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Modeling and analyzing single-cell multimodal data with deep parametric inference.
- Published in:
- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbad005
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Correction to: VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.
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- 2023
- Publication type:
- Correction Notice
Integrated mRNA sequence optimization using deep learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbad001
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Prediction of anticancer peptides based on an ensemble model of deep learning and machine learning using ordinal positional encoding.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac630
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Tracing human life trajectory using gut microbial communities by context-aware deep learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac629
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- Article
Reducing false positive rate of docking-based virtual screening by active learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac626
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scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac625
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- Article
A novel strategy for designing the magic shotguns for distantly related target pairs.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac621
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GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac620
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Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac619
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- Article
Comparative epigenome analysis using Infinium DNA methylation BeadChips.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac617
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- Article
Correction to: siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers.
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- 2023
- Publication type:
- Correction Notice
A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac616
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Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac609
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Benchmarking of computational methods for predicting circRNA-disease associations.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac613
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Systematic benchmarking of statistical methods to assess differential expression of circular RNAs.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac612
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A comparison between similarity matrices for principal component analysis to assess population stratification in sequenced genetic data sets.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac611
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- Article
slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac610
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- Article
Computational model for disease research.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac615
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- Article
Structure-preserved dimension reduction using joint triplets sampling for multi-batch integration of single-cell transcriptomic data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac608
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- Article
Benchmarking differential abundance analysis methods for correlated microbiome sequencing data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac607
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- Article
A social theory-enhanced graph representation learning framework for multitask prediction of drug–drug interactions.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac602
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A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac605
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Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac599
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- 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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- Article
AFP-MFL: accurate identification of antifungal peptides using multi-view feature learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac606
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- Article
From SNP to pathway-based GWAS meta-analysis: do current meta-analysis approaches resolve power and replication in genetic association studies?
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac600
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- Article
To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac594
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- Article
Logistic tensor decomposition with sparse subspace learning for prediction of multiple disease types of human–virus protein–protein interactions.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac604
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- Article
DSN-DDI: an accurate and generalized framework for drug–drug interaction prediction by dual-view representation learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac597
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- Article
Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac596
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- Article
Predicting lncRNA–disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac595
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- Article
Deleterious synonymous mutation identification based on selective ensemble strategy.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac598
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- Article
Discovery of fusion circular RNAs in leukemia with KMT2A::AFF1 rearrangements by the new software CircFusion.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac589
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- Article
An evolution-based machine learning to identify cancer type-specific driver mutations.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac593
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- Article
bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac591
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- Article
SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac590
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- Article
Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac587
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- Article
CCSynergy: an integrative deep-learning framework enabling context-aware prediction of anti-cancer drug synergy.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac588
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- Publication type:
- Article
Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac592
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- Article
Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac586
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- Publication type:
- Article
scGMAAE: Gaussian mixture adversarial autoencoders for diversification analysis of scRNA-seq data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac585
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- Article
SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac584
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- Article
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac583
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- Article
CODA: a combo-Seq data analysis workflow.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac582
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- Article
RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac581
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- Article
Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac580
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- Article
LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac579
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- Article
Metapath-aggregated heterogeneous graph neural network for drug–target interaction prediction.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac578
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- Publication type:
- Article
Identification of vital chemical information via visualization of graph neural networks.
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- Briefings in Bioinformatics, 2023, v. 24, n. 1, p. 1, doi. 10.1093/bib/bbac577
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- Article