Assistant Professor

Di Wu, Ph.D.,

**** ***** **** *** **, Bowling Green, KY 42103

Email: ****.***@*****.***; Mobile: 270-***-****

Pursuing a R&D position in biotechnology or pharmaceutical industries

EDUCATION

•Iowa State University, Ames, Iowa

Co-major Ph.D., Bioinformatics and Computational Biology, 2006; Applied Mathematics, 2006

•Fudan University, Shanghai, China

B.S., Microbiology, 2000

RESEARCH INTERESTS

•Bioinformatics and Medical Informatics

•Computational Structural Biology

•Protein-protein interaction and Rational Drug Design

•System Biology

•Operations Research, Constrained and Unconstrained Optimization

•Actuarial Science and Financial Engineering

PROFESSIONAL EXPERIENCES

2006- Assistant Professor (Tenure-track), Department of Mathematics, Bioinformatics and Information Sciences Center, Western Kentucky University

2009 July-Aug Visiting Scholar, Hefei University of Technology(Hefei, China), Centralsouth University(Changsha, China) and Fudan University(Shanghai China)

2001-06 Ph.D. Candidate, Program on Bioinformatics and Computational Biology, Department of Mathematics, Iowa State University

1998-00 Research Assistant, State Key Lab of Genetics and Genetic Engineering, Institute of Genetics, Fudan University

FUNDING

•PI, “Mathematical and Computational Methods in Protein Structure Determination and Refinement”, NIH KBRIN AREA, Kentucky Biomedical Research Infrastructure Network, May 2009-April 2010, Amount $16,336, granted.

•PI, “Computational Methods in Protein Structural Modeling and Refinement”, Junior Faculty Fellowship, Office of Sponsored Program, Western Kentucky University, 2009-2010, Amount $4,000, granted.

•PI, “GNM Weighted Superimpositions for Identification of Protein Motions and Domains”, NSF KY EPSCOR REG, Sept 2008-Aug 2009, Amount $12,500, granted.

•PI, “A Novel Method for Protein Structural Refinement using Coarse-Grained Models over High Performance Computing”, NIH KBRIN AREA, Kentucky Biomedical Research Infrastructure Network, May 2007-April 2009, Amount $27,000, granted.

•PI, “Refinement of NMR Protein Structures with Angle-based Statistical Potentials”, Summer Faculty Fellowship, Office of Sponsored Program, Western Kentucky University, summer 2008, Amount $6,000, granted.

•Co-PI, “Meta-Analysis of Clinical Cardiovascular Data towards Evidential Reasoning for Disease Management”, Proposal Incentive Fund (PIF), Office of Sponsored Program, Western Kentucky University, Feb 2007-Feb 2008, Amount $22,600, granted.

•Co-PI, “Kentucky EPSCoR Intensive Workshop on High Performance Computing for Informatics and Bioscience”, Kentucky NSF EPSCoR CRIG, March 2007-June 2008, Amount $10,000, granted.

PUBLICATIONS

Refereed Papers (Accepted or Published)

•Davis, R., Ernst, C., Wu.D.*, Protein Structure Determination via an Efficient Geometric Build-up Algorithm to appear in BMC Structural Biology, 2010

•Wu,D.*, Wu,Z., Superimposition of Protein Structures with Dynamically Weighted RMSD, Journal of Molecular Modeling, 2010, 16:211-222.

•Davis, R., Ernst, C., Wu.D.*, An Efficient Geometric Build-up Algorithm for Protein Structure Determination with Sparse Exact Distance Data, forthcoming in the Proceedings of IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBM) 2009, Volume , Issue , 1-4 Nov. 2009 Page(s):173 – 178.

