Jinbo Xu

发表

A conditional neural fields model for protein threading

Jian Peng, Sheng Wang, Jianzhu Ma, 2012, Bioinform..

Raptor: Optimal Protein Threading by Linear Programming

Ying Xu, Ming Li, Dongsup Kim, 2003, J. Bioinform. Comput. Biol..

Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling

Jian Peng, Sheng Wang, Jianzhu Ma, 2013, AISTATS.

Disease Gene Prioritization Using Network and Feature

Jinbo Xu, Natalia Maltsev, Bingqing Xie, 2015, J. Comput. Biol..

A position-specific distance-dependent statistical potential for protein structure and functional study.

Jinbo Xu, Feng Zhao, 2012, Structure.

Inferential modeling of 3D chromatin structure

Jinbo Xu, Jianyang Zeng, Siyu Wang, 2015, Nucleic acids research.

Folding membrane proteins by deep transfer learning

Yizhou Yu, Sheng Wang, Jinbo Xu, 2017, bioRxiv.

RaptorX server: a resource for template-based protein structure modeling.

Jianzhu Ma, Sheng Wang, Jinbo Xu, 2014, Methods in molecular biology.

Opportunities and obstacles for deep learning in biology and medicine [update in progress]

Anne E Carpenter, Srinivas C. Turaga, Brett K. Beaulieu-Jones, 2020 .

Template-based protein structure modeling using the RaptorX web server

Jian Peng, Sheng Wang, Jinbo Xu, 2012, Nature Protocols.

Study of Real-Valued Distance Prediction For Protein Structure Prediction with Deep Learning

Jinbo Xu, Jin Li, 2020, bioRxiv.

Deep graph learning of inter-protein contacts

Jinbo Xu, Ziwei Xie, 2021, bioRxiv.

ProALIGN: Directly learning alignments for protein structure prediction via exploiting context-specific alignment motifs

Jinbo Xu, D. Bu, Shiwei Sun, 2020, bioRxiv.

Predicting the clinical impact of human mutation with deep neural networks

Jörg Hakenberg, Jinbo Xu, Serafim Batzoglou, 2018, Nature Genetics.

Fast and effective protein model refinement using deep graph neural networks

Jinbo Xu, Xiaoyang Jing, 2021, Nature Computational Science.

Approximate Inference by Intersecting Semidenite Bound and

Nathan Srebro, Tamir Hazan, Jian Peng, 2012 .

Protein structure alignment beyond spatial proximity

Jianzhu Ma, Jinbo Xu, Sheng Wang, 2013, Scientific Reports.

Predicting Epigenomic Functions of Genetic Variants in the Context of Neurodevelopment via Deep Transfer Learning

Jinbo Xu, J. Duan, Xin He, 2021, bioRxiv.

Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning

Jinbo Xu, Minghua Deng, Sheng Wang, 2017 .

D ec 2 01 7 Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning

Minghua Deng, Sheng Wang, Jinbo Xu, 2017 .

Protein structure prediction enhanced with evolutionary diversity: SPEED

Michael Wilde, Jinbo Xu, Karl F Freed, 2010, Protein science : a publication of the Protein Society.

Modeling large regions in proteins: Applications to loops, termini, and folding

Michael Wilde, Jinbo Xu, Jian Peng, 2012, Protein science : a publication of the Protein Society.

iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition

Bonnie Berger, Jinbo Xu, Jian Peng, 2015, 1504.05467.

Opportunities and obstacles for deep learning in biology and medicine

Anne E Carpenter, Srinivas C. Turaga, Brett K. Beaulieu-Jones, 2017, bioRxiv.

A computational framework for boosting confidence in high-throughput protein-protein interaction datasets

Bonnie Berger, Jinbo Xu, Ulrich Stelzl, 2012, Genome Biology.

Opportunities and obstacles for deep learning in biology and medicine: 2019 update

Anne E Carpenter, Srinivas C. Turaga, Brett K. Beaulieu-Jones, 2019 .

Template‐based and free modeling by RAPTOR++ in CASP8

Jinbo Xu, Feng Zhao, Jian Peng, 2009, Proteins.

Protein structure alignment beyond spatial proximity

Jianzhu Ma, Jinbo Xu, Sheng Wang, 2013 .

