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Recent Publications
- Ying Xu, Dong Xu, Dongsup Kim, Victor Olman, Jane Razumovskaya, and Tao Jiang
Automated Assignment of Backbone NMR Peaks Using Constrained Bipartite Matching.
Computing in Science and Engineering.
In press.
- Ying Xu, Victor Olman, and Dong Xu.
Clustering Gene Expression Data Using a Graph-Theoretic
Approach: An Application of Minimum Spanning Trees.
Bioinformatics.
In press.
- Ying Xu, Victor Olman, and Dong Xu.
Minimum Spanning Trees for Gene Expression
Data Clustering.
In Proceedings of the 12th International Conference
on Genome Informatics (GIW), edited by S. Miyano, R. Shamir and T. Takagi.
Accepted.
- Dong Xu and Ying Xu. Computational Studies of Protein Structure and Function
Using Threading Program PROSPECT. In Protein Structure Prediction:
Bioinformatic Approach, edited by Igor Tsigelny. International University Line
publishers (IUL), La Jolla, CA. Invited publication.
- Ying Xu, Dong Xu, and Victor Olman.
A Practical Method for Interpretation
of Threading Scores: An Application of Neural Network.
Statistica Sinica (special issue in bioinformatics).
Invited publication.
- Dong Xu, Oakley H. Crawford, Philip F. LoCascio, and Ying Xu. Application of PROSPECT in CASP4:
Characterizing Protein Structures with New Folds.Proteins: Structure, Function, and Genetics (CASP4 Special Issue).
Invited publication.
- Ying Xu and Dong Xu.
Protein Structure Prediction
by Protein Threading and Partial Experimental Data.
In: Current topics
in computational biology. In press.
- Dong Xu, Kunnumal Baburaj, Cynthia B. Peterson, and Ying Xu.
A Model for the Three-Dimensional Structure of Vitronectin:
Predictions for the Multi-Domain Protein from Threading and Docking.
Proteins: Structure, Function, and Genetics. 44:312-320. 2001.
- Ying Xu, Dong Xu, and Harold N. Gabow.
Protein Domain Decomposition using a Graph-Theoretic Approach. Bioinformatics.
16:1091-1104. 2000.
- Ying Xu, Dong Xu. Oakley H. Crawford, and J. Ralph Einstein.
"A computational method for NMR-constrained protein threading."
Journal of Computational Biology. 7:449-467. 2000.
- Ying Xu and Dong Xu. Protein threading using PROSPECT:
Design and evaluation.Proteins: Structure, Function, and Genetics.
40:343-354. 2000.
- Dong Xu, Ying Xu, Gary Li, and Jizhong Zhou. A Computer Program
for Generating Gene-Specific Fragments for Microarrays. In Currents
in Computational Molecular Biology, edited by S. Miyano, R. Shamir and
T. Takagi. Universal Academy Press, Inc. Tokyo, Japan. Pages 3-4. 2000.
- Dong Xu, Ying Xu, and Edward C. Uberbacher.
Computational tools for protein modeling.
Current Protein and Peptide Science. 1:1-21. 2000.
- Dong Xu and Ying Xu.
Protein tertiary structure prediction.
In: Current Protocols in Protein Science,
edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield.
John Wiley & Sons, New York.
Volume 1, pages 2.7.1-2.7.17. 2000.
- Dong Xu and Ying Xu.
Protein Databases on the Internet.
In: Current Protocols in Protein Science,
edited by J. E. Coligan, B. M. Dunn, H. L. Ploegh, D. W. Speicher, and P. T. Wingfield.
John Wiley & Sons, New York.
Volume 1, pages 2.6.1-2.6.15. 2000.
- Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, and Engin Serpersu.
Protein structure determination using
protein threading and sparse NMR data.
In: The Fourth Annual International Conference on Computational
Molecular Biology, edited by R.
Shamir, S. Miyano, S. Istrail, P. Pevzner, and M. Waterman. Pages 299-307, ACM, Tokyo, Japan. 2000.
- Ying Xu, Dong Xu, Oakley H. Crawford, J. Ralph Einstein, Frank Larimer,
Edward C. Uberbacher, Michael A. Unseren, and Ge Zhang.
Protein threading by PROSPECT: a prediction experiment in CASP3.
Protein Engineering.
12:899-907, 1999.
- Dong Xu, Michael A. Unseren, Ying Xu, and Edward C. Uberbacher.
Protein fold recognition
at the secondary structure level.
Bioinformatics.
16:257-68, 2000.
- Oakley H. Crawford.
A fast, stochastic threading algorithm for proteins.
Bioinformatics, 15:66-71, 1999.
- Ying Xu, Dong Xu, and Edward C. Uberbacher.
An efficient computational method for globally optimal threading.
Journal of Computational Biology.
5:597-614, 1998.
- Ying Xu, Dong Xu, and Edward C. Uberbacher.
A new method for modeling and solving the protein fold recognition problem.
In: The Second Annual International Conference on Computational
Molecular Biology, (Istrail, S, Pevzner, P, Waterman, M, eds) pp.
285-292. ACM New York.
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