BMC Bioinformatics

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1670
SALON ontology for the formal description of sequence alignments	378
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	177
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	161
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	147
REDalign: accurate RNA structural alignment using residual encoder-decoder network	136
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	134
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	133
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	129
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	128
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	122
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	119
A two-phase clustering procedure based on allele specific expression	117
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	113
A gene based combination test using GWAS summary data	96
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	92
Abstraction-based segmental simulation of reaction networks using adaptive memoization	80
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	79
A comparative analysis of topological domain callers over RNA-associated interactome	77
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	77
Multilayer network alignment based on topological assessment via embeddings	76
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	75
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	73
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	72
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	72

Deep learning and multi-omics approach to predict drug responses in cancer	70
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	70
Machine learning for multi-omics data integration in crop improvement: a systematic review	67
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	67
Implementation of machine learning in the clinic: challenges and lessons in prospective deployment from the System for High Intensity EvaLuation During Radiation Therapy (SHIELD-RT) randomized control	65
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	65
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	64
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation	64
Mabs, a suite of tools for gene-informed genome assembly	61
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	59
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	59
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	58
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	57
SVhound: detection of regions that harbor yet undetected structural variation	57
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	57
INFLECT: an R-package for cytometry cluster evaluation using marker modality	56
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	56
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	53
SPAC: a scalable and integrated enterprise platform for single-cell spatial analysis	53
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	52
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	50
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	50
False discovery rate estimation using candidate peptides for each spectrum	50
BADASS: BActeriocin-Diversity ASsessment Software	48
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	47
AutoPrompt-SAM3D: integrated generation and selection for SAM2-based 3D medical segmentation	46
DHGCMDA: a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction	46
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	45
Using empirical biological knowledge to infer regulatory networks from multi-omics data	44
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	43
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	43
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	43
EcoliTyper: a species-optimized computational pipeline for comprehensive genotyping and surveillance of Escherichia coli	43
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures	43
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	43
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	43
Identification of fish species through tRNA-based primer design	42
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	41
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons	41
DiseaseNet: a transfer learning approach to noncommunicable disease classification	40
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	40
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	40
A novel IVN-entropy based distance-driven MARCOS framework for evaluating and ranking global green hydrogen-producing countries	39
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	39
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	39
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	39
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	38
Can large language models understand molecules?	38
A novel modality contribution confidence-enhanced multimodal deep learning framework for multiomics data	38
Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples	38

Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	37
Covariance decomposition for distance based species tree estimation	37
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	37
Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues	36
A graph neural network framework for mapping histological topology in oral mucosal tissue	36
Semantic interoperability: ontological unpacking of a viral conceptual model	36
Deafness gene screening based on a multilevel cascaded BPNN model	35
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	34
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	34
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	33
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	33
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	33
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	33
Inference of single-cell network using mutual information for scRNA-seq data analysis	33
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	33
Fractal feature selection model for enhancing high-dimensional biological problems	33
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	33
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	32
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	32
Glucostats: an efficient Python library for glucose time series feature extraction and visual analysis	32
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	32
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	32
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	32
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	31
Reducing Boolean networks with backward equivalence	31
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	31
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	31
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	30
Conformal novelty detection for multiple metabolic networks	30
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	30
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	30
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	30
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	30
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	30
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	29
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	29
Circtools 2.0: a comprehensive framework for enhanced circular RNA bioinformatics	29
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	28
NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data	28
DeShiftNet: a deformable-shifted cross-attention network for lightweight and robust organoid image segmentation	28
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information	28
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	28
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	28
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	27
The FBA solution space kernel: introduction and illustrative examples	27
Image-centric compression of protein structures improves space savings	27
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	27
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	27
SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network	27
Extract antibody and antigen names from biomedical literature	27
GVC: efficient random access compression for gene sequence variations	27
Taxanorm: a novel taxa-specific normalization approach for microbiome data	27
An approach for proteins and their encoding genes synonyms integration based on protein ontology	27
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	27
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	27
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	27
Rendering protein mutation movies with MutAmore	27
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	27
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	27
Statistical methods and resources for biomarker discovery using metabolomics	27
PhenoExam: gene set analyses through integration of different phenotype databases	26
A two-stage sperm holomorphological analysis method based on multi-output network construction	26
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	26
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	26
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	26
Adaptive enhancement of chest X-ray images using tissue attenuation and local and global fusion	26
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	26
AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions	26
Ion-pumping microbial rhodopsin protein classification by machine learning approach	26
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	26
ProTaxoVis—protein taxonomic visualisation of presence	26
DiCleave: a deep learning model for predicting human Dicer cleavage sites	25
SNPio: a Python interface for population genomic data processing	25
BIOWATCH: a R shiny application for the detection of species of interest in metabarcoding datasets	25
Multi-granularity transformer contrastive learning and feature reconstruction for prediction of disease-related miRNAs	25
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	25
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	25
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	24
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	24
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	24