Peptide Antidotes to SARS-CoV-2 (COVID-19)

Jinbo Xu, R. Stroud, Leonardo M. R. Ferreira, 2020, bioRxiv.

Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning

Jinbo Xu, J. Duan, Xin He, 2022, PLoS Comput. Biol..

1 Supplement : iWRAP : An interface threading approach for protein-protein interaction prediction

B. Berger, Jinbo Xu, J. Bienkowska, 2010 .

End-to-End deep structure generative model for protein design

Jinbo Xu, Boqiao Lai, Matthew McPartlon, 2022, bioRxiv.

Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information

Xin Gao, Ming Li, Jinbo Xu, 2008, RECOMB.

Consensus Approaches to Protein Structure Prediction

Shuai Cheng Li, Ming Li, Jinbo Xu, 2008 .

BIOINFORMATICS Designing succinct structural alphabets

Jinbo Xu, D. Cheriton, D. Bu, 2008 .

APPLES: Fast Distance-Based Phylogenetic Placement

Larry Smarr, Andrey D. Prjibelski, Pavel A. Pevzner, 2019, RECOMB.

Deep template-based protein structure prediction

Jinbo Xu, Fandi Wu, 2020, bioRxiv.

Improve the Protein Complex Prediction with Protein Language Models

Jie Tang, Jinbo Xu, J. Qiu, 2022, bioRxiv.

Improved the Protein Complex Prediction with Protein Language Models

Jie Tang, Jinbo Xu, J. Qiu, 2022, bioRxiv.

When Geometric Deep Learning Meets Pretrained Protein Language Models

Dragomir R. Radev, Jinbo Xu, Fang Wu, 2022, bioRxiv.

Fast and accurate algorithms for protein side-chain packing

Bonnie Berger, Jinbo Xu, B. Berger, 2006, JACM.

Boosting Protein Threading Accuracy

Jian Peng, Jinbo Xu, Jian Peng, 2009, RECOMB.

Global alignment of multiple protein interaction networks with application to functional orthology detection

Bonnie Berger, Rohit Singh, Jinbo Xu, 2008, Proceedings of the National Academy of Sciences.

Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology

Bonnie Berger, Jinbo Xu, Rohit Singh, 2007, RECOMB.

Lynx: a database and knowledge extraction engine for integrative medicine

Sheng Wang, Bo Feng, Jinbo Xu, 2013, Nucleic Acids Res..

Inferential modeling of 3 D chromatin structure

Jinbo Xu, Jianyang Zeng, Jinbo Xu, 2015 .

Predicting the clinical impact of human mutation with deep neural networks

S. Batzoglou, Jinbo Xu, K. Farh, 2018, Nature Genetics.

Folding membrane proteins by deep transfer learning

Yizhou Yu, Sheng Wang, Jinbo Xu, 2017, bioRxiv.

Low-homology protein threading

Jian Peng, Jinbo Xu, Jian Peng, 2010, Bioinform..

A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants

Zhiyong Wang, Xinghua Shi, Jinbo Xu, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

CNVnet: combining sparse learning and biological networks to capture joint effect of copy number variants

Zhiyong Wang, Xinghua Shi, Jinbo Xu, 2014, BCB.

Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis

Michael H. Schwartz, Jinbo Xu, T. Pan, 2018, Nature Communications.

RaptorX-Property: a web server for protein structure property prediction

Wei Li, Sheng Wang, Jinbo Xu, 2016, Nucleic Acids Res..

PredMP: a web server for de novo prediction and visualization of membrane proteins

Feng Zhao, Yu Li, Xin Gao, 2018, Bioinform..

Protein threading using context-specific alignment potential

Feng Zhao, Sheng Wang, Jianzhu Ma, 2013, Bioinform..

Learning Scale-Free Networks by Dynamic Node Specific Degree Prior

Jinbo Xu, Qingming Tang, Siqi Sun, 2015, ICML.

Learning Scale Free Network by Node Specific Degree Prior pdf

Chao Yang, Jinbo Xu, Qingming Tang, 2015, ArXiv.

Improved protein structure prediction by deep learning irrespective of co-evolution information

Jinbo Xu, Jin Li, Matthew Mcpartlon, 2020, Nature Machine Intelligence.

Distance-based protein folding powered by deep learning

Jinbo Xu, 2018, Proceedings of the National Academy of Sciences.

