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Volume 24, Issue 4, July 2023
Editorial
Editorial
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad258, https://doi.org/10.1093/bib/bbad258
Articles
emPDBA: protein-DNA binding affinity prediction by combining features from binding partners and interface learned with ensemble regression model
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad192, https://doi.org/10.1093/bib/bbad192
CMGN: a conditional molecular generation net to design target-specific molecules with desired properties
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad185, https://doi.org/10.1093/bib/bbad185
Integrating multiple traits for improving polygenic risk prediction in disease and pharmacogenomics GWAS
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad181, https://doi.org/10.1093/bib/bbad181
Census of exposed aggregation-prone regions in proteomes
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad183, https://doi.org/10.1093/bib/bbad183
Comparison and benchmark of structural variants detected from long read and long-read assembly
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad188, https://doi.org/10.1093/bib/bbad188
CIForm as a Transformer-based model for cell-type annotation of large-scale single-cell RNA-seq data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad195, https://doi.org/10.1093/bib/bbad195
WMSA 2: a multiple DNA/RNA sequence alignment tool implemented with accurate progressive mode and a fast win-win mode combining the center star and progressive strategies
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad190, https://doi.org/10.1093/bib/bbad190
Attention-based cross domain graph neural network for prediction of drug–drug interactions
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad155, https://doi.org/10.1093/bib/bbad155
SC-AIR-BERT: a pre-trained single-cell model for predicting the antigen-binding specificity of the adaptive immune receptor
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad191, https://doi.org/10.1093/bib/bbad191
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad187, https://doi.org/10.1093/bib/bbad187
Fast and accurate protein intrinsic disorder prediction by using a pretrained language model
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad173, https://doi.org/10.1093/bib/bbad173
DBGRU-SE: predicting drug–drug interactions based on double BiGRU and squeeze-and-excitation attention mechanism
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad184, https://doi.org/10.1093/bib/bbad184
MPI-VGAE: protein–metabolite enzymatic reaction link learning by variational graph autoencoders
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad189, https://doi.org/10.1093/bib/bbad189
An interpretable single-cell RNA sequencing data clustering method based on latent Dirichlet allocation
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad199, https://doi.org/10.1093/bib/bbad199
IEPAPI: a method for immune epitope prediction by incorporating antigen presentation and immunogenicity
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad171, https://doi.org/10.1093/bib/bbad171
Integrating massive RNA-seq data to elucidate transcriptome dynamics in Drosophila melanogaster
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad177, https://doi.org/10.1093/bib/bbad177
Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad186, https://doi.org/10.1093/bib/bbad186
ProgCAE: a deep learning-based method that integrates multi-omics data to predict cancer subtypes
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad196, https://doi.org/10.1093/bib/bbad196
Correction to: DeepFormer: a hybrid network based on convolutional neural network and flow-attention mechanism for identifying the function of DNA sequences
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad211, https://doi.org/10.1093/bib/bbad211
Correction: Comparison and benchmark of structural variants detected from long read and long-read assembly
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad224, https://doi.org/10.1093/bib/bbad224
Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad172, https://doi.org/10.1093/bib/bbad172
Spatially aware self-representation learning for tissue structure characterization and spatial functional genes identification
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad197, https://doi.org/10.1093/bib/bbad197
MITNet: a fusion transformer and convolutional neural network architecture approach for T-cell epitope prediction
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad202, https://doi.org/10.1093/bib/bbad202
Precision oncology: a review to assess interpretability in several explainable methods
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad200, https://doi.org/10.1093/bib/bbad200
DCiPatho: deep cross-fusion networks for genome scale identification of pathogens
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad194, https://doi.org/10.1093/bib/bbad194
MMSMAPlus: a multi-view multi-scale multi-attention embedding model for protein function prediction
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad201, https://doi.org/10.1093/bib/bbad201
Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad198, https://doi.org/10.1093/bib/bbad198
A Bayesian approach to estimate MHC-peptide binding threshold
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad208, https://doi.org/10.1093/bib/bbad208
CATAD: exploring topologically associating domains from an insight of core-attachment structure
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad204, https://doi.org/10.1093/bib/bbad204
TRAmHap: accurate prediction of transcriptional activity from DNA methylation haplotypes in bisulfite-sequencing data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad214, https://doi.org/10.1093/bib/bbad214
MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad207, https://doi.org/10.1093/bib/bbad207
scDFC: A deep fusion clustering method for single-cell RNA-seq data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad216, https://doi.org/10.1093/bib/bbad216
Machine learning modeling of RNA structures: methods, challenges and future perspectives
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad210, https://doi.org/10.1093/bib/bbad210
Improving comparative analyses of Hi-C data via contrastive self-supervised learning
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad193, https://doi.org/10.1093/bib/bbad193
Improving the identification of miRNA–disease associations with multi-task learning on gene–disease networks
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad203, https://doi.org/10.1093/bib/bbad203
A systematic review of computational methods for designing efficient guides for CRISPR DNA base editor systems
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad205, https://doi.org/10.1093/bib/bbad205
Evaluation of sequence-based predictors for phase-separating protein
