2012
Xiaohui Chen, Xinghua Shi, Xing Xu, Zhiyong
Wang, Jinbo Xu and Charles Lee.
A Two-Graph Guided Multi-task Lasso Approach for eQTL
Mapping, accepted
by AISTAT 2012. (The last two authors are
co-corresponding authors).
Jian Peng, Nathan Srebro, Tamir Hazan and Jinbo Xu. Approximate
Inference with Intersected Outer Bounds and Rounding Schemes, accepted by AISTAT 2012.
2011
Aashish N. Adhikari, Jian Peng, Michael Wilde, Jinbo Xu, Karl F. Freed and Tobin R. Sosnick. Modeling large regions in proteins: Applications
to loops, termini and folding. Protein Science, 2011. In Press.
Jian Peng and Jinbo Xu. RaptorX:
exploiting structure information for protein alignment by statistical
inference. PROTEINS, 2011. (an invited paper for the CASP9
special issue)
Sheng Wang, Jian Peng
and Jinbo Xu. Alignment of distantly-related protein structures: algorithm, bound
and implications to homology modeling. Bioinformatics, 2011.
Zhiyong Wang, Jian Peng, Feng
Zhao and Jinbo Xu. Protein 8-class secondary structure prediction using
conditional neural fields. PROTEOMICS, 2011. Early version appears at the IEEE BIBM 2010.
Zhiyong Wang and Jinbo Xu. A Conditional Random Fields Method for RNA
Sequence-Structure Relationship Modeling and Conformation Sampling.
Bioinformatics (Proceedings of ISMB/ECCB 2011).
Jian Peng and Jinbo Xu. A multiple-template approach to protein
threading. PROTEINS, 2011.
2010
Zhiyong Wang, Jian Peng, Feng
Zhao and Jinbo Xu. Protein 8-class secondary structure prediction using
conditional neural fields. IEEE BIBM 2010.
Raghavendra
Hosur, Jinbo Xu, Jadwiga Bienkowska,
and Bonnie Berger. iWRAP: An interface threading approach with
application to prediction of cancer related protein-protein interactions. Journal
of Molecular Biology, December 2010.
Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra
Hosur and Bonnie Berger.
Struct2Net: a Web-Service to Predict Protein-Protein Interactions Using a
Structure-based Approach. NAR web server issue.
(The first three authors equally contribute to this paper.)
Jian Peng and Jinbo Xu.
Low-homology Protein Threading. Bioinformatics (Proceedings of ISMB2010).
Feng Zhao, Jian Peng and Jinbo Xu. Fragment-free Approach to Protein Folding
Using Conditional Neural Fields. Bioinformatics (Proceedings of ISMB2010).
2009
Joe DeBartolo, Glen Hocky, Mike Wilde, Jinbo Xu, Karl F. Freed and Tobin R. Sosnick. Protein Structure Prediction Enhanced with
Evolutionary Diversity: SPEED. Protein Science, 2009.
Feng Zhao, Jian Peng, Joe DeBartolo, Karl F.
Freed, Tobin R. Sosnick and Jinbo Xu. A probabilistic
and continuous model of protein conformational space for template-free modeling.
Journal of Computational Biology, 2009. An early version of this paper also
appears at RECOMB 2009.
Jian Peng, Liefeng Bo and Jinbo Xu.
Conditional Neural Fields. NIPS 2009 (Conditional Neural Fields are similar to
but much more powerful than Conditional Random Fields. A software package is
available at http://ttic.uchicago.edu/~pengjian/CNF-0.1.tar.gz)
Jinbo
Xu, Jian Peng and Feng Zhao. Template-based and free modeling by RAPTOR++ in
CASP8. The CASP8 special issue of PROTEINS, 2009. (invited paper)
Jian Peng and Jinbo Xu. Boosting protein threading accuracy.
RECOMB 2009.
Feng Zhao, Jian Peng, Joe DeBartolo, Karl F.
Freed, Tobin R. Sosnick and Jinbo Xu. A probabilistic
graphical model for ab initio folding. RECOMB 2009.
Xin Gao, Dongbo Bu, Jinbo Xu and Ming
Li. Improving consensus contact prediction via server
correlation reduction.
2008
ShuaiCheng Li, Dongbo Bu, Jinbo Xu and Ming Li. Fragment-HMM: A New Approach to Protein Structure
Prediction. Protein Science, 2008.
Rohit Singh, Jinbo
Xu and Bonnie Berger. Global Alignment of Multiple Protein Interaction Networks
with Application to Functional Orthology Detection.
PNAS, 2008.
ShuaiCheng Li, Dongbo Bu, Xin Gao, Jinbo Xu and Ming Li. Design Succinct Structural
Alphabet. ISMB, 2008.
Feng Zhao, ShuaiCheng Li, Beckett W. Sterner and Jinbo Xu.
Discriminative Learning for Protein Conformation Sampling. PROTEINS: Structure,
Function and Bioinformatics, 2008.
Ben Boyerinas, Sun-Mi Park, Noam Shomron, Cydney B. Nielsen,
Christine Feig, Jinbo Xu, Christopher B. Burge and
Marcus E. Peter. Identification of Let-7-regulated oncofetal
genes for human cancer. Cancer Research, 2008.
Jing
Zhang, Xin Gao, Jinbo Xu
and Ming Li. Rapid and Accurate Protein Side Chain Packing using Local Backbone
Information, RECOMB 2008.
