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DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences.
- Published in:
- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad095
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AMHMDA: attention aware multi-view similarity networks and hypergraph learning for miRNA–disease associations identification.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad094
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- Article
Correction to: kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes.
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- 2023
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- Correction Notice
Identification of significant gene expression changes in multiple perturbation experiments using knockoffs.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad084
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MCANet: shared-weight-based MultiheadCrossAttention network for drug–target interaction prediction.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad082
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MHTAN-DTI: Metapath-based hierarchical transformer and attention network for drug–target interaction prediction.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad079
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- Article
Protein phosphorylation database and prediction tools.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad090
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- Article
GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad092
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IMperm: a fast and comprehensive IMmune Paired-End Reads Merger for sequencing data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad080
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- Article
Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad050
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- Article
Correction to: mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences.
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- 2023
- Publication type:
- Correction Notice
miWords: transformer-based composite deep learning for highly accurate discovery of pre-miRNA regions across plant genomes.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad088
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Benchmarking genome assembly methods on metagenomic sequencing data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad087
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TEINet: a deep learning framework for prediction of TCR–epitope binding specificity.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad086
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Fine-grained selective similarity integration for drug–target interaction prediction.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad085
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- Article
Auto-Kla: a novel web server to discriminate lysine lactylation sites using automated machine learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad070
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- Article
NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad077
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- Article
Machine learning on protein–protein interaction prediction: models, challenges and trends.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad076
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- Article
Correction to: Prediction of transcript structure and concentration using RNA-Seq data.
- Published in:
- 2023
- Publication type:
- Correction Notice
A comprehensive review of bioinformatics tools for chromatin loop calling.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad072
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- Article
Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad060
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- Article
PROSE: phenotype-specific network signatures from individual proteomic samples.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad075
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- Article
iATMEcell: identification of abnormal tumor microenvironment cells to predict the clinical outcomes in cancer based on cell–cell crosstalk network.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad074
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- Article
Integrative analysis of multi-omics and imaging data with incorporation of biological information via structural Bayesian factor analysis.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad073
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- Article
STEEL enables high-resolution delineation of spatiotemporal transcriptomic data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad068
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- Article
Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad071
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- Article
Collaborative deep learning improves disease-related circRNA prediction based on multi-source functional information.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad069
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- Article
DRdriver: identifying drug resistance driver genes using individual-specific gene regulatory network.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad066
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- Article
Development of a TMErisk model based on immune infiltration in tumour microenvironment to predict prognosis of immune checkpoint inhibitor treatment in hepatocellular carcinoma.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad067
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- Article
Identification of metal ion-binding sites in RNA structures using deep learning method.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad049
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- Article
MDBuilder: a PyMOL plugin for the preparation of molecular dynamics simulations.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad057
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- Article
FAMetA: a mass isotopologue-based tool for the comprehensive analysis of fatty acid metabolism.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad064
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- Article
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad063
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- Article
scSTAR reveals hidden heterogeneity with a real-virtual cell pair structure across conditions in single-cell RNA sequencing data.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad062
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- Article
IBRAP: integrated benchmarking single-cell RNA-sequencing analytical pipeline.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad061
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- Article
Designing antimicrobial peptides using deep learning and molecular dynamic simulations.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad058
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- Article
Lesion Shedding Model: unraveling site-specific contributions to ctDNA.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad059
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- Article
Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad027
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- Article
Caution towards spurious off-target signal in 10X Visium spatial transcriptomics assay from potential lncRNAs.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad031
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- Article
Comprehensive assessment of nine target prediction web services: which should we choose for target fishing?
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad014
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- Article
A computational framework of routine test data for the cost-effective chronic disease prediction.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad054
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- Article
The repertoire of copy number alteration signatures in human cancer.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad053
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- Publication type:
- Article
PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad052
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- Article
FungiExpresZ: an intuitive package for fungal gene expression data analysis, visualization and discovery.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad051
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- Article
netANOVA: novel graph clustering technique with significance assessment via hierarchical ANOVA.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad029
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- Article
SMURF: embedding single-cell RNA-seq data with matrix factorization preserving self-consistency.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad026
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- Article
Identifying spatial domain by adapting transcriptomics with histology through contrastive learning.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad048
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- Article
Dockey: a modern integrated tool for large-scale molecular docking and virtual screening.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad047
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- Article
Persistent Tor-algebra for protein–protein interaction analysis.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad046
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- Publication type:
- Article
scGAD: a new task and end-to-end framework for generalized cell type annotation and discovery.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad045
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- Article