Improved protein model quality assessment by integrating sequential and pairwise features using deep learning

Jinbo Xu, Xiaoyang Jing, Jinbo Xu, 2020, bioRxiv.

Accurate Protein Function Prediction via Graph Attention Networks with Predicted Structure Information

Jinbo Xu, Boqiao Lai, 2021, bioRxiv.

A Deep SE(3)-Equivariant Model for Learning Inverse Protein Folding

Jinbo Xu, Matthew McPartlon, Ben Lai, 2022, bioRxiv.

Analysis of distance‐based protein structure prediction by deep learning in CASP13

Jinbo Xu, Sheng Wang, Sheng Wang, 2019, Proteins.

Analysis of distance-based protein structure prediction by deep learning in CASP13

Jinbo Xu, Sheng Wang, Sheng Wang, 2019, bioRxiv.

ComplexContact: a web server for inter-protein contact prediction using deep learning

Qing Wu, Jinbo Xu, Hong Zeng, 2018, Nucleic Acids Res..

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Zhen Li, Sheng Wang, Jinbo Xu, 2016, bioRxiv.

Predicting protein‐protein interactions through sequence‐based deep learning

Behnam Neyshabur, Jinbo Xu, Aly A. Khan, 2018, Bioinform..

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields

Jian Peng, Sheng Wang, Jianzhu Ma, 2015, Scientific Reports.

Critical assessment of protein intrinsic disorder prediction

M. Y. Lobanov, David C. Jones, K. Paliwal, 2021, Nature Methods.

Raptorx: Exploiting structure information for protein alignment by statistical inference

Jinbo Xu, Jian Peng, Jian Peng, 2011, Proteins.

Network Inference by Learned Node-Specific Degree Prior pdf

Lifu Tu, Jinbo Xu, Weiran Wang, 2016, ArXiv.

Correction: An Integrative Computational Approach for Prioritization of Genomic Variants

T. Gilliam, N. Maltsev, Jianzhu Ma, 2015, PloS one.

An end-to-end deep learning method for rotamer-free protein side-chain packing

Jinbo Xu, Matthew McPartlon, 2022, bioRxiv.

Automated inference of Boolean models from molecular interaction maps using CaSQ

Anna Niarakis, Jinbo Xu, Vidisha Singh, 2020, Bioinform..

High-throughput translational medicine: challenges and solutions.

Inna Dubchak, Bhadrachalam Chitturi, Bo Feng, 2014, Advances in experimental medicine and biology.

A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling

Zhiyong Wang, Jinbo Xu, Jinbo Xu, 2011, Bioinform..

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Zhiyong Wang, Sheng Wang, Jianzhu Ma, 2014, PLoS Comput. Biol..

Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers

Sheng Wang, Xin Gao, Jinbo Xu, 2019, BCB.

Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers

Sheng Wang, Xin Gao, Jinbo Xu, 2019, BCB.

A tree-decomposition approach to protein structure prediction

Bonnie Berger, Feng Jiao, Jinbo Xu, 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

Protein 8-class secondary structure prediction using Conditional Neural Fields

Zhiyong Wang, Jinbo Xu, Feng Zhao, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling

Sheng Wang, Jinbo Xu, Siqi Sun, 2016, ECML/PKDD.

AUC-maximized Deep Convolutional Neural Fields for Sequence Labeling pdf

Sheng Wang, Jinbo Xu, Siqi Sun, 2015, ArXiv.

Rapid Protein Side-Chain Packing via Tree Decomposition

Jinbo Xu, Jinbo Xu, 2005, RECOMB.

Protein structure prediction using threading.

Jinbo Xu, Feng Jiao, Libo Yu, 2008, Methods in molecular biology.

Improving consensus contact prediction via server correlation reduction

Jinbo Xu, Dongbo Bu, Ming Li, 2009, BMC Structural Biology.

Designing succinct structural alphabets

Shuai Cheng Li, Xin Gao, Ming Li, 2008, ISMB.

Assessment of RAPTOR's linear programming approach in CAFASP3

Ming Li, Jinbo Xu, Ming Li, 2003, Proteins.

AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields

Sheng Wang, Jianzhu Ma, Jinbo Xu, 2016, Bioinform..

Predicting protein contact map using evolutionary and physical constraints by integer programming

Zhiyong Wang, Jinbo Xu, Jinbo Xu, 2013, Bioinform..

