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 Cagliari, Sardinia, Italy (Dec 3-7, 2008). CASP is the most prestigious competition in the field of protein structure prediction.

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.