•Ravindrudu, R., Wu, D., Guaratne, A., Feng Y., Wu, Z., Integrated Software Environment for Protein Structure Refinement, In the Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine 2008, Volume , Issue , 2-4 Nov. 2008 Page(s): 25-32

•Wu, D., Yuan, Y., and Wu, Z., Rigid versus unique determination of protein structures with geometric buildup, Optimization Letters (2008) 2:319–331

•Wu, D., Yuan, Y., and Wu, Z., The Solution of the Distance Geometry Problem for Protein Modeling via Geometric Buildup, Biophysical Reviews and Letters Vol: 3 Issue: 1/2 (April 2008) Page: 43 - 75

•Wu, D., Jernigan, R., and Wu, Z., Refinement of NMR-Determined Protein Structures with Database Derived Mean Force Potentials, Proteins: Structures, Functions and Bioinformatics, V68, 1:232-242, 2007.

•Wu, D., Cui, F., Jernigan, R., and Wu, Z., PIDD: Database for Protein Inter-atomic Distance Distributions, Nucleic Aids Research, V35:D202-7, 2007.

•Wu, D., and Wu, Z. An Updated Geometric Build-Up Algorithm for Solving the Molecular Distance Geometry Problem with Sparse Distance Data. Journal of Global Optimization, V37, 4:661-673, 2007.

•Xiaoyong Sun, Wu, D., Jernigan, R., and Wu, Zj., PRTAD: A Database for Protein Residue Torsion Angle Distributions. In the Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine 2007, Volume , Issue , 2-4 Nov. 2007 Page(s):24 – 31

•Narasimhan, V.L., Wu, D., Meta-Analysis of Clinical Cardiovascular Data towards Evidential Reasoning for Cardiovascular Life Cycle Management, Journal of Issues in Informing Science and Information Technology (IISIT), V4: 651-659, 2007.

•Chen, R., Jin Z., Wu, D., Tang, R., and Mao, Y. Repeated Reverse Transcription Reaction (RRTR) Protocol and Its Application. Progress in Biochemistry and Biophysics. 28-4, 560-562, 2001.

•Chen, R., Wu, D., Tang, R., Wang, J. and Mao, Y. Detection of HCV RNA by Circulatory Reverse Transcription-PCR. Chinese Journal of Virology, 2000, 3:79-82.

•Wu, D., Xue, M., Ren, D., Research Progress and Prospect of HCV. Chinese Journal of Biology, 16-6: 8-9, 1999.

*: Correspondence Author

Book Chapter

•Rakesh, L., Wu, D., Fundamentals of Computational and Mathematical Methods in Modeling of Bio-molecule and Nanomedicine, Nanomedicine: Nanomaterials, Nanotechnology & Interfaces with Perspective on Therapeutic and Diagnostic Applications (in preparation).

•Wu, D., Yuan, Y., and Wu, Z., The Solution of the Distance Geometry Problem for Protein Modeling via Geometric Buildup, BIOMAT 2007 –Proceedings of International Symposium on Mathematical and Computational Biology, Rubem Mondaini, ed., 2007.

PROFESSIONAL ACTIVITIES

Journal Referee/Editorial Board (in alphabetical order) (review regularly)

Advances and Applications in Bioinformatics and Chemistry; Bioinformatics and Biology Insights (on Editorial Board); Computational Optimization and Applications; International Journal of Computational Biosciences; International Journal of Biomedical Imaging; Neurocomputing; Online Journal of Bioinformatics (on Scientific Board); Open Access Bioinformatics; Physics Letters A; Protein Science; Journal of Biochemical Technology (on Authors Advisory Board); Journal of Global Optimization, Journal of Molecular Modeling; Proceedings of IEEE International Conference on Bioinformatics and Biomedicine, Proceedings of the 5th Int'l Conference on Bio-Inspired Models of Network, Information and Computing Systems, Theoretical Biology and Medical Modeling; Theoretical Biology Insights (on Editorial Board)

Services of Conference/Workshop/Editorship

•Program Committee of Special Track on Bioinformatics of the 5th Int'l Conference on Bio-Inspired Models of Network, Information and Computing Systems, Boston, December, 2010

•Guest Editor of Special issue in Bio-molecular Structure Determination and Refinement for International Journal of Computational Biosciences, 2009 (select five research papers for publication)

•Co-Editor of Special issue in Computational Structural Bioinformatics for BMC Structural Biology, 2009 (select seven research papers for publication)