Fragment‐HMM: A new approach to protein structure prediction

Shuai Cheng Li, Ming Li, Dongbo Bu, 2008, Protein science : a publication of the Protein Society.

Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning

Zhiyong Wang, Sheng Wang, Jianzhu Ma, 2013, Bioinform..

FragQA: predicting local fragment quality of a sequence-structure alignment.

Shuai Cheng Li, Ming Li, Dongbo Bu, 2007, Genome informatics. International Conference on Genome Informatics.

Struct2Net: a web service to predict protein–protein interactions using a structure-based approach

Bonnie Berger, Jinbo Xu, Rohit Singh, 2010, Nucleic Acids Res..

Learning structured densities via infinite dimensional exponential families

Mladen Kolar, Jinbo Xu, Siqi Sun, 2015, NIPS.

Protein threading using residue co-variation and deep learning

Sheng Wang, Jinbo Xu, Dongbo Bu, 2018, Bioinform..

Lynx: a knowledge base and an analytical workbench for integrative medicine

Jinbo Xu, Dinanath Sulakhe, Natalia Maltsev, 2015, Nucleic Acids Res..

RaptorX-Single: single-sequence protein structure prediction by integrating protein language models

Jinbo Xu, Xiaoyang Jing, Fandi Wu, 2023, bioRxiv.

An Integrative Computational Approach for Prioritization of Genomic Variants

Inna Dubchak, Jianzhu Ma, Jinbo Xu, 2014, PloS one.

CoinFold: a web server for protein contact prediction and contact-assisted protein folding

Wei Li, Sheng Wang, Jinbo Xu, 2016, Nucleic Acids Res..

ISMB 2014 Proceedings Papers Committee

William Stafford Noble, Noah M. Daniels, D. Heckerman, 2014, Bioinformatics.

Analysis of deep learning methods for blind protein contact prediction in CASP12

Sheng Wang, Siqi Sun, Jinbo Xu, 2017, bioRxiv.

Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization

Jinbo Xu, Qixing Huang, Somaye Hashemifar, 2016, RECOMB.

InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems

Stan Z. Li, Jinbo Xu, Xianyuan Zhan, 2023, ArXiv.

The landscape of tolerated genetic variation in humans and primates.

Aashish N. Adhikari, S. Batzoglou, Martin Kuhlwilm, 2023, Science.

A Two-Graph Guided Multi-task Lasso Approach for eQTL Mapping

Xiaohui Chen, Xing Xu, Zhiyong Wang, 2012, AISTATS.

A multiple‐template approach to protein threading

Jinbo Xu, Jian Peng, Jian Peng, 2011, Proteins.

Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space

Zhiyong Wang, Xinghua Shi, Jinbo Xu, 2014, J. Comput. Biol..

Improved the heterodimer protein complex prediction with protein language models.

Jie Tang, Jinbo Xu, J. Qiu, 2023, Briefings in Bioinformatics.

RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning

Minghua Deng, Sheng Wang, Jinbo Xu, 2018, BMC Bioinformatics.

Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis

Sheng Wang, Jinbo Xu, Tian-Ming Zhou, 2017, bioRxiv.

Improving consensus contact prediction via server correlation reduction

Ming Li, Jinbo Xu, D. Bu, 2009, BMC Structural Biology.

Structure Learning Constrained by Node-Specific Degree Distribution

Feng Zhao, Jianzhu Ma, Jinbo Xu, 2015, UAI.

Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage

Jian Peng, Sheng Wang, Jianzhu Ma, 2015, BCB.

Bermuda: Bidirectional de novo assembly of transcripts with new insights for handling uneven coverage

Jianzhu Ma, Jinbo Xu, Sheng Wang, 2015, 1506.05538.

Critical assessment of protein intrinsic disorder prediction

Silvio C. E. Tosatto, Marco Necci, Damiano Piovesan, 2020, Nature Methods.

Approximate Inference by Intersecting Semidefinite Bound and Local Polytope

Tamir Hazan, Jian Peng, Nathan Srebro, 2012, AISTATS.

Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction

Bonnie Berger, Jinbo Xu, Rohit Singh, 2005, Pacific Symposium on Biocomputing.

A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning

Jinbo Xu, Sheng Wang, Xiaoyang Jing, 2020, Protein-Protein Interaction Networks.

