Jinbo Xu

ORCID

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 50

Top Venues

Publications

Chongshan Liang, Yi Dai, Jun Xia, Jinbo Xu, Jintao Peng, Weixia Xu, Ming Xie, Jie Liu, Zhiquan Lai, Sheng Ma, Qi Zhu
The Self-adaptive and Topology-aware MPI_Bcast leveraging Collective offload on Tianhe Express Interconnect. IPDPS (2024)
Huimei Liao, Siyuan Leng, Junhai Yang, Jinbo Xu, Junhao Zhang, Jinling Tang
A Robust and Efficient Risk Assessment Framework for Multi-Step Attacks. ICICT (2024)
Jinbo Xu, Yong Wang, Xiaoyu He, Yiqun Zou
Support-Query Mutual Promotion and Classification Correction Network for Few-Shot Object Detection. IEEE Signal Process. Lett. 31 (2024)
Bo Chen, Ziwei Xie, Jiezhong Qiu, Zhaofeng Ye, Jinbo Xu, Jie Tang
Improved the heterodimer protein complex prediction with protein language models. Briefings Bioinform. 24 (4) (2023)
Wenyi Xu, Jinbo Xu, Zhipeng Zhang
Research on the Aesthetic Connotation of New Media Ink Painting Art Based on Grounded Theory. HCI (24) (2023)
Alessio Del Conte, Adel Bouhraoua, Mahta Mehdiabadi, Damiano Clementel, Alexander Miguel Monzon, Alex S. Holehouse, Daniel A. Griffith, Ryan J. Emenecker, Ashwini Patil, Ronesh Sharma, Tatsuhiko Tsunoda, Alok Sharma, Yi Jun Tang, Bin Liu, Claudio Mirabello, Björn Wallner, Burkhard Rost, Dagmar Ilzhöfer, Maria Littmann, Michael Heinzinger, Lea I M. Krautheimer, Michael Bernhofer, Liam J. McGuffin, Isabelle Callebaut, Tristan Bitard Feildel, Jian Liu, Jianlin Cheng, Zhiye Guo, Jinbo Xu, Sheng Wang, Nawar Malhis, Jörg Gsponer, Chol-Song Kim, Kun-Sop Han, Myong-Chol Ma, Lukasz A. Kurgan, Sina Ghadermarzi, Akila Katuwawala, Bi Zhao, Zhenling Peng, Zhonghua Wu, Gang Hu, Kui Wang, Md. Tamjidul Hoque, Md Wasi Ul Kabir, Michele Vendruscolo, Pietro Sormanni, Min Li, Fuhao Zhang, Pengzhen Jia, Yida Wang, Michail Yu. Lobanov, Oxana V. Galzitskaya, Wim F. Vranken, Adrián Díaz, Thomas Litfin, Yaoqi Zhou, Jack Hanson, Kuldip K. Paliwal, Zsuzsanna Dosztányi, Gábor Erdös, Silvio C. E. Tosatto, Damiano Piovesan
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins. Nucleic Acids Res. 51 (W1) (2023)
Fandi Wu, Xiaoyang Jing, Xiao Luo, Jinbo Xu
Improving protein structure prediction using templates and sequence embedding. Bioinform. 39 (1) (2023)
Fang Wu, Huiling Qin, Siyuan Li, Stan Z. Li, Xianyuan Zhan, Jinbo Xu
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems. CoRR (2023)
Jinbo Xu, Yueqing Wei
Analysis of the Attainable Design Paths of Non-heritage Cultural Tourism Immersion Experience - An Example of the Tujia City Living Room Project in Enshi Prefecture. HCI (48) (2022)
Fang Wu, Tao Yu, Dragomir Radev, Jinbo Xu
When Geometric Deep Learning Meets Pretrained Protein Language Models. CoRR (2022)
Ziwei Xie, Jinbo Xu
Deep graph learning of inter-protein contacts. Bioinform. 38 (4) (2022)
Boqiao Lai, Jinbo Xu
Accurate protein function prediction via graph attention networks with predicted structure information. Briefings Bioinform. 23 (1) (2022)
Ngoc Hieu Tran, Jinbo Xu, Ming Li
A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction. Briefings Bioinform. 23 (1) (2022)
Boqiao Lai, Sheng Qian, Hanwei Zhang, Siwei Zhang, Anna A. Kozlova, Jubao Duan, Jinbo Xu, Xin He
Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning. PLoS Comput. Biol. 18 (5) (2022)
Lupeng Kong, Fusong Ju, Wei-Mou Zheng, Jianwei Zhu, Shiwei Sun, Jinbo Xu, Dongbo Bu
ProALIGN: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs. J. Comput. Biol. 29 (2) (2022)
Fengyuan Hu, Jia Lu, Louise S. Matheson, Manuel D. Díaz-Muñoz, Alexander Saveliev, Jinbo Xu, Martin Turner
ORFLine: a bioinformatic pipeline to prioritize small open reading frames identifies candidate secreted small proteins from lymphocytes. Bioinform. 37 (19) (2021)
