Briefings in Bioinformatics

Article	Citations
Letter regarding article named ‘Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy’	806
ExsgRNA: reduce off-target efficiency by on-target mismatched sgRNA	346
MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification	233
Incomplete time-series gene expression in integrative study for islet autoimmunity prediction	165
Correction to: Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design	161
Towards molecular structure discovery from cryo-ET density volumes via modelling auxiliary semantic prototypes	156
Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences	154
BioGSF: a graph-driven semantic feature integration framework for biomedical relation extraction	140
Complex p53 dynamics regulated by miR-125b in cellular responses to reactive oxidative stress and DNA damage	135
bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data	122
Fast heritability estimation based on MINQUE and batch training	120
Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data	117
Integrating network pharmacology and in silico analysis deciphers Withaferin-A’s anti-breast cancer potential via hedgehog pathway and target network interplay	117
eSCAN: scan regulatory regions for aggregate association testing using whole-genome sequencing data	116
Learning discriminative and structural samples for rare cell types with deep generative model	115
HIP: a method for high-dimensional multi-view data integration and prediction accounting for subgroup heterogeneity	115
CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences	113
An initial game-theoretic assessment of enhanced tissue preparation and imaging protocols for improved deep learning inference of spatial transcriptomics from tissue morphology	113
Interpretable modeling of time-resolved single-cell gene–protein expression with CrossmodalNet	109
SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network	108
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly	108
iDRPro-SC: identifying DNA-binding proteins and RNA-binding proteins based on subfunction classifiers	106
Identification of vital chemical information via visualization of graph neural networks	102
Application of deep learning in cancer epigenetics through DNA methylation analysis	98
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles	97

Assessing protein model quality based on deep graph coupled networks using protein language model	97
Clover: tree structure-based efficient DNA clustering for DNA-based data storage	94
Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer	94
Forman persistent Ricci curvature (FPRC)-based machine learning models for protein–ligand binding affinity prediction	93
preMLI: a pre-trained method to uncover microRNA–lncRNA potential interactions	92
Artificial intelligence in drug discovery: applications and techniques	92
Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference	87
spaCI: deciphering spatial cellular communications through adaptive graph model	86
Improved model quality assessment using sequence and structural information by enhanced deep neural networks	86
Letter to the editor: testing the effectiveness of MyPROSLE in classifying patients with lupus nephritis	86
ETLD: an encoder-transformation layer-decoder architecture for protein contact and mutation effects prediction	85
Defining the single base importance of human mRNAs and lncRNAs	85
COWID: an efficient cloud-based genomics workflow for scalable identification of SARS-COV-2	83
Genome optimization via virtual simulation to accelerate maize hybrid breeding	81
DeepMiceTL: a deep transfer learning based prediction of mice cardiac conduction diseases using early electrocardiograms	80
Representation of molecules for drug response prediction	77
IndGOterm: a qualitative method for the identification of individually dysregulated GO terms in cancer	77
Accurate flexible refinement for atomic-level protein structure using cryo-EM density maps and deep learning	77
KDGene: knowledge graph completion for disease gene prediction using interactional tensor decomposition	76
SEGCECO: Subgraph Embedding of Gene expression matrix for prediction of CEll-cell COmmunication	75
MGCNSS: miRNA–disease association prediction with multi-layer graph convolution and distance-based negative sample selection strategy	74
IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network	74
Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA	73
Correction to: siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers	73
Knowledge bases and software support for variant interpretation in precision oncology	73
GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms	73
A strategy combining denoising and cryo-EM single particle analysis	73
Evaluation of propensity score methods for causal inference with high-dimensional covariates	73
Heavy chain sequence-based classifier for the specificity of human antibodies	73
Improving drug response prediction via integrating gene relationships with deep learning	69
Quantitative estimation of intracellular oxidative stress in human tissues	69
Potential of dissimilarity measure-based computation of protein thermal stability data for determining protein interactions	68
Corrigendum to: Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein	68
GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences	67
Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data	66
BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing	66
Machine learning modeling of RNA structures: methods, challenges and future perspectives	65
Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions	64
SuperCUT, an unsupervised multimodal image registration with deep learning for biomedical microscopy	63
ML-PLIC: a web platform for characterizing protein–ligand interactions and developing machine learning-based scoring functions	63
Deep reinforcement learning identifies personalized intermittent androgen deprivation therapy for prostate cancer	63
A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks	63
Improving drug-target affinity prediction via feature fusion and knowledge distillation	63
Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design	62
HiCDiff: single-cell Hi-C data denoising with diffusion models	62
HTINet2: herb–target prediction via knowledge graph embedding and residual-like graph neural network	62
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks	62
Self-supervised learning with chemistry-aware fragmentation for effective molecular property prediction	62
SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm	62
An inductive transfer learning force field (ITLFF) protocol builds protein force fields in seconds	61

INTREPPPID—an orthologue-informed quintuplet network for cross-species prediction of protein–protein interaction	61
Meta-DHGNN: method for CRS-related cytokines analysis in CAR-T therapy based on meta-learning directed heterogeneous graph neural network	61
Prediction of allosteric druggable pockets of cyclin-dependent kinases	61
An overview of machine learning methods for monotherapy drug response prediction	61
CRAFT: a bioinformatics software for custom prediction of circular RNA functions	60
Canalizing kernel for cell fate determination	60
A Markov random field model-based approach for differentially expressed gene detection from single-cell RNA-seq data	59
CoraL: interpretable contrastive meta-learning for the prediction of cancer-associated ncRNA-encoded small peptides	59
Harnessing large language models’ zero-shot and few-shot learning capabilities for regulatory research	59
Ensemble classification based signature discovery for cancer diagnosis in RNA expression profiles across different platforms	58
Statistical challenges in longitudinal microbiome data analysis	58
Evaluation of graphical models for multi-group metabolomics data	58
dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility	58
AESurv: autoencoder survival analysis for accurate early prediction of coronary heart disease	58
A hybrid positive unlabeled learning framework for uncovering scaffolds across human proteome by measuring the propensity to drive phase separation	57
MLysPRED: graph-based multi-view clustering and multi-dimensional normal distribution resampling techniques to predict multiple lysine sites	57
siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers	57
TPD: a web tool for tipping-point detection based on dynamic network biomarker	57
MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models	57
Clustered tree regression to learn protein energy change with mutated amino acid	57
A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota	56
iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network	56
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics	56
Removing unwanted variation between samples in Hi-C experiments	55
Distant metastasis identification based on optimized graph representation of gene interaction patterns	55
Predicting multiple types of miRNA–disease associations using adaptive weighted nonnegative tensor factorization with self-paced learning and hypergraph regularization	55
DaDL-SChlo: protein subchloroplast localization prediction based on generative adversarial networks and pre-trained protein language model	54
Revealing cell–cell communication pathways with their spatially coupled gene programs	53
Single-cell RNA sequencing data imputation using bi-level feature propagation	53
Evaluating large language models for annotating proteins	53
mbDecoda: a debiased approach to compositional data analysis for microbiome surveys	53
HighFold: accurately predicting structures of cyclic peptides and complexes with head-to-tail and disulfide bridge constraints	53
C-RCPred: a multi-objective algorithm for interactive secondary structure prediction of RNA complexes integrating user knowledge and SHAPE data	52
MATTE: a pipeline of transcriptome module alignment for anti-noise phenotype-gene-related analysis	52
scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks	52
A practical assembly guideline for genomes with various levels of heterozygosity	51
BayeSMART: Bayesian clustering of multi-sample spatially resolved transcriptomics data	51
Multi-model predictive analysis of RNA solvent accessibility based on modified residual attention mechanism	51
Veterinary systems biology for bridging the phenotype–genotype gap via computational modeling for disease epidemiology and animal welfare	51
A comprehensive assessment of hurdle and zero-inflated models for single cell RNA-sequencing analysis	50
A robust statistical approach for finding informative spatially associated pathways	50
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework	50
Optimized patient-specific immune checkpoint inhibitor therapies for cancer treatment based on tumor immune microenvironment modeling	50
To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities	49
Analysis of affinity purification-related proteomic data for studying protein–protein interaction networks in cells	49
Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings	49
