My research interest
lies in Computational Biology and Bioinformatics. I am now working on the
following topics: protein structure alignment, protein structure prediction,
protein side-chain packing, protein-protein interaction prediction, DNA/protein
sequence search and biological network analysis.
Recent
Highlights
1. A poster on our paper
entitled Boosting Protein Threading
Accuracy won the Best Poster Award in RECOMB 2009 held in Tucson, Arizona
(May 17-21, 2009). RECOMB is one of the best conferences in the field of
Computational Biology and Bioinformatics.
2. The
following poster won the Best Poster Award in
CASP8 conference held in
J. DeBartolo, G. Hockey, F. Zhao, J. Peng,
A. Augustyn, A. Adhikar, J.
Xu, K. F. Freed and T. R. Sosnick.
Structure
prediction combining the template-based RAPTOR algorithm with the ItFix ab initio method.
3. My protein structure
prediction program RAPTOR ranked No.2-No.4 among
all automated programs in CASP8, according to several assessments (Grishin, McGuffin, Zhang) and the
CASP8 official ranking. The abstract
about RAPTOR in CASP8 is available at RAPTOR-CASP8.doc.
Please note that RAPTOR in CASP8 is very different from previous RAPTORs and there is only one RAPTOR participating in
CASP8. Here I give a list of people who contributed to RAPTOR in CASP8.
1) Jinbo Xu and his
students Jian Peng and Feng Zhao at TTI-Chicago: major contributors
2) Tobin Sosnick, Karl
Freed and Joe DeBartolo at U Chicago: the energy
function in the ab initio folding module
3) Beckett W. Sterner and Shuaicheng
Li: two summer intern students involved in the very early stage of the ab initio folding module
4) Libo Yu: template database
generation
5) Brendan McConkey:
template database generation and one threading energy function
6) Xin Gao:
RAPTOR web server setup and running RAPTOR in the very early stage of CASP8
7) Ming Li: providing some computing resources
This new version RAPTOR
does not do any fragment assembly at all. We are working on a totally new web
server to provide free protein modeling service. The binary code of some
modules in the new version RAPTOR will also be available for download
gradually.
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,
accepted by RECOMB 2007.
Jinbo Xu, Feng Jiao and Bonnie Berger. A
Parameterized Algorithm for Protein Structure Alignment. Accepted,
RECOMB 2006. [pdf]
Rohit Singh, Jinbo Xu and Bonnie Berger. Struct2Net: Integrating Structure into
Protein-Protein Interaction Prediction. Accepted, 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 SCATD. 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. Accepted.[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.,
Protein threading by nonlinearly combining
evolutionary and non-evolutionary information. The
Protein threading by
nonlinearly combining evolutionary and non-evolutionary information. MIT, March 2009.
Computer Algorithms for
Structural Bioinformatics. INFORMS Annual Meeting,
October 2008.
Computer Algorithms for
Structural Bioinformatics.
Global Alignment of
Multiple Protein Interaction Networks. UIC, April 2008.
Protein Conformation
Sampling Using Conditional Random Fields. MIT, Feb 2008.
Knowledge-Based Protein
Structure Prediction. TTI-Japan, April 2007.
Knowledge-Based Protein
Structure Prediction. Inst of Comp Tech, Chinese
Knowledge-Based Protein
Structure Prediction.
A Parameterized
Algorithm for Protein Structure Alignment.
A Parameterized
Algorithm for Protein Structure Alignment. MIT, May 2006.
Protein Structure
Prediction.
Northwestern University, May 2006.
A Parameterized
Algorithm for Protein Structure Alignment. UIC, November 2005.
Protein Side-Chain
Packing.
Fast and Accurate
Protein Side-Chain Prediction. DIMACS Workshop on Information Processing by
Protein Structures in Molecular Recognition, DIMACS Center, CoRE
Building, Rutgers University, June 13-14, 2005.
RAPTOR: protein threading by linear programming.
ACE: consensus method to fold recognition.
CASP6,
Protein Structure
Prediction by Linear Programming.
Protein Structure
Prediction.
ICTS,