Fan Ding, Nan Jiang, Jianzhu Ma, Jian Peng, Jinbo Xu, Yexiang Xue
PALM: Probabilistic area loss Minimization for Protein Sequence Alignment. UAI (2021)
Fan Ding, Jianzhu Ma, Jinbo Xu, Yexiang Xue
XOR-CD: Linearly Convergent Constrained Structure Generation. ICML (2021)
Xiaoyang Jing, Jinbo Xu
Improved protein model quality assessment by integrating sequential and pairwise features using deep learning. Bioinform. 36 (22-23) (2021)
Jin Li, Jinbo Xu
Study of real-valued distance prediction for protein structure prediction with deep learning. Bioinform. 37 (19) (2021)
Fandi Wu, Jinbo Xu
Deep template-based protein structure prediction. PLoS Comput. Biol. 17 (5) (2021)
Xiaoyang Jing, Jinbo Xu
Fast and effective protein model refinement using deep graph neural networks. Nat. Comput. Sci. 1 (7) (2021)
Jinbo Xu, Matthew McPartlon, Jin Li
Improved protein structure prediction by deep learning irrespective of co-evolution information. Nat. Mach. Intell. 3 (7) (2021)
Sara Sadat Aghamiri, Vidisha Singh, Aurélien Naldi, Tomás Helikar, Sylvain Soliman, Anna Niarakis, Jinbo Xu
Automated inference of Boolean models from molecular interaction maps using CaSQ. Bioinform. 36 (16) (2020)
Sheng Wang, Shiyang Fei, Zongan Wang, Yu Li, Jinbo Xu, Feng Zhao, Xin Gao
PredMP: a web server for de novo prediction and visualization of membrane proteins. Bioinform. 35 (4) (2019)
Zhen Li, Chongming Ni, Jinbo Xu, Xin Gao, Shuguang Cui, Sheng Wang
Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers. BCB (2019)
Zhen Li, Chongming Ni, Jinbo Xu, Xin Gao, Shuguang Cui, Sheng Wang
Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers. BCB (2019)
Jinbo Xu
stance-Based Protein Folding Powered by Deep Learning. RECOMB (2019)
Hong Zeng, Sheng Wang, Tian-Ming Zhou, Feifeng Zhao, Xiufeng Li, Qing Wu, Jinbo Xu
ComplexContact: a web server for inter-protein contact prediction using deep learning. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Tian-Ming Zhou, Sheng Wang, Jinbo Xu
Deep Learning Reveals Many More Inter-protein Residue-Residue Contacts than Direct Coupling Analysis. RECOMB (2018)
Somaye Hashemifar, Behnam Neyshabur, Aly A. Khan, Jinbo Xu
Predicting protein-protein interactions through sequence-based deep learning. Bioinform. 34 (17) (2018)
Jianwei Zhu, Sheng Wang, Dongbo Bu, Jinbo Xu
Protein threading using residue co-variation and deep learning. Bioinform. 34 (13) (2018)
Yujuan Gao, Sheng Wang, Minghua Deng, Jinbo Xu
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. BMC Bioinform. (4) (2018)
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PLoS Comput. Biol. 13 (1) (2017)
Sheng Wang, Zhen Li, Yizhou Yu, Jinbo Xu
Folding membrane proteins by deep transfer learning. CoRR (2017)
Zhen Li, Sheng Wang, Yizhou Yu, Jinbo Xu
Predicting membrane protein contacts from non-membrane proteins by deep transfer learning. CoRR (2017)
Jinbo Xu
Folding Large Proteins by Ultra-Deep Learning. BCB (2017)
Zhiyong Wang, Benika Hall, Jinbo Xu, Xinghua Shi
A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (5) (2017)
Zhen Li, Sheng Wang, Yizhou Yu, Jinbo Xu
Folding Membrane Proteins by Deep Transfer Learning. RECOMB (2017)
Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu
ModuleAlign: module-based global alignment of protein-protein interaction networks. Bioinform. 32 (17) (2016)
Sheng Wang, Wei Li, Renyu Zhang, Shiwang Liu, Jinbo Xu
CoinFold: a web server for protein contact prediction and contact-assisted protein folding. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Sheng Wang, Wei Li, Shiwang Liu, Jinbo Xu
RaptorX-Property: a web server for protein structure property prediction. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Dinanath Sulakhe, Bingqing Xie, Andrew Taylor, Mark D'Souza, Sandhya Balasubramanian, Somaye Hashemifar, Steven White, Utpal J. Dave, Gady Agam, Jinbo Xu, Sheng Wang, T. Conrad Gilliam, Natalia Maltsev
