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Volume 25, Issue 1, January 2024
A granularity-level information fusion strategy on hypergraph transformer for predicting synergistic effects of anticancer drugs
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad522, https://doi.org/10.1093/bib/bbad522
sRNAfrag: a pipeline and suite of tools to analyze fragmentation in small RNA sequencing data
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad515, https://doi.org/10.1093/bib/bbad515
MHCLMDA: multihypergraph contrastive learning for miRNA–disease association prediction
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad524, https://doi.org/10.1093/bib/bbad524
From data to diagnosis: how machine learning is revolutionizing biomarker discovery in idiopathic inflammatory myopathies
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad514, https://doi.org/10.1093/bib/bbad514
Articles
Evidential deep learning for trustworthy prediction of enzyme commission number
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad401, https://doi.org/10.1093/bib/bbad401
CellGO: a novel deep learning-based framework and webserver for cell-type-specific gene function interpretation
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad417, https://doi.org/10.1093/bib/bbad417
FormulationAI: a novel web-based platform for drug formulation design driven by artificial intelligence
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad419, https://doi.org/10.1093/bib/bbad419
Transfer learning for clustering single-cell RNA-seq data crossing-species and batch, case on uterine fibroids
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad426, https://doi.org/10.1093/bib/bbad426
Assessing protein model quality based on deep graph coupled networks using protein language model
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad420, https://doi.org/10.1093/bib/bbad420
Identifying phenotype-associated subpopulations through LP_SGL
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad424, https://doi.org/10.1093/bib/bbad424
Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad432, https://doi.org/10.1093/bib/bbad432
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad425, https://doi.org/10.1093/bib/bbad425
Identifying the potential miRNA biomarkers based on multi-view networks and reinforcement learning for diseases
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad427, https://doi.org/10.1093/bib/bbad427
Characterization on the oncogenic effect of the missense mutations of p53 via machine learning
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad428, https://doi.org/10.1093/bib/bbad428
Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad429, https://doi.org/10.1093/bib/bbad429
Drug repositioning based on weighted local information augmented graph neural network
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad431, https://doi.org/10.1093/bib/bbad431
BatmanNet: bi-branch masked graph transformer autoencoder for molecular representation
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad400, https://doi.org/10.1093/bib/bbad400
VirusHound-I: prediction of viral proteins involved in the evasion of host adaptive immune response using the random forest algorithm and generative adversarial network for data augmentation
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad434, https://doi.org/10.1093/bib/bbad434
A benchmark study on current GWAS models in admixed populations
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad437, https://doi.org/10.1093/bib/bbad437
Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad379, https://doi.org/10.1093/bib/bbad379
Integrating somatic mutation profiles with structural deep clustering network for metabolic stratification in pancreatic cancer: a comprehensive analysis of prognostic and genomic landscapes
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad430, https://doi.org/10.1093/bib/bbad430
KGDiff: towards explainable target-aware molecule generation with knowledge guidance
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad435, https://doi.org/10.1093/bib/bbad435
Accurate TCR-pMHC interaction prediction using a BERT-based transfer learning method
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad436, https://doi.org/10.1093/bib/bbad436
MESPool: Molecular Edge Shrinkage Pooling for hierarchical molecular representation learning and property prediction
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad423, https://doi.org/10.1093/bib/bbad423
VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad444, https://doi.org/10.1093/bib/bbad444
iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad443, https://doi.org/10.1093/bib/bbad443
Using the PharmCAT tool for Pharmacogenetic clinical decision support
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad452, https://doi.org/10.1093/bib/bbad452
Advancing the accuracy of SARS-CoV-2 phosphorylation site detection via meta-learning approach
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad433, https://doi.org/10.1093/bib/bbad433
A transformer-based genomic prediction method fused with knowledge-guided module
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad438, https://doi.org/10.1093/bib/bbad438
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad440, https://doi.org/10.1093/bib/bbad440
Robust knowledge-guided biclustering for multi-omics data
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad446, https://doi.org/10.1093/bib/bbad446
CellTICS: an explainable neural network for cell-type identification and interpretation based on single-cell RNA-seq data
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad449, https://doi.org/10.1093/bib/bbad449
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad441, https://doi.org/10.1093/bib/bbad441
RMTLysPTM: recognizing multiple types of lysine PTM sites by deep analysis on sequences
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad450, https://doi.org/10.1093/bib/bbad450
ICBcomb: a comprehensive expression database for immune checkpoint blockade combination therapy
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad457, https://doi.org/10.1093/bib/bbad457
scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad447, https://doi.org/10.1093/bib/bbad447
WSGMB: weight signed graph neural network for microbial biomarker identification