Clustering scRNA-seq data with the cross-view collaborative information fusion strategy	48
Pioneering bioinformatics with agent-based modelling: an innovative protocol to accurately forecast skin or respiratory allergic reactions to chemical sensitizers	48
Cancerous time estimation for interpreting the evolution of lung adenocarcinoma	48
DEWNA: dynamic entropy weight network analysis and its application to the DNA-binding proteome in A549 cells with cisplatin-induced damage	47
NetTDP: permutation-based true discovery proportions for differential co-expression network analysis	47
Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping	47
Omics data analysis and integration for COVID-19 patients – editorial	47
Assessing polygenic risk score models for applications in populations with under-represented genomics data: an example of Vietnam	46
Correction: Insights from analyses of low complexity regions with canonical methods for protein sequence comparison	46
Ensemble classification based feature selection: a case of identification on plant pentatricopeptide repeat proteins	46
ZoomQA: residue-level protein model accuracy estimation with machine learning on sequential and 3D structural features	45
A similarity-based deep learning approach for determining the frequencies of drug side effects	45
WEDGE: imputation of gene expression values from single-cell RNA-seq datasets using biased matrix decomposition	45
Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation	44
Improved inter-protein contact prediction using dimensional hybrid residual networks and protein language models	44
The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis	44
Bridging-BPs: a novel approach to predict potential drug–target interactions based on a bridging heterogeneous graph and BPs2vec	44
Reducing false positive rate of docking-based virtual screening by active learning	43
Computational insights into the cross-talk between medin and Aβ: implications for age-related vascular risk factors in Alzheimer’s disease	43
Combining power of different methods to detect associations in large data sets	43
Correction to: Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology	42
Open tools for quantitative anonymization of tabular phenotype data: literature review	42
EGFI: drug–drug interaction extraction and generation with fusion of enriched entity and sentence information	42
Detection of transcription factors binding to methylated DNA by deep recurrent neural network	42
Differential variability analysis of single-cell gene expression data	42
Learning multi-scale heterogenous network topologies and various pairwise attributes for drug–disease association prediction	42
Protein–DNA binding sites prediction based on pre-trained protein language model and contrastive learning	42
FEED: a feature selection method based on gene expression decomposition for single cell clustering	41
Evaluating the efficacy of MEANGS for mitochondrial genome assembly of cartilaginous and ray-finned fish species	41
RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome	41
Two-stage-vote ensemble framework based on integration of mutation data and gene interaction network for uncovering driver genes	40
Integrative COVID-19 biological network inference with probabilistic core decomposition	40
BiGATAE: a bipartite graph attention auto-encoder enhancing spatial domain identification from single-slice to multi-slices	40
Inter-domain distance prediction based on deep learning for domain assembly	40

Deep neural network learning biological condition information refines gene-expression-based cell subtypes	40
Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity	40
A fast and accurate method for SARS-CoV-2 genomic tracing	40
Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network	40
Challenges in distinguishing functional proteins from polyproteins in databases: implications for drug discovery	40
TransAC4C—a novel interpretable architecture for multi-species identification of N4-acetylcytidine sites in RNA with single-base resolution	40
Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19	39
GAABind: a geometry-aware attention-based network for accurate protein–ligand binding pose and binding affinity prediction	39
FedSPL: federated self-paced learning for privacy-preserving disease diagnosis	39
A review on the application of bioinformatics tools in food microbiome studies	39
Identification of drug-side effect association via restricted Boltzmann machines with penalized term	39
Analysis of super-enhancer using machine learning and its application to medical biology	39
Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision	39
PharmBERT: a domain-specific BERT model for drug labels	38
iAMP-Attenpred: a novel antimicrobial peptide predictor based on BERT feature extraction method and CNN-BiLSTM-Attention combination model	38
LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays	38
DSEATM: drug set enrichment analysis uncovering disease mechanisms by biomedical text mining	38
Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST	38
eQTLHap: a tool for comprehensive eQTL analysis considering haplotypic and genotypic effects	38
Network analytics for drug repurposing in COVID-19	38
Scalable batch-correction approach for integrating large-scale single-cell transcriptomes	38
ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues	38
EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning	37
A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia	37
Translational informatics for human microbiota: data resources, models and applications	37
