Jinbo Xu

Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu: A conditional neural fields model for protein threading. Bioinformatics 28(12): 59-66 (2012)

Xiaohui Chen, Xinghua Shi, Xing Xu, Zhiyong Wang, Ryan Mills, Charles Lee, Jinbo Xu: A Two-Graph Guided Multi-task Lasso Approach for eQTL Mapping. Journal of Machine Learning Research - Proceedings Track 22: 208-217 (2012)

Jian Peng, Tamir Hazan, Nathan Srebro, Jinbo Xu: Approximate Inference by Intersecting Semidefinite Bound and Local Polytope. Journal of Machine Learning Research - Proceedings Track 22: 868-876 (2012)

Zhiyong Wang, Jinbo Xu: A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling. Bioinformatics [ISMB/ECCB] 27(13): 102-110 (2011)

Sheng Wang, Jian Peng, Jinbo Xu: Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinformatics 27(18): 2537-2545 (2011)

Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li: Finding Nearly Optimal GDT Scores. Journal of Computational Biology 18(5): 693-704 (2011)

Weixia Xu, Jinbo Xu, Zhengbin Pang: A Parallel Processing Scheme for Large-Size Sliding-Window Applications. HPCC 2011: 35-39

Jian Peng, Jinbo Xu: Low-homology protein threading. Bioinformatics [ISMB] 26(12): 294-300 (2010)

Feng Zhao, Jian Peng, Jinbo Xu: Fragment-free approach to protein folding using conditional neural fields. Bioinformatics [ISMB] 26(12): 310-317 (2010)

Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu: A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling. Journal of Computational Biology 17(6): 783-798 (2010)

Rohit Singh, Daniel Park, Jinbo Xu, Raghavendra Hosur, Bonnie Berger: Struct2Net: a web service to predict protein-protein interactions using a structure-based approach. Nucleic Acids Research 38(Web-Server-Issue): 508-515 (2010)

Zhiyong Wang, Feng Zhao, Jian Peng, Jinbo Xu: Protein 8-class secondary structure prediction using Conditional Neural Fields. BIBM 2010: 109-114

Jinbo Xu, Yong Dou, Zhengbin Pang: A Reconfigurable Architecture for Rotation Invariant Multi-View Face Detection Based on a Novel Two-Stage Boosting Method. EURASIP J. Adv. Sig. Proc. 2009 (2009)

Xin Gao, Jinbo Xu, Shuai Cheng Li, Ming Li: Predicting Local Quality of a Sequence-Structure Alignment. J. Bioinformatics and Computational Biology 7(5): 789-810 (2009)

Dongbo Bu, Ming Li, Shuai Cheng Li, Jianbo Qian, Jinbo Xu: Finding compact structural motifs. Theor. Comput. Sci. 410(30-32): 2834-2839 (2009)

Jinbo Xu, Yong Dou, YuXing Tang, Xiaodong Wang: Implementation of Rotation Invariant Multi-View Face Detection on FPGA. APPT 2009: 82-94

Yong Dou, Jie Zhou, Xiaoyang Chen, Yuanwu Lei, Jinbo Xu: FPGA accelerating three QR decomposition algorithms in the unified pipelined framework. FPL 2009: 410-416

Jian Peng, Liefeng Bo, Jinbo Xu: Conditional Neural Fields. NIPS 2009: 1419-1427

Jian Peng, Jinbo Xu: Boosting Protein Threading Accuracy. RECOMB 2009: 31-45

Feng Zhao, Jian Peng, Joe DeBartolo, Karl F. Freed, Tobin R. Sosnick, Jinbo Xu: A Probabilistic Graphical Model for Ab Initio Folding. RECOMB 2009: 59-73

Fei Xia, Yong Dou, Jinbo Xu: Hardware BLAST Algorithms with Multi-seeds Detection and Parallel Extension. ARC 2008: 39-50

Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li: Finding Largest Well-Predicted Subset of Protein Structure Models. CPM 2008: 44-55

Jie Zhou, Yong Dou, Yuanwu Lei, Jinbo Xu, Yazhuo Dong: Double Precision Hybrid-Mode Floating-Point FPGA CORDIC Co-processor. HPCC 2008: 182-189

Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li: Designing succinct structural alphabets. ISMB 2008: 182-189

Jinbo Xu, Yong Dou, Jie Zhou: Rectangularly Multi-Module Memory System with Table-Based Dynamic Addressing Scheme. NAS 2008: 334-341

Rohit Singh, Jinbo Xu, Bonnie Berger: Global Alignment of Multiple Protein Interaction Networks. Pacific Symposium on Biocomputing 2008: 303-314

Jing Zhang, Xin Gao, Jinbo Xu, Ming Li: Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information. RECOMB 2008: 285-299

Bonnie Berger, Rohit Singh, Jinbo Xu: Graph algorithms for biological systems analysis. SODA 2008: 142-151

Jinbo Xu, Feng Jiao, Bonnie Berger: A Parameterized Algorithm for Protein Structure Alignment. Journal of Computational Biology 14(5): 564-577 (2007)

Yong Dou, Jinbo Xu: FPGA-Accelerated Active Shape Model for Real-Time People Tracking. Asia-Pacific Computer Systems Architecture Conference 2007: 268-279

Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu: Finding Compact Structural Motifs. CPM 2007: 142-149

Jinbo Xu, Yong Dou, Junfeng Li, Xingming Zhou, Qiang Dou: FPGA Accelerating Algorithms of Active Shape Model in People Tracking Applications. DSD 2007: 432-435

Rohit Singh, Jinbo Xu, Bonnie Berger: Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology. RECOMB 2007: 16-31

Jinbo Xu, Bonnie Berger: Fast and accurate algorithms for protein side-chain packing. J. ACM 53(4): 533-557 (2006)

Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma: Optimizing Multiple Spaced Seeds for Homology Search. Journal of Computational Biology 13(7): 1355-1368 (2006)

Jinbo Xu, Yong Dou: Robust and real-time automatic target recognition using partial hausdorff distance measure on reconfigurable hardware. FPT 2006: 25-32

Rohit Singh, Jinbo Xu, Bonnie Berger: Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction. Pacific Symposium on Biocomputing 2006: 403-414

Jinbo Xu, Feng Jiao, Bonnie Berger: A Parameterized Algorithm for Protein Structure Alignment. RECOMB 2006: 488-499

Jinbo Xu: Fold Recognition by Predicted Alignment Accuracy. IEEE/ACM Trans. Comput. Biology Bioinform. 2(2): 157-165 (2005)

Jinbo Xu, Libo Yu, Ming Li: Consensus fold recognition by predicted model quality. APBC 2005: 73-83

Jinbo Xu, Feng Jiao, Bonnie Berger: A Tree-Decomposition Approach to Protein Structure Prediction. CSB 2005: 247-256

Thomas Tang, Jinbo Xu, Ming Li: Discovering Sequence-Structure Motifs from Protein Segments and Two Applications. Pacific Symposium on Biocomputing 2005

Jinbo Xu: Rapid Protein Side-Chain Packing via Tree Decomposition. RECOMB 2005: 423-439

Jinbo Xu, Ming Li, Ying Xu: Protein Threading by Linear Programming: Theoretical Analysis and Computational Results. J. Comb. Optim. 8(4): 403-418 (2004)

Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma: Optimizing Multiple Spaced Seeds for Homology Search. CPM 2004: 47-58

Jinbo Xu, Ming Li, Dongsup Kim, Ying Xu: Raptor: Optimal Protein Threading by Linear Programming. J. Bioinformatics and Computational Biology 1(1): 95-118 (2003)

Zhi-Zhong Chen, Tao Jiang, Guo-Hui Lin, Jianjun Wen, Dong Xu, Jinbo Xu, Ying Xu: Approximation algorithms for NMR spectral peak assignment. Theor. Comput. Sci. 1-3(299): 211-229 (2003)

Jinbo Xu, Ming Li, Guo-Hui Lin, Dongsup Kim, Ying Xu: Protein Threading by Linear Programming. Pacific Symposium on Biocomputing 2003: 264-275

Jinbo Xu: Speedup LP Approach to Protein Threading via Graph Reduction. WABI 2003: 374-388