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad213, https://doi.org/10.1093/bib/bbad213
Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad220, https://doi.org/10.1093/bib/bbad220
MCFF-MTDDI: multi-channel feature fusion for multi-typed drug–drug interaction prediction
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad215, https://doi.org/10.1093/bib/bbad215
TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad209, https://doi.org/10.1093/bib/bbad209
scHiMe: predicting single-cell DNA methylation levels based on single-cell Hi-C data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad223, https://doi.org/10.1093/bib/bbad223
Deep enhanced constraint clustering based on contrastive learning for scRNA-seq data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad222, https://doi.org/10.1093/bib/bbad222
PharmBERT: a domain-specific BERT model for drug labels
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad226, https://doi.org/10.1093/bib/bbad226
GraphGPSM: a global scoring model for protein structure using graph neural networks
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad219, https://doi.org/10.1093/bib/bbad219
Improved structure-related prediction for insufficient homologous proteins using MSA enhancement and pre-trained language model
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad217, https://doi.org/10.1093/bib/bbad217
DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad231, https://doi.org/10.1093/bib/bbad231
A feature extraction free approach for protein interactome inference from co-elution data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad229, https://doi.org/10.1093/bib/bbad229
Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad218, https://doi.org/10.1093/bib/bbad218
Improved the heterodimer protein complex prediction with protein language models
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad221, https://doi.org/10.1093/bib/bbad221
MPCLCDA: predicting circRNA–disease associations by using automatically selected meta-path and contrastive learning
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad227, https://doi.org/10.1093/bib/bbad227
Structure-based pathogenicity relationship identifier for predicting effects of single missense variants and discovery of higher-order cancer susceptibility clusters of mutations
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad206, https://doi.org/10.1093/bib/bbad206
DAmiRLocGNet: miRNA subcellular localization prediction by combining miRNA–disease associations and graph convolutional networks
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad212, https://doi.org/10.1093/bib/bbad212
Leveraging trans-ethnic genetic risk scores to improve association power for complex traits in underrepresented populations
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad232, https://doi.org/10.1093/bib/bbad232
A novel statistical method for decontaminating T-cell receptor sequencing data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad230, https://doi.org/10.1093/bib/bbad230
C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad225, https://doi.org/10.1093/bib/bbad225
DKADE: a novel framework based on deep learning and knowledge graph for identifying adverse drug events and related medications
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad228, https://doi.org/10.1093/bib/bbad228
Network integration and protein structural binding analysis of neurodegeneration-related interactome
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad237, https://doi.org/10.1093/bib/bbad237
Predicting potential small molecule–miRNA associations utilizing truncated schatten p-norm
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad234, https://doi.org/10.1093/bib/bbad234
An integrated deep learning framework for the interpretation of untargeted metabolomics data
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad244, https://doi.org/10.1093/bib/bbad244
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad240, https://doi.org/10.1093/bib/bbad240
E-value: a superior alternative to P-value and its adjustments in DNA methylation studies
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad241, https://doi.org/10.1093/bib/bbad241
iEnhance: a multi-scale spatial projection encoding network for enhancing chromatin interaction data resolution
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad245, https://doi.org/10.1093/bib/bbad245
DeepAlgPro: an interpretable deep neural network model for predicting allergenic proteins
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad246, https://doi.org/10.1093/bib/bbad246
Large-scale predicting protein functions through heterogeneous feature fusion
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad243, https://doi.org/10.1093/bib/bbad243
Comprehensive evaluation of deep and graph learning on drug–drug interactions prediction
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad235, https://doi.org/10.1093/bib/bbad235
An interpretable block-attention network for identifying regulatory feature interactions
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad250, https://doi.org/10.1093/bib/bbad250
iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad251, https://doi.org/10.1093/bib/bbad251
Predicting potential microbe–disease associations based on multi-source features and deep learning
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad255, https://doi.org/10.1093/bib/bbad255
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA)
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad248, https://doi.org/10.1093/bib/bbad248
ProJect: a powerful mixed-model missing value imputation method
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad233, https://doi.org/10.1093/bib/bbad233
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad242, https://doi.org/10.1093/bib/bbad242
GCFMCL: predicting miRNA-drug sensitivity using graph collaborative filtering and multi-view contrastive learning
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad247, https://doi.org/10.1093/bib/bbad247
ZetaDesign: an end-to-end deep learning method for protein sequence design and side-chain packing
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad257, https://doi.org/10.1093/bib/bbad257
Orchestrating information across tissues via a novel multitask GAT framework to improve quantitative gene regulation relation modeling for survival analysis
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad238, https://doi.org/10.1093/bib/bbad238
iBT-Net: an incremental broad transformer network for cancer drug response prediction
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad256, https://doi.org/10.1093/bib/bbad256
An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad252, https://doi.org/10.1093/bib/bbad252
Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results
Briefings in Bioinformatics, Volume 24, Issue 4, July 2023, bbad254, https://doi.org/10.1093/bib/bbad254
