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Recent Deep Learning Methodology Development for RNA–RNA Interaction Prediction.
- Published in:
- Symmetry (20738994), 2022, v. 14, n. 7, p. N.PAG, doi. 10.3390/sym14071302
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- Publication type:
- Article
A Non-homogeneous Firefly Algorithm and Its Convergence Analysis.
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- Journal of Optimization Theory & Applications, 2016, v. 170, n. 2, p. 616, doi. 10.1007/s10957-016-0875-4
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- Publication type:
- Article
Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy.
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- International Journal of Molecular Sciences, 2021, v. 22, n. 9, p. 4408, doi. 10.3390/ijms22094408
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- Publication type:
- Article
RBPsuite: RNA-protein binding sites prediction suite based on deep learning.
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- BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-07291-6
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- Publication type:
- Article
Prediction of Protein-Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures.
- Published in:
- 2016
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- Publication type:
- journal article
TargetFreeze: Identifying Antifreeze Proteins via a Combination of Weights using Sequence Evolutionary Information and Pseudo Amino Acid Composition.
- Published in:
- 2015
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- Publication type:
- journal article
MINDG: a drug–target interaction prediction method based on an integrated learning algorithm.
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- Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae147
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- Publication type:
- Article
MLNGCF: circRNA–disease associations prediction with multilayer attention neural graph-based collaborative filtering.
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- Bioinformatics, 2023, v. 39, n. 8, p. 1, doi. 10.1093/bioinformatics/btad499
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- Publication type:
- Article
De novo drug design by iterative multiobjective deep reinforcement learning with graph-based molecular quality assessment.
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- Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad157
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- Publication type:
- Article
GraphLoc: a graph neural network model for predicting protein subcellular localization from immunohistochemistry images.
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- Bioinformatics, 2022, v. 38, n. 21, p. 4941, doi. 10.1093/bioinformatics/btac634
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- Publication type:
- Article
CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.
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- Bioinformatics, 2022, v. 38, n. 3, p. 720, doi. 10.1093/bioinformatics/btab744
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- Publication type:
- Article
Accurate inference of gene regulatory interactions from spatial gene expression with deep contrastive learning.
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- Bioinformatics, 2022, v. 38, n. 3, p. 746, doi. 10.1093/bioinformatics/btab718
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- Publication type:
- Article
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning.
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- Bioinformatics, 2021, v. 37, n. 16, p. 2308, doi. 10.1093/bioinformatics/btab127
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- Publication type:
- Article
TFvelo: gene regulation inspired RNA velocity estimation.
- Published in:
- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-45661-w
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- Publication type:
- Article
ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43597-1
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- Publication type:
- Article
A New Supervised Over-Sampling Algorithm with Application to Protein-Nucleotide Binding Residue Prediction.
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- PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0107676
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- Publication type:
- Article
Revealing the Hidden Relationship by Sparse Modules in Complex Networks with a Large-Scale Analysis.
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- PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0066020
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- Publication type:
- Article
Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade.
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- Proteins, 2016, v. 84, p. 233, doi. 10.1002/prot.24918
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- Publication type:
- Article
Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.
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- Proteins, 2016, v. 84, p. 76, doi. 10.1002/prot.24930
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- Publication type:
- Article
Improving accuracy of protein contact prediction using balanced network deconvolution.
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- Proteins, 2015, v. 83, n. 3, p. 485, doi. 10.1002/prot.24744
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- Publication type:
- Article
LabCaS: Labeling calpain substrate cleavage sites from amino acid sequence using conditional random fields.
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- Proteins, 2013, v. 81, n. 4, p. 622, doi. 10.1002/prot.24217
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- Publication type:
- Article
Large-scale plant protein subcellular location prediction.
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- Journal of Cellular Biochemistry, 2007, v. 100, n. 3, p. 665, doi. 10.1002/jcb.21096
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- Publication type:
- Article
TargetCrys: protein crystallization prediction by fusing multi-view features with two-layered SVM.
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- Amino Acids, 2016, v. 48, n. 11, p. 2533, doi. 10.1007/s00726-016-2274-4
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- Publication type:
- Article
Learning protein multi-view features in complex space.
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- Amino Acids, 2013, v. 44, n. 5, p. 1365, doi. 10.1007/s00726-013-1472-6
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- Publication type:
- Article
SOMPNN: an efficient non-parametric model for predicting transmembrane helices.
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- Amino Acids, 2012, v. 42, n. 6, p. 2195, doi. 10.1007/s00726-011-0959-2
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- Publication type:
- Article
Fast protein structure comparison through effective representation learning with contrastive graph neural networks.
- Published in:
- PLoS Computational Biology, 2022, v. 18, n. 3, p. 1, doi. 10.1371/journal.pcbi.1009986
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- Publication type:
- Article
High-accuracy protein model quality assessment using attention graph neural networks.
