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Volume 23, Issue 6, November 2022
Deep learning joint models for extracting entities and relations in biomedical: a survey and comparison
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac342, https://doi.org/10.1093/bib/bbac342
Predicting ncRNA–protein interactions based on dual graph convolutional network and pairwise learning
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac339, https://doi.org/10.1093/bib/bbac339
A geometric deep learning framework for drug repositioning over heterogeneous information networks
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac384, https://doi.org/10.1093/bib/bbac384
Jupytope: computational extraction of structural properties of viral epitopes
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac362, https://doi.org/10.1093/bib/bbac362
LDAformer: predicting lncRNA-disease associations based on topological feature extraction and Transformer encoder
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac370, https://doi.org/10.1093/bib/bbac370
MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac372, https://doi.org/10.1093/bib/bbac372
Integrating multi-omics summary data using a Mendelian randomization framework
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac376, https://doi.org/10.1093/bib/bbac376
Attention-aware contrastive learning for predicting T cell receptor–antigen binding specificity
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac378, https://doi.org/10.1093/bib/bbac378
MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac380, https://doi.org/10.1093/bib/bbac380
Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac397, https://doi.org/10.1093/bib/bbac397
csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac392, https://doi.org/10.1093/bib/bbac392
Deep learning models for disease-associated circRNA prediction: a review
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac364, https://doi.org/10.1093/bib/bbac364
Multi-modality artificial intelligence in digital pathology
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac367, https://doi.org/10.1093/bib/bbac367
Clustered tree regression to learn protein energy change with mutated amino acid
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac374, https://doi.org/10.1093/bib/bbac374
EXPERT: transfer learning-enabled context-aware microbial community classification
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac396, https://doi.org/10.1093/bib/bbac396
CORN—Condition Orientated Regulatory Networks: bridging conditions to gene networks
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac402, https://doi.org/10.1093/bib/bbac402
FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac408, https://doi.org/10.1093/bib/bbac408
Critical assessment of pan-genomic analysis of metagenome-assembled genomes
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac413, https://doi.org/10.1093/bib/bbac413
SPRoBERTa: protein embedding learning with local fragment modeling
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac401, https://doi.org/10.1093/bib/bbac401
Machine learning-based tumor-infiltrating immune cell-associated lncRNAs for predicting prognosis and immunotherapy response in patients with glioblastoma
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac386, https://doi.org/10.1093/bib/bbac386
Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac403, https://doi.org/10.1093/bib/bbac403
A review and performance evaluation of clustering frameworks for single-cell Hi-C data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac385, https://doi.org/10.1093/bib/bbac385
How does the structure of data impact cell–cell similarity? Evaluating how structural properties influence the performance of proximity metrics in single cell RNA-seq data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac387, https://doi.org/10.1093/bib/bbac387
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac404, https://doi.org/10.1093/bib/bbac404
DGHNE: network enhancement-based method in identifying disease-causing genes through a heterogeneous biomedical network
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac405, https://doi.org/10.1093/bib/bbac405
Updated review of advances in microRNAs and complex diseases: towards systematic evaluation of computational models
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac407, https://doi.org/10.1093/bib/bbac407
Efficacy difference of antipsychotics in Alzheimer’s disease and schizophrenia: explained with network efficiency and pathway analysis methods
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac394, https://doi.org/10.1093/bib/bbac394
Linking research of biomedical datasets
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac373, https://doi.org/10.1093/bib/bbac373
BioGPT: generative pre-trained transformer for biomedical text generation and mining
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac409, https://doi.org/10.1093/bib/bbac409
LION: an integrated R package for effective prediction of ncRNA–protein interaction
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac420, https://doi.org/10.1093/bib/bbac420
PlantBind: an attention-based multi-label neural network for predicting plant transcription factor binding sites
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac425, https://doi.org/10.1093/bib/bbac425
Decoding brain memory formation by single-cell RNA sequencing
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac412, https://doi.org/10.1093/bib/bbac412
Predicting multiple types of miRNA–disease associations using adaptive weighted nonnegative tensor factorization with self-paced learning and hypergraph regularization
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac390, https://doi.org/10.1093/bib/bbac390
FCCCSR_Glu: a semi-supervised learning model based on FCCCSR algorithm for prediction of glutarylation sites
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac421, https://doi.org/10.1093/bib/bbac421
Microbe-bridged disease-metabolite associations identification by heterogeneous graph fusion
