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PUBLICATIONS
Refereed Journal Papers
Wu,
D.,
Yuan, Y., and Wu,
Z., Generating Rigid Protein Structures with Sparse Sets of
Inter-Atomic and Inter-Residual Distances, Optimization Letters
(accepted), 2007.
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, Jan; 35: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.
Wu,
D.,
Smith, S., Mahan,
H., Jernigan, R., and Wu, Z., The Study of Protein Dynamics of NMR
ensembles through Local DME, submitted and under revision, 2007.
Sun, X., Wu, D., Jernigan, R., and
Wu, Zj.,
PRTAD: A Database for Protein Residue Torsion Angle Distributions,
submitted and under revision,
2007.
Submitted Journal Papers or Manuscripts
Wu,
D., and Wu, Z., A
Fast Linear Programming Method in Metabolic Pathways, preprint, 2007.
Mahan, H., Smith, S., Roh,
K., Wu, D., and Wu, Z., An Optimization Algorithm for Multiple
Structure Alignment, preprint, 2007.
Wu,
D.,
et al, A Novel
Protein Structural Alignment Method using GNM, preprint, 2007.
Refereed
Conference Journal Papers
Narasimhan,
V.L., Wu,
D., Meta-Analysis of Clinical Cardiovascular Data towards
Evidential Reasoning for Cardiovascular Life Cycle Management, accepted
by Informing Science and Information Technology Education Joint
Conference, Ljubljana, Slovenia, June 22-25, 2007.
Others
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.
CONFERENCES
AND POSTERS
Presentations
2007
Protein Structure Modeling and Refinement (Invited). Mini-Symposium on on Mathematics of Proteomics, Protein Structures and Dynamics, 2008 Annual Meeting of The Society of Mathematical Biology, University of Toronto, Ontario, Canada, July 30 - August 2, 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
2006
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.
Before
What can we get from Local DME?
SIAM
Conference on the Life Sciences,
Portland
,
Oregon
,
July 11-14, 2004.
Posters
2007
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.
2006
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.
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