- Published in:
- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbac614
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- Publication type:
- Article
Leveraging scaffold information to predict protein–ligand binding affinity with an empirical graph neural network.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac603
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- Publication type:
- Article
MDGF-MCEC: a multi-view dual attention embedding model with cooperative ensemble learning for CircRNA-disease association prediction.
- Published in:
- Briefings in Bioinformatics, 2022, v. 23, n. 5, p. 1, doi. 10.1093/bib/bbac289
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- Publication type:
- Article
Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning.
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- Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbac026
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- Publication type:
- Article
SIFLoc: a self-supervised pre-training method for enhancing the recognition of protein subcellular localization in immunofluorescence microscopic images.
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- Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab605
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- Publication type:
- Article
Learning protein subcellular localization multi-view patterns from heterogeneous data of imaging, sequence and networks.
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- Briefings in Bioinformatics, 2022, v. 23, n. 2, p. 1, doi. 10.1093/bib/bbab539
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- Publication type:
- Article
circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier.
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- Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab394
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- Publication type:
- Article
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network.
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- Briefings in Bioinformatics, 2021, v. 22, n. 6, p. 1, doi. 10.1093/bib/bbab279
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- Publication type:
- Article
RNA-binding protein recognition based on multi-view deep feature and multi-label learning.
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- Briefings in Bioinformatics, 2021, v. 22, n. 3, p. 1, doi. 10.1093/bib/bbaa174
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- Publication type:
- Article
Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks.
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- BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4889-1
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- Publication type:
- Article
Semantic-Based Implicit Feature Transform for Few-Shot Classification.
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- International Journal of Computer Vision, 2024, v. 132, n. 11, p. 5014, doi. 10.1007/s11263-024-02113-8
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- Publication type:
- Article
AttSiOff: a self-attention-based approach on siRNA design with inhibition and off-target effect prediction.
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- Med-X, 2024, v. 2, n. 1, p. 1, doi. 10.1007/s44258-024-00019-1
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- Publication type:
- Article
Improving segmentation and classification of renal tumors in small sample 3D CT images using transfer learning with convolutional neural networks.
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- International Journal of Computer Assisted Radiology & Surgery, 2022, v. 17, n. 7, p. 1303, doi. 10.1007/s11548-022-02587-2
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- Publication type:
- Article
Virus-PLoc: A fusion classifier for predicting the subcellular localization of viral proteins within host and virus-infected cells.
- Published in:
- Biopolymers, 2007, v. 85, n. 3, p. 233, doi. 10.1002/bip.20640
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- Publication type:
- Article
Incorporating label correlations into deep neural networks to classify protein subcellular location patterns in immunohistochemistry images.
- Published in:
- Proteins, 2022, v. 90, n. 2, p. 493, doi. 10.1002/prot.26244
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- Publication type:
- Article
Consistency and variation of protein subcellular location annotations.
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- Proteins, 2021, v. 89, n. 2, p. 242, doi. 10.1002/prot.26010
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- Publication type:
- Article
Predicting gene regulatory interactions based on spatial gene expression data and deep learning.
- Published in:
- PLoS Computational Biology, 2019, v. 15, n. 9, p. 1, doi. 10.1371/journal.pcbi.1007324
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- Publication type:
- Article
ToxDL: deep learning using primary structure and domain embeddings for assessing protein toxicity.
- Published in:
- Bioinformatics, 2020, v. 36, n. 21, p. 5159, doi. 10.1093/bioinformatics/btaa656
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- Publication type:
- Article
Protein–ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data.
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- Bioinformatics, 2020, v. 36, n. 10, p. 3018, doi. 10.1093/bioinformatics/btaa110
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- Publication type:
- Article
ImPLoc: a multi-instance deep learning model for the prediction of protein subcellular localization based on immunohistochemistry images.
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- Bioinformatics, 2020, v. 36, n. 7, p. 2244, doi. 10.1093/bioinformatics/btz909
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- Publication type:
- Article
Learning complex subcellular distribution patterns of proteins via analysis of immunohistochemistry images.
- Published in:
- Bioinformatics, 2020, v. 36, n. 6, p. 1908, doi. 10.1093/bioinformatics/btz844
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- Publication type:
- Article
Artificial intelligence-based multi-objective optimization protocol for protein structure refinement.
- Published in:
- Bioinformatics, 2020, v. 36, n. 2, p. 437, doi. 10.1093/bioinformatics/btz544
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- Publication type:
- Article
AnnoFly: annotating Drosophila embryonic images based on an attention-enhanced RNN model.
- Published in:
- Bioinformatics, 2019, v. 35, n. 16, p. 2834, doi. 10.1093/bioinformatics/bty1064
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- Publication type:
- Article
Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks.
- Published in:
- Bioinformatics, 2018, v. 34, n. 20, p. 3427, doi. 10.1093/bioinformatics/bty364
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- Publication type:
- Article