2013

Dinanath Sulakhe, Sandhya Balasubramanian, BingqingXie, Bo Feng, Andrew Taylor, Sheng Wang, Eduardo Berrocal, Paul Dave, Jinbo Xu, Daniela Bornigen, Conrad Gilliam and Natalia Maltsev. Lynx: a database and knowledge extraction engine for integrative medicine. NAR (to appear)

 

Zhiyong Wang, Jinbo Xu and Xinghua Shi, Finding Alternative eQTLs by Exploring Sparse Model Space”, To appear in Proceedings of the RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges (RECOMB/ISCB RegSys 2013), Toronto, Canada, November 2013.

 

Fan Yang, Jinbo Xu and Jianyang Zeng. Drug-Target Interaction Prediction by Integrating Chemical, Genomic, Functional and Pharmacological Data. Pacific Symposium on Biocomputing (PSB). The Big Island of Hawaii. January 3-7, 2014. PDFSupplementary Material.

 

Sheng Wang, Jian Peng, Jianzhu Ma and Jinbo Xu. Protein structure alignment beyond spatial proximity. Scientific Reports, 2013.

 

Zhiyong Wang and Jinbo Xu. Predicting protein contact map using evolutionary and physical constraints by integer programming, ISMB 2013. An extended version contains many more technical details and results. [The presentation file] [The server]

 

Jianzhu Ma, Sheng Wang, Feng Zhao and Jinbo Xu. Protein threading using context-specific alignment potential, ISMB 2013.

 

Jianzhu Ma, Jian Peng, Sheng Wang and Jinbo Xu. Estimating the partition function of graphical models using Langevin importance sampling, AI and Statistics (AISTATS) 2013.

 

Morten Källberg, Gohar Margaryan, Sheng Wang, Jianzhu Ma and Jinbo Xu. RaptorX Server: A Resource for Template-based Protein Structure Modeling. Methods in Molecular Biology 2013. (Book Chapter)

 

2012

Raghavendra Hosur, Jian Peng, Arunachalam Vinayagam, Ulrich Stelzl, Jinbo Xu, Norbert Perrimon, Jadwiga Bienkowska and Bonnie Berger.  Coev2Net: a computational framework for boosting confidence in high-throughput protein-protein interaction dataset. Genome Biology, August 2012.

 

Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu and Jinbo Xu. Template-based protein structure modeling using the RaptorX web server. Nature Protocols, 2012.

 

Feng Zhao and Jinbo Xu. A position-specific distance-dependent statistical potential for protein structure and functional study. STRUCTURE, Cell Press, 2012.

 

Jianzhu Ma, Jian Peng, Sheng Wang and Jinbo Xu. A Conditional Neural Fields model for protein threading. Bioinformatics (Proceedings of ISMB), 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. AISTATS 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. AISTATS 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.

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. BMC Structural Biology 2009, 9:28

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, PSB, Jan 2008.

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, CSB, August 2007.

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.