•Co-Editor of Proceedings of IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBM) 2009, 2009

•Co-Organizer of 29th Annual Mathematics Symposium at Western Kentucky University, Bowling Green, KY, Nov 5-6, 2009

•Chair of Computational Structural Biology Workshop, IEEE International Conference on Bioinformatics & Biomedicine, sponsored by IEEE, Washington D.C., Nov 1-4, 2009, sponsored by IEEE and NSF (managing review process for 33 research papers)

•Co-Chair, Intensive International Workshop on High Performance Computing for Informatics and Biosciences, IIWHPC2007, sponsored by NSF KY EPSCoR, Bowling Green, Kentucky, Oct 5-7, 2007.

Summer Programs

•Supervisor in Mathematics, Summer Program for Verbally and Mathematically Precocious Youth, Bowling Green, Kentucky, June 28 – July 18, 2009, June 23- July 11, 2008 & June 24- July 14, 2007.

PROFESSIONAL DEVELOPMENT

SAS Certificate in Data Mining for Educators

SAS Programming Essentials I for Educators

Applied Analytics Using SAS Enterprise Miner 5

SAS Programming Essentials II for Educators

Customer Segmentation with Numeric and Textual Data using SAS

Issues in Linear Model Building and Data Mining

(Please request the document if needed)

Actuarial Science (Passed Exams of Society of Actuary)

Exam P Probability

Exam FM Financial Mathematics

Exam MFE Exam M Financial Economics

(Plan to get ASA -Associate of Society of Actuary)

(The transcript is available, please request the document if needed)

PUBLISHED CONFERENCE AND POSTER ABSTACTS

Presentations

•A Novel Computational Method in Protein Structure Determination and Refinement, 2010 Annual Kentucky MAA, University of Kentucky, Lexington, Kentucky, March 26-27, 2010

•An Efficient Geometric Build-up Algorithm for Molecular Distance Geometry Problem with Sparse Distance Data, the IEEE International Conference on Bioinformatics and Biomedicine 2009, Washington D.C., November 1-4, 2009

•Colloquium Talk, School of Chemical Engineering and School of Mathematics, CentralSouth University, Changsha, China, Aug 2009.

•Colloquium Talk, School of Computer Science and Informatics Sciences, Hefei University of Technology, Hefei, China, July 2009.

•Colloquium Talk, Department of Computer Science, New Mexico State University, June 2009.

•Second Derivatives in the Study of Protein Fluctuations, 2009 Annual Kentucky MAA, Kentucky State University, Frankfort, Kentucky, March 27-28, 2009

•Colloquium Talk, Department of Mathematics, Central Michigan University, Nov 2008

•Integrated Software Environment for Protein Structure Refinement, the IEEE International Conference on Bioinformatics and Biomedicine 2008, Philadelphia, PA, November 3-5, 2008

•Geometric Databases of Protein Structures (Selected Short Presentation), UT-ORNL-KBRIN Bioinformatics Summit 2008, Lake Barkley State Resort Park, Cadiz, KY, March 28-30, 2008.

•NMR Protein Structure Refinement through angle-based potentials (Invited), Special Session on Mathematical Modeling in Biological Systems, Fall 2007 American Mathematical Society Southeastern Meeting, Murfreesboro, Tennessee, November 3 – 4, 2007.

•NMR Protein Structure Refinement with PMF and Superimposition of NMR ensembles through weighted-RMSD (Invited), The Fall 2007 Workshop for Young Researchers in Mathematical Biology (WYRMB), Mathematical Biosciences Institute, Columbus, Ohio, September 11-14, 2007

•Applications of Singular Value Decomposition to Biological Systems, 2007 Annual Kentucky MAA, Northern Kentucky University, Highland Heights, Kentucky, March 30-31, 2007

•Distance Geometry in Protein Structural Modeling, 26th Annual Mathematics Symposium at Western Kentucky University, Bowling Green, Kentucky, November 17-18, 2006

•NMR Protein Structure Refinement with Mean Force Potentials, American Mathematics Society 2006 Fall Central Section Meeting, Cincinnati, Ohio, October 21-22, 2006.