Lynx: a knowledge base and an analytical workbench for integrative medicine. Nucleic Acids Res. 44 (Database-Issue) (2016)
Sheng Wang, Jianzhu Ma, Jinbo Xu
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. Bioinform. 32 (17) (2016)
Qingming Tang, Lifu Tu, Weiran Wang, Jinbo Xu
Network Inference by Learned Node-Specific Degree Prior. CoRR (2016)
Somaye Hashemifar, Qixing Huang, Jinbo Xu
Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization. RECOMB (2016)
Somaye Hashemifar, Qixing Huang, Jinbo Xu
Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization. J. Comput. Biol. 23 (11) (2016)
Sheng Wang, Siqi Sun, Jinbo Xu
AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling. ECML/PKDD (2) (2016)
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. CoRR (2016)
Somaye Hashemifar, Qixing Huang, Jinbo Xu
Joint alignment of multiple protein-protein interaction networks via convex optimization. CoRR (2016)
Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. BCB (2015)
Jinbo Xu, Weixia Xu, Zhengbin Pang
A low-latency fine-grained dynamic shared cache management scheme for chip multi-processor. IPCCC (2015)
Somaye Hashemifar, Behnam Neyshabur, Jinbo Xu
Joint inference of tissue-specific networks with a scale free topology. BIBM (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinform. 31 (21) (2015)
Jianzhu Ma, Feng Zhao, Jinbo Xu
Structure Learning Constrained by Node-Specific Degree Distribution. UAI (2015)
Qingming Tang, Siqi Sun, Chao Yang, Jinbo Xu
Learning Scale Free Network by Node Specific Degree Prior. CoRR (2015)
Sheng Wang, Siqi Sun, Jinbo Xu
AUC-maximized Deep Convolutional Neural Fields for Sequence Labeling. CoRR (2015)
Qi Lv, Yong Dou, Xin Niu, Jiaqing Xu, Jinbo Xu, Fei Xia
Urban Land Use and Land Cover Classification Using Remotely Sensed SAR Data through Deep Belief Networks. J. Sensors 2015 (2015)
Qingming Tang, Chao Yang, Jian Peng, Jinbo Xu
Exact Hybrid Covariance Thresholding for Joint Graphical Lasso. ECML/PKDD (2) (2015)
Qingming Tang, Siqi Sun, Jinbo Xu
Learning Scale-Free Networks by Dynamic Node Specific Degree Prior. ICML (2015)
Siqi Sun, Mladen Kolar, Jinbo Xu
Learning structured densities via infinite dimensional exponential families. NIPS (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. RECOMB (2015)
Siqi Sun, Hai Wang, Jinbo Xu
Inferring Block Structure of Graphical Models in Exponential Families. AISTATS (2015)
Siqi Sun, Jianzhu Ma, Sheng Wang, Jinbo Xu
Predicting diverse M-best protein contact maps. BIBM (2015)
Qingming Tang, Chao Yang, Jian Peng, Jinbo Xu
Exact Hybrid Covariance Thresholding for Joint Graphical Lasso. CoRR (2015)
Qi Lv, Yong Dou, Xin Niu, Jiaqing Xu, Jinbo Xu
Classification of Tiangong-1 hyperspectral remote sensing image via contextual sparse coding. ICMLC (2015)
Bingqing Xie, Gady Agam, Sandhya Balasubramanian, Jinbo Xu, T. Conrad Gilliam, Natalia Maltsev, Daniela Börnigen
Disease Gene Prioritization Using Network and Feature. J. Comput. Biol. 22 (4) (2015)
Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
Protein secondary structure prediction using deep convolutional neural fields. CoRR (2015)
Zhiyong Wang, Jinbo Xu, Xinghua Shi
CNVnet: combining sparse learning and biological networks to capture joint effect of copy number variants. BCB (2014)
Zhiyong Wang, Jinbo Xu, Xinghua Shi
Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space. J. Comput. Biol. 21 (5) (2014)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. RECOMB (2014)
Dinanath Sulakhe, Sandhya Balasubramanian, Bingqing Xie, Bo Feng, Andrew Taylor, Sheng Wang, Eduardo Berrocal, Utpal J. Dave, Jinbo Xu, Daniela Börnigen, T. Conrad Gilliam, Natalia Maltsev
