Jianlin Cheng
Orcid: 0000-0003-0305-2853
According to our database1,
Jianlin Cheng
authored at least 105 papers
between 2004 and 2024.
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Bibliography
2024
Bioinform., February, 2024
2023
Single-cell Hi-C data enhancement with deep residual and generative adversarial networks.
Bioinform., August, 2023
Predicted structural proteome of <i>Sphagnum divinum</i> and proteome-scale annotation.
Bioinform., August, 2023
CAID prediction portal: a comprehensive service for predicting intrinsic disorder and binding regions in proteins.
Nucleic Acids Res., July, 2023
Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer.
Bioinform., May, 2023
Bioinform., January, 2023
Efficient Acceleration of Deep Learning Inference on Resource-Constrained Edge Devices: A Review.
Proc. IEEE, 2023
Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs.
CoRR, 2023
Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action.
CoRR, 2023
A gated graph transformer for protein complex structure quality assessment and its performance in CASP15.
Bioinform., 2023
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function.
Bioinform., 2023
Proceedings of the International Conference on Machine Learning and Applications, 2023
Towards a Domain-Agnostic Knowledge Graph-as-a-Service Infrastructure for Active Cyber Defense with Intelligent Agents.
Proceedings of the 52nd IEEE Applied Imagery Pattern Recognition Workshop, 2023
2022
Deep learning for reconstructing protein structures from cryo-EM density maps: recent advances and future directions.
CoRR, 2022
Deep Learning Prediction of Severe Health Risks for Pediatric COVID-19 Patients with a Large Feature Set in 2021 BARDA Data Challenge.
CoRR, 2022
DRLComplex: Reconstruction of protein quaternary structures using deep reinforcement learning.
CoRR, 2022
CoRR, 2022
CoRR, 2022
Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps.
BMC Bioinform., 2022
DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network.
BMC Bioinform., 2022
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction.
BMC Bioinform., 2022
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers.
Bioinform., 2022
Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions.
Briefings Bioinform., 2022
Machine Learning Embedded Smartphone Application for Early-Stage Diabetes Risk Assessment.
Proceedings of the IEEE International Symposium on Medical Measurements and Applications, 2022
Proceedings of the Tenth International Conference on Learning Representations, 2022
2021
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction.
CoRR, 2021
Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network.
BMC Bioinform., 2021
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network.
BMC Bioinform., 2021
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks.
BMC Bioinform., 2021
Bioinform., 2021
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function.
Proceedings of the IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments, 2021
2020
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM.
BMC Bioinform., 2020
Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction.
BMC Bioinform., 2020
Analysis of several key factors influencing deep learning-based inter-residue contact prediction.
Bioinform., 2020
CATA++: A Collaborative Dual Attentive Autoencoder Method for Recommending Scientific Articles.
IEEE Access, 2020
Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020
2019
AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images.
BMC Bioinform., 2019
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure.
Bioinform., 2019
PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects.
Bioinform., 2019
Proceedings of the 18th IEEE International Conference On Machine Learning And Applications, 2019
Protein Tertiary Structure Modeling Driven by Deep Learning and Contact Distance Prediction in CASP13.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019
2018
BMC Bioinform., 2018
Bioinform., 2018
DNCON2: improved protein contact prediction using two-level deep convolutional neural networks.
Bioinform., 2018
DeepHCF: A Deep Learning Based Hybrid Collaborative Filtering Approach for Recommendation Systems.
Proceedings of the 17th IEEE International Conference on Machine Learning and Applications, 2018
Proceedings of the 17th IEEE International Conference on Machine Learning and Applications, 2018
Proceedings of the 11th International Conference on Developments in eSystems Engineering, 2018
2017
ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.
BMC Bioinform., 2017
Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts.
BMC Bioinform., 2017
QAcon: single model quality assessment using protein structural and contact information with machine learning techniques.
Bioinform., 2017
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017
2016
Nucleic Acids Res., 2016
DeepQA: improving the estimation of single protein model quality with deep belief networks.
BMC Bioinform., 2016
BMC Bioinform., 2016
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data.
Bioinform., 2016
UniCon3D: <i>de novo</i> protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.
Bioinform., 2016
Bioinform., 2016
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016
2015
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods.
EURASIP J. Bioinform. Syst. Biol., 2015
Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.
BMC Bioinform., 2015
A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11.
BMC Bioinform., 2015
Large-scale model quality assessment for improving protein tertiary structure prediction.
Bioinform., 2015
From gigabyte to kilobyte: a bioinformatics protocol for mining large RNA-Seq transcriptomics data.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015
MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction.
Proceedings of the 6th ACM Conference on Bioinformatics, 2015
2014
Enhancing HMM-based protein profile-profile alignment with structural features and evolutionary coupling information.
BMC Bioinform., 2014
SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.
BMC Bioinform., 2014
2013
Predicting gene regulatory networks of soybean nodulation from RNA-Seq transcriptome data.
BMC Bioinform., 2013
Three-Level Prediction of Protein Function by Combining Profile-Sequence Search, Profile-Profile Search, and Domain Co-Occurrence Networks.
BMC Bioinform., 2013
A study and benchmark of DNcon: a method for protein residue-residue contact prediction using deep networks.
BMC Bioinform., 2013
BMC Bioinform., 2013
Automated protein structure refinement using i3Drefine software and its assessment in CASP10.
Proceedings of the ACM Conference on Bioinformatics, 2013
Proceedings of the ACM Conference on Bioinformatics, 2013
2012
Recursive protein Modeling: a Divide and Conquer Strategy for protein Structure Prediction and its Case Study in CASP9.
J. Bioinform. Comput. Biol., 2012
BMC Genom., 2012
Bioinform., 2012
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012
2011
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning.
BMC Bioinform., 2011
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts.
BMC Bioinform., 2011
Bioinform., 2011
2010
BMC Bioinform., 2010
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8.
Bioinform., 2010
2009
Nucleic Acids Res., 2009
BMC Bioinform., 2009
Sequence-Based Prediction of Protein Folding Rates Using Contacts, Secondary Structures and Support Vector Machines.
Proceedings of the 2009 IEEE International Conference on Bioinformatics and Biomedicine, 2009
2008
TMBpro: secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins.
Bioinform., 2008
Proceedings of the International Joint Conference on Neural Networks, 2008
2007
Nucleic Acids Res., 2007
Improved residue contact prediction using support vector machines and a large feature set.
BMC Bioinform., 2007
HHMMVE: A Visual Editor for Profile Hidden Markov Model.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2007
2006
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006
DOMpro: Protein Domain Prediction Using Profiles, Secondary Structure, Relative Solvent Accessibility, and Recursive Neural Networks.
Data Min. Knowl. Discov., 2006
Bioinform., 2006
2005
Nucleic Acids Res., 2005
IEEE Intell. Syst., 2005
Data Min. Knowl. Discov., 2005
Three-stage prediction of protein ?-sheets by neural networks, alignments and graph algorithms.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005
2004
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004