Drug-target interaction prediction by integrating chemical, genomic, functional and pharmacological data.

Fan Yang, Jinbo Xu, Jianyang Zeng, 2013, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Integration of pre-trained protein language models into geometric deep learning networks

Dragomir R. Radev, Stan Z. Li, Jinbo Xu, 2023, Communications biology.

Deep Learning for Flexible and Site-Specific Protein Docking and Design

Jinbo Xu, Matthew McPartlon, 2023, bioRxiv.

RaptorX-Single: single-sequence protein structure prediction by integrating protein language models

Jinbo Xu, Xiaoyang Jing, Fandi Wu, 2023, bioRxiv.

Protein fold recognition using the gradient boost algorithm.

Dale Schuurmans, Jinbo Xu, Feng Jiao, 2006, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions.

Bonnie Berger, Jinbo Xu, Raghavendra Hosur, 2010, Journal of molecular biology.

PureseqTM: efficient and accurate prediction of transmembrane topology from amino acid sequence only

Renmin Han, Sheng Wang, Xin Gao, 2019, bioRxiv.

Folding Large Proteins by Ultra-Deep Learning

Jinbo Xu, Jinbo Xu, 2017, BCB.

Title: Analysis of distance-based protein structure prediction by deep learning in CASP13 Short Title: Deep learning for distance-based folding Authors:

Sheng Wang, Jinbo Xu, 2019 .

A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling

Feng Zhao, Jian Peng, Jinbo Xu, 2010, J. Comput. Biol..

Fragment-free approach to protein folding using conditional neural fields

Feng Zhao, Jian Peng, Jinbo Xu, 2010, Bioinform..

A Probabilistic Graphical Model for Ab Initio Folding

Feng Zhao, Jian Peng, Jinbo Xu, 2009, RECOMB.

Inferring Block Structure of Graphical Models in Exponential Families

Hai Wang, Jinbo Xu, Siqi Sun, 2015, AISTATS.

Improving protein structure prediction using templates and sequence embedding

Jinbo Xu, Xiaoyang Jing, Fandi Wu, 2022, Bioinform..

Fast and effective protein model refinement by deep graph neural networks

Jinbo Xu, Xiaoyang Jing, Jinbo Xu, 2020, bioRxiv.

Predicting Local Quality of a Sequence-Structure Alignment

Shuai Cheng Li, Xin Gao, Ming Li, 2009, J. Bioinform. Comput. Biol..

Discriminative learning for protein conformation sampling

Jinbo Xu, Feng Zhao, Shuaicheng Li, 2008, Proteins.

Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis

Sheng Wang, Jinbo Xu, Tian-Ming Zhou, 2017, bioRxiv.

CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins

Silvio C. E. Tosatto, M. Y. Lobanov, Md. Wasi Ul Kabir, 2023, Nucleic Acids Res..

AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields

Jianzhu Ma, Sheng Wang, Jinbo Xu, 2016, Bioinform..

An end-to-end deep learning method for protein side-chain packing and inverse folding

Jinbo Xu, Matthew McPartlon, 2023, Proceedings of the National Academy of Sciences of the United States of America.

Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling

Jian Peng, Sheng Wang, Jinbo Xu, 2011, Bioinform..

Graph algorithms for biological systems analysis

Bonnie Berger, Jinbo Xu, Rohit Singh, 2008, SODA '08.

Optimizing Multiple Spaced Seeds for Homology Search

Bin Ma, Daniel G. Brown, Ming Li, 2004, CPM.

Approximation algorithms for NMR spectral peak assignment

Zhi-Zhong Chen, Tao Jiang, Ying Xu, 2003, Theor. Comput. Sci..

Forecasting residue‐residue contact prediction accuracy

Malgorzata Kotulska, J. Xu, Gert Vriend, 2017, Bioinform..

Folding membrane proteins by deep transfer learning

Yizhou Yu, Sheng Wang, Jinbo Xu, 2017, bioRxiv.

Predicting membrane protein contacts from non-membrane proteins by deep transfer learning pdf

Zhen Li, Yizhou Yu, Sheng Wang, 2017, ArXiv.

Joint inference of tissue-specific networks with a scale free topology

Behnam Neyshabur, Jinbo Xu, Somaye Hashemifar, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).