Lynx: a database and knowledge extraction engine for integrative medicine. Nucleic Acids Res. 42 (Database-Issue) (2014)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. PLoS Comput. Biol. 10 (3) (2014)
Siqi Sun, Yuancheng Zhu, Jinbo Xu
Adaptive Variable Clustering in Gaussian Graphical Models. AISTATS (2014)
Somaye Hashemifar, Jinbo Xu
HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks. Bioinform. 30 (17) (2014)
Yuanwu Lei, Lei Guo, Yong Dou, Sheng Ma, Jinbo Xu
FPGA Implementation of a Special-Purpose VLIW Structure for Double-Precision Elementary Function. ACM Trans. Reconfigurable Technol. Syst. 7 (2) (2014)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. CoRR (2014)
Jinbo Xu, Weixia Xu, Kefei Wang, Zhengbin Pang
Low-latency last-level cache structure based on grouped cores in Chip Multi-Processor. IPCCC (2014)
Zhiyong Wang, Jinbo Xu
Predicting protein contact map using evolutionary and physical constraints by integer programming. Bioinform. 29 (13) (2013)
Rongchun Li, Yong Dou, Jie Zhou, Baofeng Li, Jinbo Xu
From WiFi to WiMAX: Efficient GPU-based Parameterized Transceiver across Different OFDM Protocols. KSII Trans. Internet Inf. Syst. 7 (8) (2013)
Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. AISTATS (2013)
Caixia Sun, Yongwen Wang, Jinbo Xu
Achieving Predictable Performance in SMT Processors by Instruction Fetch Policy. NCCET (2013)
Pingjing Lu, Bao Li, Zhengbin Pang, Ying Zhang, Shaogang Wang, Jinbo Xu, Yan Liu
An Effective Framework of Program Optimization for High Performance Computing. NCCET (2013)
Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu
Protein threading using context-specific alignment potential. Bioinform. 29 (13) (2013)
Zhiyong Wang, Jinbo Xu
Predicting protein contact map using evolutionary and physical constraints by integer programming (extended version). CoRR (2013)
Yuanwu Lei, Yong Dou, Lei Guo, Jinbo Xu, Jie Zhou, Yazhuo Dong, Hongjian Li
VLIW coprocessor for IEEE-754 quadruple-precision elementary functions. ACM Trans. Archit. Code Optim. 10 (3) (2013)
Dan Zou, Yong Dou, Qiang Wang, Jinbo Xu, Baofeng Li
Direction-Optimizing Breadth-First Search on CPU-GPU Heterogeneous Platforms. HPCC/EUC (2013)
Jianzhu Ma, Sheng Wang, Jinbo Xu
Protein contact prediction by joint evolutionary coupling analysis across multiple families. CoRR (2013)
Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
A conditional neural fields model for protein threading. Bioinform. 28 (12) (2012)
Jian Peng, Tamir Hazan, Nathan Srebro, Jinbo Xu
Approximate Inference by Intersecting Semidefinite Bound and Local Polytope. AISTATS (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. AISTATS (2012)
Weixia Xu, Jinbo Xu, Zhengbin Pang
A Parallel Processing Scheme for Large-Size Sliding-Window Applications. HPCC (2011)
Zhiyong Wang, Jinbo Xu
A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling. Bioinform. 27 (13) (2011)
Sheng Wang, Jian Peng, Jinbo Xu
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinform. 27 (18) (2011)
Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
Finding Nearly Optimal GDT Scores. J. Comput. Biol. 18 (5) (2011)
Feng Zhao, Jian Peng, Jinbo Xu
Fragment-free approach to protein folding using conditional neural fields. Bioinform. 26 (12) (2010)
Zhiyong Wang, Feng Zhao, Jian Peng, Jinbo Xu
Protein 8-class secondary structure prediction using Conditional Neural Fields. BIBM (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 Res. 38 (Web-Server-Issue) (2010)
Jian Peng, Jinbo Xu
Low-homology protein threading. Bioinform. 26 (12) (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. J. Comput. Biol. 17 (6) (2010)

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Publication Activity (10 Years)

Top Topics

Top Venues

Jinbo Xu