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad448, https://doi.org/10.1093/bib/bbad448
Multi-task bioassay pre-training for protein-ligand binding affinity prediction
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad451, https://doi.org/10.1093/bib/bbad451
Response to the letter ‘testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis’
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad454, https://doi.org/10.1093/bib/bbad454
Clustering malignant cell states using universally variable genes
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad460, https://doi.org/10.1093/bib/bbad460
Differentiable rotamer sampling with molecular force fields
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad456, https://doi.org/10.1093/bib/bbad456
GAABind: a geometry-aware attention-based network for accurate protein–ligand binding pose and binding affinity prediction
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad462, https://doi.org/10.1093/bib/bbad462
MSIpixel: a fully automated pipeline for compound annotation and quantitation in mass spectrometry imaging experiments
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad463, https://doi.org/10.1093/bib/bbad463
CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad380, https://doi.org/10.1093/bib/bbad380
Model-based evaluation of spatiotemporal data reduction methods with unknown ground truth through optimal visualization and interpretability metrics
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad455, https://doi.org/10.1093/bib/bbad455
Cofea: correlation-based feature selection for single-cell chromatin accessibility data
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad458, https://doi.org/10.1093/bib/bbad458
Unraveling viral drug targets: a deep learning-based approach for the identification of potential binding sites
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad459, https://doi.org/10.1093/bib/bbad459
KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad461, https://doi.org/10.1093/bib/bbad461
LDA-VGHB: identifying potential lncRNA–disease associations with singular value decomposition, variational graph auto-encoder and heterogeneous Newton boosting machine
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad466, https://doi.org/10.1093/bib/bbad466
GTAD: a graph-based approach for cell spatial composition inference from integrated scRNA-seq and ST-seq data
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad469, https://doi.org/10.1093/bib/bbad469
THItoGene: a deep learning method for predicting spatial transcriptomics from histological images
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad464, https://doi.org/10.1093/bib/bbad464
MMP3C: an in-silico framework to depict cancer metabolic plasticity using gene expression profiles
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad471, https://doi.org/10.1093/bib/bbad471
AMGDTI: drug–target interaction prediction based on adaptive meta-graph learning in heterogeneous network
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad474, https://doi.org/10.1093/bib/bbad474
CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad475, https://doi.org/10.1093/bib/bbad475
A review of genetic variant databases and machine learning tools for predicting the pathogenicity of breast cancer
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad479, https://doi.org/10.1093/bib/bbad479
RNet: a network strategy to predict RNA binding preferences
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad482, https://doi.org/10.1093/bib/bbad482
SpliceWiz: interactive analysis and visualization of alternative splicing in R
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad468, https://doi.org/10.1093/bib/bbad468
‘Bingo’—a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad472, https://doi.org/10.1093/bib/bbad472
Identify gestational diabetes mellitus by deep learning model from cell-free DNA at the early gestation stage
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad492, https://doi.org/10.1093/bib/bbad492
Opportunities and challenges for ChatGPT and large language models in biomedicine and health
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad493, https://doi.org/10.1093/bib/bbad493
SilenceREIN: seeking silencers on anchors of chromatin loops by deep graph neural networks
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad494, https://doi.org/10.1093/bib/bbad494
A critical assessment of clustering algorithms to improve cell clustering and identification in single-cell transcriptome study
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad497, https://doi.org/10.1093/bib/bbad497
Advancing single-cell RNA-seq data analysis through the fusion of multi-layer perceptron and graph neural network
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad481, https://doi.org/10.1093/bib/bbad481
Joint deep autoencoder and subgraph augmentation for inferring microbial responses to drugs
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad483, https://doi.org/10.1093/bib/bbad483
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad486, https://doi.org/10.1093/bib/bbad486
Protein–DNA binding sites prediction based on pre-trained protein language model and contrastive learning
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad488, https://doi.org/10.1093/bib/bbad488
SGCAST: symmetric graph convolutional auto-encoder for scalable and accurate study of spatial transcriptomics
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad490, https://doi.org/10.1093/bib/bbad490
MrGPS: an m6A-related gene pair signature to predict the prognosis and immunological impact of glioma patients
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad498, https://doi.org/10.1093/bib/bbad498
H2Opred: a robust and efficient hybrid deep learning model for predicting 2’-O-methylation sites in human RNA
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad476, https://doi.org/10.1093/bib/bbad476
MulinforCPI: enhancing precision of compound–protein interaction prediction through novel perspectives on multi-level information integration
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad484, https://doi.org/10.1093/bib/bbad484
ACE configurator for ELISpot: optimizing combinatorial design of pooled ELISpot assays with an epitope similarity model
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad495, https://doi.org/10.1093/bib/bbad495