Bonnie Berger, Rohit Singh and Jinbo Xu. Graph
Algorithms for Biological Systems Analysis, SODA 2008. (invited paper).
Rohit Singh, Jinbo
Xu and Bonnie Berger. Global Alignment of Multiple Protein Interaction
Networks,
2007
Jinbo
Xu. Solving the Contact Map Overlap Problem via Tree Decomposition and a
DEE-Like Pruning Strategy, accepted by the 46th IEEE Conference on Decision and
Control, Dec 2007. (Invited Paper)
Xin Gao, Dongbo Bu, Shuai Cheng Li, Jinbo Xu and Ming Li. FragQA: predicting local fragment quality of a
sequence-structure alignment, GIW 2007. (Best Paper Award)
Xin Gao, Dongbo Bu, ShuaiCheng Li, Ming Li, and Jinbo Xu. Consensus Contact
Prediction by Linear Programming,
Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li and Jinbo Xu. Finding Compact Structural
Motifs in Many Proteins, accepted by Combinatorial Pattern Matching (CPM), July
2007.
Jinbo
Xu, Feng Jiao and Bonnie Berger, A Paramterized Algorithm for Protein Structure Alignment.
Journal of Computational Biology, Vol. 14, No. 5, pp.564-577, 2007. Early version appears at RECOMB 2006.
Dongbo Bu, Shuaicheng Li, Xin Gao, Libo Yu, Jinbo Xu and Ming
Li. Consensus Approaches to Protein Structure Prediction. Book Chapter in
Machine Learning in Bioinformatics, Eds: Yan-Qing
Zhang and Jagath C. Rajapakse,
John Wiley & Sons, 2007.
Rohit Singh, Jinbo Xu and Bonnie Berger. Pairwise
Global Alignment of Protein Interaction Networks By Matching Neighborhood,
accepted by RECOMB 2007.
Jinbo
Xu, Libo Yu and Feng Jiao.
Protein Structure Prediction Using Threading. Book Chapter in Protein Structure
Prediction: Methods and Protocols, Humana Press 2007.
2006
Jinbo Xu and Bonnie Berger. Fast and
Accurate Algorithms for Protein Side-Chain Packing. the Journal of the ACM,
2006. Early version appears at RECOMB2005.
Feng Jiao, Jinbo
Xu, Libo Yu, Dale Schuurmans. Protein Fold Recognition Using Gradient Boost
Algorithm. CSB 2006.
Jinbo
Xu, Feng Jiao, Bonnie Berger. A Parameterized Algorithm for Protein Structure
Alignment. RECOMB 2006, Venice, Italy.
Rohit
Singh, Jinbo Xu, Bonnie Berger. Struct2Net: Integrating Structure into
Protein-Protein Interaction Prediction. PSB 2006. (the first two authors
contribute equally)
2005
Jinbo
Xu. Protein Fold Recognition by Predicted Alignment Accuracy. IEEE/ACM Trans.
on Computational Biology and Bioinformatics. 2005.
Jinbo Xu, Feng Jiao, Bonnie Berger. A Tree-Decomposition
Approach to Protein Structure Prediction. CSB 2005, Stanford, USA.
Jinbo
Xu. Rapid Protein Side-Chain Packing via Tree Decomposition. RECOMB 2005,
Boston, USA.
Jinbo Xu, Libo Yu, Ming Li. Consensus Fold
Recognition by Predicted Model Quality. APBC 2005, Singapore.
Thomas
Tang, Jinbo Xu, Ming Li. Discovery of Sequence-Structure Motifs from Protein
Segments and Two Applications. PSB 2005. Hawaii, USA.
2004
Jinbo
Xu, Ying Xu, Ming Li. Protein Threading by Linear Programming: Theoretical
Analysis and Computational Results, Journal of Combinatorial Optimization,
2004.
Jinbo Xu, Daniel Brown, Ming Li, Bin Ma. Optimizing
multiple spaced seeds for homology search. Combinatorial Pattern Matching 2004.
An extended version has been accepted by Journal of Computational Biology.
2003
Jinbo
Xu, Ying Xu, Dongsup Kim, 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), an absolutely blind test of structure prediction servers
organized by protein structure community. RAPTOR also ranks third among all
non-meta servers in CASP6 according to http://www.bioinformatics.buffalo.edu/casp6/.
Jinbo
Xu, 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 the novelty and
performance.)
Jinbo
Xu, Ying Xu, Guohui Lin, Dongsup
Kim, Ming Li. Protein Structure Prediction By Linear Programming, PSB 2003.
Jinbo
Xu. Speed up LP Approach to Protein Threading via Graph Reduction, WABI 2003.
2002
Guohui Lin, Jinbo Xu
et al. Approximation Algorithms for NMR Spectral Peak Assignment, Theoretical
Computer Science, vol. 299, pages 211-229, 2002.
2001 and Before
Guoliang Chen, Jinbo
Xu. Communication Strategy of Butterfly-Style Computing on LogP
Model, (Chinese) Journal of Computers, no.8, pg. 702-710, 1997.
Jinbo
Xu, Guoliang Chen. Design and Analysis of Parallel
FFT on CCC Model, (Chinese) Journal of Research and Development of Computer,
no.12, 1997.
Jie Lin, Jinbo
Xu, Naijie Gu and Guoliang Chen. Paralell String
Matching Algorithm on Distributed Systems. (Chinese) Journal of Software, vol.
11, no.6, pp. 771-778, 2000.