•Distance-based Protein Structure Modeling, job candidate talk, Department of Mathematics, Western Kentucky University, Bowling Green, Kentucky, April 25, 2006.

•A Rigid Geometric Build-up Algorithm for Solving a Distance Geometry Problem, 2006 Iowa Mathematics Meeting, MAA- Iowa Section, Ames, Iowa, April 7-8, 2006.

•What can we get from Local DME? SIAM Conference on the Life Sciences, Portland, Oregon, July 11-14, 2004.

Poster Presentations

•Wu, D., Protein Structure Determination and Refinement via Short and Long Range Potentials, UT-ORNL-KBRIN Bioinformatics Summit 2010, Lake Barkley State Resort Park, Cadiz, KY, March 19-21, 2010.

•Wu, D., An Integrated Software Environment for Protein Structure Refinement, UT-ORNL-KBRIN Bioinformatics Summit 2009, Fall Creek Falls State Park, Pikeville, Tennessee, March 20-22, 2009.

•Davis, R., Ernst, C., and Wu, D., The Molecular Distance Geometry Problem Incorporating Clique Detection, UT-ORNL-KBRIN Bioinformatics Summit 2009, Fall Creek Falls State Park, Pikeville, Tennessee, March 20-22, 2009.

•Quiton, J., and Wu, D., Computing infrastructure initiative and methods in biological modeling, survival analysis and statistical data mining, 14th Annual Kentucky EPSCOR Conference, Louisville, KY, Oct 3, 2008

•Wu, D., Geometric Databases of Protein Structures, UT-ORNL-KBRIN Bioinformatics Summit 2008, Lake Barkley State Resort Park, Cadiz, KY, March 28-30, 2008.

•Wu, D., Garabato, B., A Novel Method for the Superimposition of Protein Structures through Weighted RMSD, UT-ORNL-KBRIN Bioinformatics Summit 2007, Paris Landing State Park, Buchanan, Tennessee, April 13-15, 2007.

•Wu, D., and Wu, Z., Protein Structure Determination through Geometric Build-up Algorithms, Sixth Annual Joint Bioinformatics Symposium-Systems Biology, Ames, Iowa, July 13-14, 2006.

•Wu, D., Cui, F., Jernigan, R., Wu, Z., NMR-determined Protein Structure Refinement with Database Derived Mean-Force Potentials, Sixth Annual Joint Bioinformatics Symposium-Systems Biology, Ames, Iowa, July 13-14, 2006.

•Wu, D., and Wu, Z., Geometric Build-Up Algorithms for Protein Structure Determination, Wisconsin 32nd Steenbock Symposium on Dynamics of Proteins and Macromolecular Assemblies, Madison, Wisconsin, May 18-21, 2006.

•Cui, F., Wu, D., Jernigan, R., and Wu, Z., Refinement of Protein Structures with Database-Derived Distance Constraints and Mean-Force Potentials, Wisconsin 32nd Steenbock Symposium on Dynamics of Proteins and Macromolecular Assemblies, Madison, Wisconsin, May 18-21, 2006.

Workshops

•Summer Program II for Educators Teaching Text Mining , SAS World Headquarters Training Center, Cary NC, July 20-24, 2009

•Summer Program I for Educators Teaching Data Mining, SAS World Headquarters Training Center, Cary NC, July 21-25, 2008

•The IMA Thematic Year on Molecular and Cellular Biology, Workshop: Protein Folding, the Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN, January 14-18, 2008.

•The IMA Thematic Year on Molecular and Cellular Biology, Tutorial: Mathematics of Proteins, the Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN, January 10-11, 2008.

•Intensive International Workshop on High Performance Computing for Informatics and Biosciences, Bowling Green, Kentucky, Oct 5 - 6, 2007.

•The IMA Summer Program on Classical and Quantum Approaches in Molecular Modeling, the Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, MN, July 23-Aug 3, 2007.

REFERENCES

Available upon request

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