Selected Publications (A Full List >>>)
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. [pdf]
Rohit Singh, Jinbo Xu and Bonnie Berger. Struct2Net: Integrating Structure into
Protein-Protein Interaction Prediction. PSB 2006. URL:
http://theory.lcs.mit.edu/struct2net/
(The first two authors contribute equally to the paper.)
Jinbo Xu. Rapid Protein Side-Chain Packing via
Tree Decomposition. RECOMB 2005. [ps][pdf] A software package based
on this approach can be downloaded at TreePack.
A full
version of this paper appeared at the Journal of the ACM.
Jinbo Xu. Protein Fold Recognition by Predicted
Alignment Accuracy. IEEE/ACM Trans. on Computational Biology and
Bioinformatics, 2005. [ps][pdf]
Jinbo Xu,
Daniel Brown, Ming Li and Bin Ma. Optimizing Multiple Spaced
Seeds for Homology Search. Journal of Computational Biology, 2005.[ps][pdf]
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. (an
invited paper, the only one voted by all the CASP5/CAFASP3 attendees according
to novelty and performance.) [ps][pdf]
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.[ps] [pdf] 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.,