Structural coverage of the human interactome
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad496, https://doi.org/10.1093/bib/bbad496
Specific network information gain for detecting the critical state of colorectal cancer based on gut microbiome
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad465, https://doi.org/10.1093/bib/bbad465
Attention is all you need: utilizing attention in AI-enabled drug discovery
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad467, https://doi.org/10.1093/bib/bbad467
The role of ncRNA regulatory mechanisms in diseases—case on gestational diabetes
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad489, https://doi.org/10.1093/bib/bbad489
NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad499, https://doi.org/10.1093/bib/bbad499
stAA: adversarial graph autoencoder for spatial clustering task of spatially resolved transcriptomics
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad500, https://doi.org/10.1093/bib/bbad500
Development of innovative multi-epitope mRNA vaccine against Pseudomonas aeruginosa using in silico approaches
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad502, https://doi.org/10.1093/bib/bbad502
CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad505, https://doi.org/10.1093/bib/bbad505
DLTKcat: deep learning-based prediction of temperature-dependent enzyme turnover rates
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad506, https://doi.org/10.1093/bib/bbad506
Subgenome phasing for complex allopolyploidy: case-based benchmarking and recommendations
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad513, https://doi.org/10.1093/bib/bbad513
methylClass: an R package to construct DNA methylation-based classification models
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad485, https://doi.org/10.1093/bib/bbad485
Integrated bulk and single-cell transcriptomes reveal pyroptotic signature in prognosis and therapeutic options of hepatocellular carcinoma by combining deep learning
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad487, https://doi.org/10.1093/bib/bbad487
Consensus clustering with missing labels (ccml): a consensus clustering tool for multi-omics integrative prediction in cohorts with unequal sample coverage
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad501, https://doi.org/10.1093/bib/bbad501
CrossFuse-XGBoost: accurate prediction of the maximum recommended daily dose through multi-feature fusion, cross-validation screening and extreme gradient boosting
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad511, https://doi.org/10.1093/bib/bbad511
Deep neural network learning biological condition information refines gene-expression-based cell subtypes
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad512, https://doi.org/10.1093/bib/bbad512
scFed: federated learning for cell type classification with scRNA-seq
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad507, https://doi.org/10.1093/bib/bbad507
Genotype imputation accuracy and the quality metrics of the minor ancestry in multi-ancestry reference panels
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad509, https://doi.org/10.1093/bib/bbad509
Predicting drug–target binding affinity with cross-scale graph contrastive learning
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad516, https://doi.org/10.1093/bib/bbad516
Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad504, https://doi.org/10.1093/bib/bbad504
Accurate identification of structural variations from cancer samples
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad520, https://doi.org/10.1093/bib/bbad520
Review
An in-depth comparison of linear and non-linear joint embedding methods for bulk and single-cell multi-omics
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad416, https://doi.org/10.1093/bib/bbad416
From intuition to AI: evolution of small molecule representations in drug discovery
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad422, https://doi.org/10.1093/bib/bbad422
A Hitchhiker's guide to RNA–RNA structure and interaction prediction tools
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad421, https://doi.org/10.1093/bib/bbad421
Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad439, https://doi.org/10.1093/bib/bbad439
Integrative approaches based on genomic techniques in the functional studies on enhancers
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad442, https://doi.org/10.1093/bib/bbad442
Drug–drug interaction prediction: databases, web servers and computational models
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad445, https://doi.org/10.1093/bib/bbad445
Explainable artificial intelligence for omics data: a systematic mapping study
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad453, https://doi.org/10.1093/bib/bbad453
Applying polygenic risk score methods to pharmacogenomics GWAS: challenges and opportunities
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad470, https://doi.org/10.1093/bib/bbad470
VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad480, https://doi.org/10.1093/bib/bbad480
Quantification of biases in predictions of protein–protein binding affinity changes upon mutations
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad491, https://doi.org/10.1093/bib/bbad491
Network pharmacology: towards the artificial intelligence-based precision traditional Chinese medicine
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad518, https://doi.org/10.1093/bib/bbad518
Diagnostic Prediction of portal vein thrombosis in chronic cirrhosis patients using data-driven precision medicine model
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad478, https://doi.org/10.1093/bib/bbad478
Correction
Correction to: Breaking the barriers of data scarcity in drug–target affinity prediction
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad477, https://doi.org/10.1093/bib/bbad477
Correction to: Recent application of artificial intelligence on histopathologic image-based prediction of gene mutation in solid cancers
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbad503, https://doi.org/10.1093/bib/bbad503
Correction to: sciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution
Briefings in Bioinformatics, Volume 25, Issue 1, January 2024, bbae009, https://doi.org/10.1093/bib/bbae009
