Jinbo Xu
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Jinbo Xucomputer-science Degrees
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Computer Science
Jinbo Xu's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science Stanford University
- Bachelors Computer Science Tsinghua University
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(Suggest an Edit or Addition)Jinbo Xu's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Template-based protein structure modeling using the RaptorX web server (2012) (1475)
- Opportunities and obstacles for deep learning in biology and medicine (2017) (1310)
- Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model (2016) (729)
- Global alignment of multiple protein interaction networks with application to functional orthology detection (2008) (619)
- Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields (2015) (462)
- RaptorX-Property: a web server for protein structure property prediction (2016) (411)
- Raptorx: Exploiting structure information for protein alignment by statistical inference (2011) (342)
- Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology (2007) (328)
- Distance-based protein folding powered by deep learning (2018) (314)
- Raptor: Optimal Protein Threading by Linear Programming (2003) (271)
- RaptorX server: a resource for template-based protein structure modeling. (2014) (237)
- Predicting the clinical impact of human mutation with deep neural networks (2018) (227)
- Predicting protein‐protein interactions through sequence‐based deep learning (2018) (178)
- Conditional Neural Fields (2009) (171)
- Protein structure alignment beyond spatial proximity (2013) (151)
- Protein threading using context-specific alignment potential (2013) (139)
- Predicting protein contact map using evolutionary and physical constraints by integer programming (2013) (129)
- Protein 8-class secondary structure prediction using Conditional Neural Fields (2010) (125)
- Improved protein structure prediction by deep learning irrespective of co-evolution information (2020) (113)
- Struct2Net: a web service to predict protein–protein interactions using a structure-based approach (2010) (111)
- A multiple‐template approach to protein threading (2011) (109)
- HubAlign: an accurate and efficient method for global alignment of protein–protein interaction networks (2014) (108)
- Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning (2013) (105)
- ComplexContact: a web server for inter-protein contact prediction using deep learning (2018) (92)
- Rapid Protein Side-Chain Packing via Tree Decomposition (2005) (90)
- AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields (2016) (89)
- Analysis of deep learning methods for blind protein contact prediction in CASP12 (2017) (88)
- Low-homology protein threading (2010) (88)
- Fast and accurate algorithms for protein side-chain packing (2006) (87)
- Inferential modeling of 3D chromatin structure (2015) (83)
- A conditional neural fields model for protein threading (2012) (83)
- Global Alignment of Multiple Protein Interaction Networks (2007) (82)
- Analysis of distance‐based protein structure prediction by deep learning in CASP13 (2019) (78)
- MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014) (71)
- Folding membrane proteins by deep transfer learning (2017) (71)
- Optimizing Multiple Spaced Seeds for Homology Search (2004) (70)
- Boosting Protein Threading Accuracy (2009) (69)
- Fragment‐HMM: A new approach to protein structure prediction (2008) (68)
- Protein threading using residue co-variation and deep learning (2018) (67)
- Struct2Net: Integrating Structure into Protein-Protein Interaction Prediction (2005) (61)
- iWRAP: An interface threading approach with application to prediction of cancer-related protein-protein interactions. (2010) (59)
- A Two-Graph Guided Multi-task Lasso Approach for eQTL Mapping (2012) (58)
- Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling (2011) (56)
- CoinFold: a web server for protein contact prediction and contact-assisted protein folding (2016) (55)
- A tree-decomposition approach to protein structure prediction (2005) (55)
- Fold recognition by predicted alignment accuracy (2005) (54)
- A position-specific distance-dependent statistical potential for protein structure and functional study. (2012) (54)
- A Parameterized Algorithm for Protein Structure Alignment (2006) (52)
- Template‐based and free modeling by RAPTOR++ in CASP8 (2009) (48)
- A computational framework for boosting confidence in high-throughput protein-protein interaction datasets (2012) (46)
- Analysis of distance-based protein structure prediction by deep learning in CASP13 (2019) (46)
- Discriminative learning for protein conformation sampling (2008) (40)
- Fragment-free approach to protein folding using conditional neural fields (2010) (40)
- Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis (2018) (40)
- RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning (2018) (39)
- Protein Threading by Linear Programming (2002) (37)
- Lynx: a database and knowledge extraction engine for integrative medicine (2013) (36)
- ModuleAlign: module-based global alignment of protein-protein interaction networks (2016) (35)
