Selected Publications (A Full List >>>)

Jian Peng and Jinbo Xu. A multiple-template approach to protein threading. PROTEINS, 2011. In Press.

Jian Peng and Jinbo Xu. Boosting Protein Threading Accuracy. RECOMB 2009. (A poster on this paper won the best poster award in RECOMB 2009.)

Feng Zhao, ShuaiCheng Li, Beckett W. Sterner and Jinbo Xu. Discriminative Learning for Protein Conformation Sampling. PROTEINS: Structure, Function and Bioinformatics, 2008.

Rohit Singh, Jinbo Xu and Bonnie Berger. Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood, RECOMB 2007.

Jinbo Xu, Feng Jiao and Bonnie Berger. A Parameterized Algorithm for Protein Structure Alignment. RECOMB 2006.

Rohit Singh, Jinbo Xu and Bonnie Berger. Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. PSB 2006. (The first two authors contribute equally to the paper.)

Jinbo Xu. Rapid Protein Side-Chain Packing via Tree Decomposition. RECOMB 2005. A software package TreePack is developed based upon this paper. (A full version of this paper appeared at the Journal of the ACM.)

Jinbo Xu, Daniel Brown, Ming Li and Bin Ma. Optimizing Multiple Spaced Seeds for Homology Search. Journal of Computational Biology, 2005.

Jinbo Xu and Ming Li. Assessment of RAPTOR's Linear Programming Approach in CAFASP3, CASP5 (Fifth Critical Assessment of Structure Prediction) special issue, Proteins: Structure, Function and Genetics. Oct, 2003. (invited paper, the only one voted by all the CASP5/CAFASP3 attendees according to novelty and performance.)

Jinbo Xu, Ying Xu, Dongsup Kim and Ming Li. RAPTOR: Optimal Protein Threading by Linear Programming, the inaugural issue, Journal of Bioinformatics and Computational Biology, April 2003. A software package RAPTOR has been developed based on the method proposed in this paper. RAPTOR ranks first among all non-meta servers in CAFASP3 (Third Critical Assessment of Fully Automated Structure Prediction). RAPTOR also ranks third among all non-meta servers in CASP6 according to http://www.bioinformatics.buffalo.edu/casp6/. RAPTOR has been commercialized to BioinformaticsSolutions Inc., Waterloo, Canada and has been licensed to some pharmaceutical companies such as Merck.