Community cohesion looseness in gene networks reveals individualized drug targets and resistance	37
A deep learning model to identify gene expression level using cobinding transcription factor signals	37
InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop	36
Positive-unlabeled learning in bioinformatics and computational biology: a brief review	36
ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes	36
RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks	36
Mix-Key: graph mixup with key structures for molecular property prediction	36
miProBERT: identification of microRNA promoters based on the pre-trained model BERT	36
Bioinformatics helping to mitigate the impact of COVID-19 – Editorial	35
Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics	35
DTSyn: a dual-transformer-based neural network to predict synergistic drug combinations	35
Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases	35
Corrigendum to: Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption	35
Adaptive sequencing using nanopores and deep learning of mitochondrial DNA	35
KGANSynergy: knowledge graph attention network for drug synergy prediction	34
Innovative super-resolution in spatial transcriptomics: a transformer model exploiting histology images and spatial gene expression	34
An enhanced cascade-based deep forest model for drug combination prediction	34
High-quality pan-genome of Escherichia coli generated by excluding confounding and highly similar strains reveals an association between unique gene clusters and genomic islands	34
Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption	34
Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks	34
DNA Bloom Filter enables anti-contamination and file version control for DNA-based data storage	33
Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy	33
CLT-seq as a universal homopolymer-sequencing concept reveals poly(A)-tail-tuned ncRNA regulation	33
Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration	33
BayesKAT: bayesian optimal kernel-based test for genetic association studies reveals joint genetic effects in complex diseases	33
Benchmarking digital PCR partition classification methods with empirical and simulated duplex data	33
CORN—Condition Orientated Regulatory Networks: bridging conditions to gene networks	32
Unveiling promising drug targets for autism spectrum disorder: insights from genetics, transcriptomics, and proteomics	32
Shall genomic correlation structure be considered in copy number variants detection?	32
labelSeg: segment annotation for tumor copy number alteration profiles	32
Identifying and training deep learning neural networks on biomedical-related datasets	32
APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures	31
Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome	31
FitDock: protein–ligand docking by template fitting	31
AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches	31
Structural coverage of the human interactome	31
MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification	31
A cloud-based learning module for biomarker discovery	31
SatXplor—a comprehensive pipeline for satellite DNA analyses in complex genome assemblies	31
ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism	31
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network	31
Heterogeneous graph contrastive learning with gradient balance for drug repositioning	31
Correction to: HHOMR: a hybrid high-order moment residual model for miRNA-disease association prediction	31
Identifying multi-functional bioactive peptide functions using multi-label deep learning	31
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data	31
Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity	30
Comparison of approaches to transcriptomic analysis in multi-sampled tumors	30
Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review	30
idenMD-NRF: a ranking framework for miRNA-disease association identification	30
A Hitchhiker's guide to RNA–RNA structure and interaction prediction tools	30
Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers	30
Computational anti-COVID-19 drug design: progress and challenges	30
Protein phosphorylation database and prediction tools	30
Locus-specific expression analysis of transposable elements	30
Prediction of disease-free survival for precision medicine using cooperative learning on multi-omic data	30
SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition	30
Comprehensive characterization genetic regulation and chromatin landscape of enhancer-associated long non-coding RNAs and their implication in human cancer	30
Contrastively generative self-expression model for single-cell and spatial multimodal data	30
scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding	30
Inflated false discovery rate due to volcano plots: problem and solutions	30
Matching single cells across modalities with contrastive learning and optimal transport	29
Feature extraction approaches for biological sequences: a comparative study of mathematical features	29
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	29
Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies	29
Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution	29
Computational model for ncRNA research	29
Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation	29
Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing	29
Exploring the immune evasion of SARS-CoV-2 variant harboring E484K by molecular dynamics simulations	29
A high-dimensional omnibus test for set-based association analysis	28