- Automated inference of Boolean models from molecular interaction maps using CaSQ (2020) (33)
- Basic Local Alignment Search Tool (2020) (33)
- Protein structure prediction using threading. (2008) (32)
- Improving consensus contact prediction via server correlation reduction (2009) (31)
- Protein structure prediction enhanced with evolutionary diversity: SPEED (2010) (29)
- PredMP: a web server for de novo prediction and visualization of membrane proteins (2018) (28)
- Assessment of RAPTOR's linear programming approach in CAFASP3 (2003) (26)
- Learning structured densities via infinite dimensional exponential families (2015) (24)
- Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization (2016) (23)
- Modeling large regions in proteins: Applications to loops, termini, and folding (2012) (23)
- A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling (2010) (23)
- AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling (2016) (23)
- Drug-target interaction prediction by integrating chemical, genomic, functional and pharmacological data. (2013) (21)
- Fast and effective protein model refinement using deep graph neural networks (2021) (20)
- Protein Structure Prediction by Linear Programming (2003) (19)
- Approximation algorithms for NMR spectral peak assignment (2003) (17)
- Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis (2017) (17)
- Critical assessment of protein intrinsic disorder prediction (2021) (17)
- Designing succinct structural alphabets (2008) (17)
- A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling (2011) (16)
- Learning Scale-Free Networks by Dynamic Node Specific Degree Prior (2015) (16)
- Deep graph learning of inter-protein contacts (2021) (15)
- Peptide Antidotes to SARS-CoV-2 (COVID-19) (2020) (15)
- Deep template-based protein structure prediction (2020) (14)
- Finding Largest Well-Predicted Subset of Protein Structure Models (2008) (14)
- Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling (2013) (14)
- Study of Real-Valued Distance Prediction For Protein Structure Prediction with Deep Learning (2020) (14)
- Inferring Block Structure of Graphical Models in Exponential Families (2015) (13)
- Disease Gene Prioritization Using Network and Feature (2015) (13)
- Protein fold recognition using the gradient boost algorithm. (2006) (13)
- High-throughput translational medicine: challenges and solutions. (2014) (12)
- Improved protein model quality assessment by integrating sequential and pairwise features using deep learning (2020) (12)
- A Deep SE(3)-Equivariant Model for Learning Inverse Protein Folding (2022) (12)
- Protein Homology Detection Through Alignment of Markov Random Fields (2015) (12)
- Consensus fold recognition by predicted model quality (2005) (11)
- Graph algorithms for biological systems analysis (2008) (11)
- Accurate Protein Function Prediction via Graph Attention Networks with Predicted Structure Information (2021) (10)
- Adaptive Variable Clustering in Gaussian Graphical Models (2014) (10)
- FragQA: predicting local fragment quality of a sequence-structure alignment. (2007) (10)
- A Probabilistic Graphical Model for Ab Initio Folding (2009) (9)
- Protein Threading by Linear Programming: Theoretical Analysis and Computational Results (2004) (9)
- Approximate Inference by Intersecting Semidefinite Bound and Local Polytope (2012) (9)
- Finding compact structural motifs (2007) (8)
- Finding Nearly Optimal GDT Scores (2011) (8)
- A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning (2020) (8)
- Inferential modeling of 3 D chromatin structure (2015) (8)
- An Integrative Computational Approach for Prioritization of Genomic Variants (2014) (8)
- Lynx: a knowledge base and an analytical workbench for integrative medicine (2015) (7)
- Discovering Sequence-Structure Motifs from Protein Segments and Two Applications (2004) (7)
- PureseqTM: efficient and accurate prediction of transmembrane topology from amino acid sequence only (2019) (7)
- Fast and effective protein model refinement by deep graph neural networks (2020) (6)
- AUC-maximized Deep Convolutional Neural Fields for Sequence Labeling (2015) (6)
- Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning (2017) (6)
- iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition (2015) (5)
- An end-to-end deep learning method for rotamer-free protein side-chain packing (2022) (5)
- Predicting Local Quality of a Sequence-Structure Alignment (2009) (5)
- Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning (2022) (4)
- Rapid and Accurate Protein Side Chain Prediction with Local Backbone Information (2008) (4)
- Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space (2014) (4)
- ProALIGN: Directly learning alignments for protein structure prediction via exploiting context-specific alignment motifs (2020) (4)
- A Sparse Learning Framework for Joint Effect Analysis of Copy Number Variants (2017) (4)
- Speedup LP Approach to Protein Threading via Graph Reduction (2003) (4)
- Predicting membrane protein contacts from non-membrane proteins by deep transfer learning (2017) (4)
- XOR-CD: Linearly Convergent Constrained Structure Generation (2021) (3)
- Joint inference of tissue-specific networks with a scale free topology (2015) (3)
- Exact Hybrid Covariance Thresholding for Joint Graphical Lasso (2015) (3)
