My research
interest lies in computational biology and bioinformatics. In particular, I am
applying machine learning and optimization algorithms to studying molecular
biology, e.g., comparative analysis of various biological data such as protein
sequence/structure, RNA sequence/structure and biological network.
We have
received financial or computational resources support from the following
grants:
1) Jinbo Xu. NSF CAREER award (total cost ~$500k for 5 years, July
2012-June 2017)
2)
Jinbo Xu. NSF DBI-0960390
(total cost ~$408k for 3 years, July 2010-June 2013)
3) Jinbo
Xu. NIH R01GM089753. (total cost ~$1.35M for 5 years,
May 2010-April 2015)
4) Bonnie Berger (PI), Jinbo Xu and Jadwiga Bienkowska. NIH R01GM081871 (2008-2012).
5) Tobin Sosnick
(PI), Karl Freed and Jinbo Xu.
NIH R01GM081642 (2007-2010).
6) Jinbo Xu. (NSF-sponsored) TeraGrid TG-MCB100062 (3.7M CPU
hours, 2010-2011)
7) Jinbo Xu. (NSF-sponsored) TeraGrid
TG-CCR100005 (200k CPU hours, 2009)
In addition,
we are also grateful to OSG, SharcNet and U Chicago
CI for their computational resources.
Recent
Highlights
1.
Our
new protein structure prediction program RaptorX was ranked No.2
among ~80 CASP9 participating servers (when all test domains are
considered). RaptorX also generated significantly
better alignments than other servers for the 50 hardest TBM (template-based
modeling) targets in CASP9 and voted as one of the most interesting and
innovative methods by the CASP9 community. Our team was invited to give three
talks at the CASP9 meeting. The RaptorX server now is
online at http://raptorx.uchicago.edu.
2.
Our
graduate student Mr. Jian Peng
wins the prestigious Microsoft Research PhD Fellowship
2010. Pnly 10 out of 176 applications received this
award in 2010. A complete list of the 10 awardees is available at http://research.microsoft.com/en-us/collaboration/awards/apply-us.aspx#2010Fellows.
3.
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.
4.
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.
5. Our 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.