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac423, https://doi.org/10.1093/bib/bbac423
dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac424, https://doi.org/10.1093/bib/bbac424
Artificial intelligence-driven prediction of multiple drug interactions
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac427, https://doi.org/10.1093/bib/bbac427
High-dimensional genomic feature selection with the ordered stereotype logit model
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac414, https://doi.org/10.1093/bib/bbac414
The GR2D2 estimator for the precision matrices
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac426, https://doi.org/10.1093/bib/bbac426
ILGBMSH: an interpretable classification model for the shRNA target prediction with ensemble learning algorithm
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac429, https://doi.org/10.1093/bib/bbac429
Machine learning alternative to systems biology should not solely depend on data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac436, https://doi.org/10.1093/bib/bbac436
Predicting the structure of unexplored novel fentanyl analogues by deep learning model
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac418, https://doi.org/10.1093/bib/bbac418
ncRNAInter: a novel strategy based on graph neural network to discover interactions between lncRNA and miRNA
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac411, https://doi.org/10.1093/bib/bbac411
CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac422, https://doi.org/10.1093/bib/bbac422
Line graph attention networks for predicting disease-associated Piwi-interacting RNAs
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac393, https://doi.org/10.1093/bib/bbac393
Integrating bioinformatic strategies in spatial life science research
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac415, https://doi.org/10.1093/bib/bbac415
Deep learning radiomics under multimodality explore association between muscle/fat and metastasis and survival in breast cancer patients
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac432, https://doi.org/10.1093/bib/bbac432
MuSiC2: cell-type deconvolution for multi-condition bulk RNA-seq data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac430, https://doi.org/10.1093/bib/bbac430
Computational methods to explore chromatin state dynamics
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac439, https://doi.org/10.1093/bib/bbac439
An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac441, https://doi.org/10.1093/bib/bbac441
NetTDP: permutation-based true discovery proportions for differential co-expression network analysis
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac417, https://doi.org/10.1093/bib/bbac417
PPMS: A framework to Profile Primary MicroRNAs from Single-cell RNA-sequencing datasets
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac419, https://doi.org/10.1093/bib/bbac419
DeepLncPro: an interpretable convolutional neural network model for identifying long non-coding RNA promoters
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac447, https://doi.org/10.1093/bib/bbac447
Data-driven patient stratification of UK Biobank cohort suggests five endotypes of multimorbidity
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac410, https://doi.org/10.1093/bib/bbac410
iDVIP: identification and characterization of viral integrase inhibitory peptides
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac406, https://doi.org/10.1093/bib/bbac406
Handcrafted versus non-handcrafted (self-supervised) features for the classification of antimicrobial peptides: complementary or redundant?
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac428, https://doi.org/10.1093/bib/bbac428
Open tools for quantitative anonymization of tabular phenotype data: literature review
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac440, https://doi.org/10.1093/bib/bbac440
Quantum computing algorithms: getting closer to critical problems in computational biology
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac437, https://doi.org/10.1093/bib/bbac437
AgingBank: a manually curated knowledgebase and high-throughput analysis platform that provides experimentally supported multi-omics data relevant to aging in multiple species
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac438, https://doi.org/10.1093/bib/bbac438
A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA–DNA interactions
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac445, https://doi.org/10.1093/bib/bbac445
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac431, https://doi.org/10.1093/bib/bbac431
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac369, https://doi.org/10.1093/bib/bbac369
MHADTI: predicting drug–target interactions via multiview heterogeneous information network embedding with hierarchical attention mechanisms
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac434, https://doi.org/10.1093/bib/bbac434
A systematic assessment of cell type deconvolution algorithms for DNA methylation data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac449, https://doi.org/10.1093/bib/bbac449
ICSDA: a multi-modal deep learning model to predict breast cancer recurrence and metastasis risk by integrating pathological, clinical and gene expression data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac448, https://doi.org/10.1093/bib/bbac448
Multi-modal chemical information reconstruction from images and texts for exploring the near-drug space
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac461, https://doi.org/10.1093/bib/bbac461
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac433, https://doi.org/10.1093/bib/bbac433
A comprehensive survey of the approaches for pathway analysis using multi-omics data integration
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac435, https://doi.org/10.1093/bib/bbac435
Identification of drug-side effect association via restricted Boltzmann machines with penalized term
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac458, https://doi.org/10.1093/bib/bbac458
A novel generation adversarial network framework with characteristics aggregation and diffusion for brain disease classification and feature selection
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac454, https://doi.org/10.1093/bib/bbac454
A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac453, https://doi.org/10.1093/bib/bbac453
EMLI-ICC: an ensemble machine learning-based integration algorithm for metastasis prediction and risk stratification in intrahepatic cholangiocarcinoma
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac450, https://doi.org/10.1093/bib/bbac450
Propagation, detection and correction of errors using the sequence database network
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac416, https://doi.org/10.1093/bib/bbac416
Identification of potential driver mutations in glioblastoma using machine learning
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac451, https://doi.org/10.1093/bib/bbac451
Correction to: A comprehensive benchmarking of WGS-based deletion structural variant callers
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac492, https://doi.org/10.1093/bib/bbac492
Interaction-based transcriptome analysis via differential network inference
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac466, https://doi.org/10.1093/bib/bbac466
Computational model for ncRNA research
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac472, https://doi.org/10.1093/bib/bbac472
Omics data analysis and integration for COVID-19 patients – editorial
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac471, https://doi.org/10.1093/bib/bbac471
LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac455, https://doi.org/10.1093/bib/bbac455
CoaDTI: multi-modal co-attention based framework for drug–target interaction annotation
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac446, https://doi.org/10.1093/bib/bbac446
Alignment-free metal ion-binding site prediction from protein sequence through pretrained language model and multi-task learning
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac444, https://doi.org/10.1093/bib/bbac444
Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2–host protein–protein interaction network
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac456, https://doi.org/10.1093/bib/bbac456
A new framework for drug–disease association prediction combing light-gated message passing neural network and gated fusion mechanism
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac457, https://doi.org/10.1093/bib/bbac457
GAE-LGA: integration of multi-omics data with graph autoencoders to identify lncRNA–PCG associations
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac452, https://doi.org/10.1093/bib/bbac452
Predicting the potential human lncRNA–miRNA interactions based on graph convolution network with conditional random field
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac463, https://doi.org/10.1093/bib/bbac463
Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac470, https://doi.org/10.1093/bib/bbac470
CysModDB: a comprehensive platform with the integration of manually curated resources and analysis tools for cysteine posttranslational modifications
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac460, https://doi.org/10.1093/bib/bbac460
Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac442, https://doi.org/10.1093/bib/bbac442
High-resolution shotgun metagenomics: the more data, the better?
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac443, https://doi.org/10.1093/bib/bbac443
Predicting drug–target binding affinity through molecule representation block based on multi-head attention and skip connection
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac468, https://doi.org/10.1093/bib/bbac468
ACP_MS: prediction of anticancer peptides based on feature extraction
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac462, https://doi.org/10.1093/bib/bbac462
Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac459, https://doi.org/10.1093/bib/bbac459
BISC: accurate inference of transcriptional bursting kinetics from single-cell transcriptomic data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac464, https://doi.org/10.1093/bib/bbac464
Correction: Insights from analyses of low complexity regions with canonical methods for protein sequence comparison
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac474, https://doi.org/10.1093/bib/bbac474
Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac467, https://doi.org/10.1093/bib/bbac467
e-TSN: an interactive visual exploration platform for target–disease knowledge mapping from literature
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac465, https://doi.org/10.1093/bib/bbac465
Deep learning identifies explainable reasoning paths of mechanism of action for drug repurposing from multilayer biological network
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac469, https://doi.org/10.1093/bib/bbac469
vsRNAfinder: a novel method for identifying high-confidence viral small RNAs from small RNA-Seq data
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac496, https://doi.org/10.1093/bib/bbac496
DAESTB: inferring associations of small molecule–miRNA via a scalable tree boosting model based on deep autoencoder
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac478, https://doi.org/10.1093/bib/bbac478
Ensembles of knowledge graph embedding models improve predictions for drug discovery
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac481, https://doi.org/10.1093/bib/bbac481
MNMDCDA: prediction of circRNA–disease associations by learning mixed neighborhood information from multiple distances
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac479, https://doi.org/10.1093/bib/bbac479
Privacy-aware estimation of relatedness in admixed populations
Briefings in Bioinformatics, Volume 23, Issue 6, November 2022, bbac473, https://doi.org/10.1093/bib/bbac473