- De Novo Protein Structure Prediction by Big Data and Deep Learning (2017) (3)
- End-to-End deep structure generative model for protein design (2022) (3)
- Author Correction: Predicting the clinical impact of human mutation with deep neural networks (2018) (3)
- Consensus Approaches to Protein Structure Prediction (2008) (2)
- Structure Learning Constrained by Node-Specific Degree Distribution (2015) (2)
- Protein contact prediction by joint evolutionary coupling analysis across multiple families (2013) (2)
- FragQA: predicting local fragment quality of a sequence-structure alignment (2007) (2)
- Improved the Protein Complex Prediction with Protein Language Models (2022) (2)
- A computational framework for boosting confidence in high-throughput protein-protein interaction datasets (2012) (1)
- CNVnet: combining sparse learning and biological networks to capture joint effect of copy number variants (2014) (1)
- Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers (2019) (1)
- Computational Methods for Protein–Protein Interaction Network Alignment (2021) (1)
- When Geometric Deep Learning Meets Pretrained Protein Language Models (2022) (1)
- Solving the contact map overlap problem via tree decomposition and a DEE-like pruning strategy (2007) (1)
- Folding Large Proteins by Ultra-Deep Learning (2017) (1)
- ISMB 2014 Proceedings Papers Committee (2014) (1)
- Learning Scale Free Network by Node Specific Degree Prior (2015) (1)
- Predicting Epigenomic Functions of Genetic Variants in the Context of Neurodevelopment via Deep Transfer Learning (2021) (1)
- Learning Networks by Node Specific Degree Prior (2015) (1)
- A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction (2021) (1)
- Deep Learning for Flexible and Site-Specific Protein Docking and Design (2023) (1)
- Efficient fragment-free approach to protein folding (2010) (0)
- A multiple-template approach for protein threading (2011) (0)
- Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage (2015) (0)
- Title: Analysis of distance-based protein structure prediction by deep learning in CASP13 Short Title: Deep learning for distance-based folding Authors: (2019) (0)
- Faculty Opinions recommendation of Protein homology model refinement by large-scale energy optimization. (2019) (0)
- Deep ResNet models for template-free protein modeling (2021) (0)
- Opportunities and obstacles for deep learning in biology and medicine [update in progress] (2020) (0)
- RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning (2018) (0)
- Predicting diverse M-best protein contact maps (2015) (0)
- Supplementary Material for “ RaptorX-Angle : real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning ” (2017) (0)
- The training data set for the deep ResNet models used by RaptorX-3DModeling (2021) (0)
- predicted contacts and 3D models of 510 non-redundant membrane proteins with solved structures in PDBTM (2017) (0)
- Approximate Inference by Intersecting Semidenite Bound and (2012) (0)
- Joint Multi-family Evolutionary Coupling Analysis for Protein Contact Prediction (2013) (0)
- Analysis of tissue-specific co-expression networks (2014) (0)
- Correction: An Integrative Computational Approach for Prioritization of Genomic Variants (2015) (0)
- Network Inference by Learned Node-Specific Degree Prior (2016) (0)
- Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis (2018) (0)
- RaptorX-Single: single-sequence protein structure prediction by integrating protein language models (2023) (0)
- 1 Supplement : iWRAP : An interface threading approach for protein-protein interaction prediction (2010) (0)
- 3DCOMB: Alignment of distantly-related protein structures (2011) (0)
- InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems (2023) (0)
- D ec 2 01 7 Real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning (2017) (0)
- Improving protein structure prediction using templates and sequence embedding (2022) (0)
- Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers (2019) (0)
- Bermuda: Bidirectional de novo assembly of transcripts with new insights for handling uneven coverage (2015) (0)
- Opportunities and obstacles for deep learning in biology and medicine: 2019 update (2019) (0)
- Author Correction: Predicting the clinical impact of human mutation with deep neural networks (2018) (0)
- PALM: Probabilistic area loss Minimization for Protein Sequence Alignment (2021) (0)
- Rapid and Accurate Protein Side Chain Prediction Using Local Backbone Information Only (2007) (0)
- Predicting the clinical impact of human mutation with deep neural networks (2018) (0)
- Folding Membrane Proteins by Contacts Inferred from Non-Membrane Proteins and Near-Atomic Level Refinement (2017) (0)
- Finding Compact Structural Motifs in Many Proteins (2009) (0)
- Consensus contact prediction by linear programming. (2007) (0)
- BIOINFORMATICS Designing succinct structural alphabets (2008) (0)
- Protein sequence labelling by AUC-maximized Deep Convolutional Neural Fields (2015) (0)
- Workshop for Protein Complexes and Quantitative Proteomics: Theory, Computation and Experiment 蛋白质复合物和定量蛋白质组学: 理论、计算与实验研讨会 (2020) (0)
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What Schools Are Affiliated With Jinbo Xu?
Jinbo Xu is affiliated with the following schools:
