ISRN Bioinformatics                                                          
  • 1996  Research Assistantship from Northeastern University, Boston, USA
  • 1994 Award in Science and Technology Competition in Institute of Thermalphysics Engineering, Chinese Academy of Science, Beijing, China
  • 1992 Research Assistantship from Institute of Thermalphysics Engineering, Chinese Academy of Science, Beijing, China

 

REFERENCES

References will be provided upon request