EDUCATION |
DUKE UNIVERSITY (Durham, NC), Dec. 2007 |
| Ph.D. in Computational Biology & Bioinformatics (Dept. of Statistical Science) |
| Advisor: Mike West, Department of Statistical Science & Institute for Genome Sciences & Policy |
Co-Advisor: Jen-Tsan Ashley Chi, Department of Molecular Genetics and Microbiology &
Institute of Genome Sciences & Policy |
| Dissertation: Bayesian Analysis in Cancer Pathway Studies and Probabilistic Pathway Annotation |
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BEIJING INSTITUTE OF TECHNOLOGY (Beijing, China), Sep. 2000
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Ph.D. in Information and Signal Processing (Advisor: Youan Ke)
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Dissertation: Fast Volume Rendering Based on Feature-Cells Extraction for Medical Volumetric Data |
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BEIJING INSTITUTE OF TECHNOLOGY (Beijing, China), Jul. 1995
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B.S. in Electronics Engineering
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RESEARCH & WORK EXPERIENCE |
DUKE UNIVERSITY (Durham, NC), Aug. 2003–present |
Graduate Student, Program in Computational Biology & Bioinformatics |
Bayesian Statistical Modeling and Computational Methods in Cancer Biology and Clinical Genomics |
· Developed a model-based approach to the problem of biological pathway annotation in genome-wide gene expression profiles; provided solution by using Markov chain Monte Carlo (MCMC) and variational methods; applied the approach to identify pathway activities associated with cancer micro-environments |
Generalized Linear Models in Clinical Genomics and Biology |
· Implemented regularized kernel logistic regression and Bayesian sparse logistic regression based on MCMC methods for classification and feature selection in lung cancer gene expression profiles
· Studied and implemented non-ordered categorical generalized linear model and MCMC methods for ant activity and invasion status analysis |
Bayesian Computational Methods in Structure Biology |
· Developed empirical Bayesian approaches to protein secondary structure prediction based on Hidden Markov Models |
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NATIONAL UNIVERSITY OF SINGAPORE (Singapore), Aug. 2000–May. 2002 |
Research Fellow, Bioinformatics Center - Center for Natural Product Research |
Natural Sample Mass Spectrum Data Processing and Analysis for Drug Discovery |
· Developed the algorithms for LCMS data purification, visualization, composition analysis and identification of replicated natural products and biologically active compounds |
· Developed the software package MassSpec Data Proc; integrated it with natural sample database for bioassay-guided compound isolation |
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BEIJING INSTITUTE OF TECHNOLOGY (Beijing, China), Sep. 1995–Sep. 2000 |
Graduate Student, Department of Electronics Engineering |
3D Reconstruction and Visualization for Slicing Medical Images |
· Developed algorithms based on 3D-wavelet analysis for volume image feature-cell extraction to accelerate volume rendering visualization of slicing medical images |
TEACHING EXPERIENCE |
DUKE UNIVERSITY (Durham, NC), Jan. 2007–May 2007 |
| Teaching assistant, Program in Computational Biology & Bioinformatics |
| Statistical Methods for Computational Biology |
BEIJING INSTITUTE OF TECHNOLOGY (Beijing, China), Mar. 1998–May 1998 |
| Teaching assistant, Program in Computational Biology & Bioinformatics |
Internal Information Exchange in Computer systems |
HONORS & AWARDS |
· Radar Technology Advancement scholarships, Beijing Institute of Technology, 1994, 1995 |
| · People scholarships for Academic distinction, Beijing Institute of Technology, 1992, 1993, 1994, 1995 |
| · Honors Graduate, Beijing 1995 |
PH.D. COURSEWORK |
Probability and Statistical Models | Statistical Learning: Algorithm and Theory | Generalized Linear Models | Statistical Methods for Computational Biology | Algorithms in Computational Biology | Gene Expression Analysis: Computational Functional Genomics | Genome Informatics and Sequence Analysis | Genome Tools and Technology | Computational Structure Biology | Functional Analysis | Linear Algebra and Matrix Analysis | Statistical Signal Processing | Signal Theory and Application | Computer Structure and System Analysis | Bayesian Experimental Design |
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SKILLS |
Bioinformatics: - Data mining from multiple resources
- Good data visualization skills
- Familiar with Affymetrix GeneChip arrays and annotation/analysis tools
- Familiar with bioinformatics resources, such as National Center for Bioinformatics
(NCBI) databases, Ensambl, UCSC genome browsers, and related analysis tools.
- Experience in sequence alignment and gene expression clustering tools |
Computation:
MATLAB, C/C++, Perl, R/S, VB;
Markov chain Monte Carlo methods;
Software development |
| Languages: English, Chinese |
| ARTICLES IN PREPARATION |
[1] |
H. Shen, J. Lucas, L. Chen, J. Chi and M. West (2007). Bayesian modelling for pathway annotation using genomic signatures. Statistical Science Discussion Paper, Department of Statistical Science, Duke University, in prep. |
[2] |
H. Shen and M. West (2007). Probabilistic pathway annotation analysis: a Bayesian approach to cancer signaling pathway exploration. Statistical Science Discussion Paper, Department of Statistical Science, Duke University, in prep. |
[3] |
H. Shen, C. Ji and M. West (2007). Monte Carlo variational methods for marginal likelihood approximation. Statistical Science Discussion Paper, Department of Statistical Science, Duke University, in prep. |
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| PROFESSIONAL PRESENTATIONS |
| [1] |
Dissection of Lactic Acidosis Response Complexity in Human Breast Cancers Using Genomic
Signatures. Meeting of the National Cancers of Integrative and Systems Biology, 13-14 Nov.
2007, Washington DC, USA |
[2] |
Bayesian gene set enrichment analysis of genome-wide expression profiles. Joint Statistical
Meeting, 29 Jul.-2 Aug. 2007, Salt Lake City, UT, USA |
[3] |
Probabilistic Pathway Annotation Analysis. Meeting of the National Cancers of Integrative and
Systems Biology, 12-14 Jun. 2007, Cambridge, MA, USA |
[4] |
Bio-Instrument Signal Processing: A Prospective GRID-Based Application to Enhance Drug Discovery. BioGRID’01 Symposium, 26 Oct. 2001, National University of Singapore. (Slides) |
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