A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	24
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	24
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets	24
A deep learning architecture for combining and imputing heterogeneous metabolomics datasets	24
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	24
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	24
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures	23
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	23
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	23
PRED-LD: efficient imputation of GWAS summary statistics	23
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	23
Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction	22
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions	22
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App	22
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	22
GGAR: gradient guided adaptive regularization enhances deep learning classification of brassica species using codon usage bias	22
Multi-objective data enhancement for deep learning-based ultrasound analysis	22
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	22
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	22
Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation	21
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions	21
SEMgsa: topology-based pathway enrichment analysis with structural equation models	21
ACVI-Med, an open source variant interpretation tool for medical genomics	21
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	21
Automatic generation of pseudoknotted RNAs taxonomy	21
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction	21
Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis	21
circGPA: circRNA functional annotation based on probability-generating functions	21
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation	21
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	21
Genealyzer: web application for the analysis and comparison of gene expression data	21
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	21
Predicting molecular recognition features in protein sequences with MoRFchibi 2.0	20
MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host	20
IMSE: interaction information attention and molecular structure based drug drug interaction extraction	20
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	20
DANSE: a pipeline for dynamic modelling of time-series multi-omics data	20
DCI-SiteDTA: drug-target affinity prediction based on binding sites detection and site-aware dual cross-interaction block	20
Interpretable deep learning methods for multiview learning	20
Phylo-rs: an extensible phylogenetic analysis library in rust	20
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	20
FindCSV: a long-read based method for detecting complex structural variations	20
A voting-based machine learning approach for classifying biological and clinical datasets	20
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	20
JCBIE: a joint continual learning neural network for biomedical information extraction	20
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations	20
UniPTMs: a unified multi-type PTM site prediction model via master–slave architecture-based multi-stage fusion strategy and hierarchical contrastive loss	19
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	19
Denoising self-supervised learning for disease-gene association prediction	19
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants	19
Optimizing diabetes classification with a machine learning-based framework	19
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models	19
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	19
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery	19
Metacells untangle large and complex single-cell transcriptome networks	19
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers	19
Using individual barcodes to increase quantification power of massively parallel reporter assays	19
Drug response prediction using graph representation learning and Laplacian feature selection	18
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP	18
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants	18
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	18
A novel two-way rebalancing strategy for identifying carbonylation sites	18
DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts	18
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	18
KEGG orthology prediction of bacterial proteins using natural language processing	18
eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings	18
SynBioTools: a one-stop facility for searching and selecting synthetic biology tools	18
Scellpam: an R package/C++ library to perform parallel partitioning around medoids on scRNAseq data sets	18
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	18
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	18
MBECS: Microbiome Batch Effects Correction Suite	18
Control of false discoveries in grouped hypothesis testing for eQTL data	18
A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification	18
BioLake: an RNA expression analysis framework for prostate cancer biomarker powered by data lakehouse	17
ASV portal: an interface to DNA-based biodiversity data in the Living Atlas	17
An information-theoretic approach to single cell sequencing analysis	17
RSCUcaller: an R package for analyzing differences in relative synonymous codon usage (RSCU)	17
BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data	17
expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer	17
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics	17
ClearFinder: a Python GUI for annotating cells in cleared mouse brain	17
SeQual-Stream: approaching stream processing to quality control of NGS datasets	17
Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis	17
Slideflow: deep learning for digital histopathology with real-time whole-slide visualization	17
M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy	17
Prediction of disease-related miRNAs by voting with multiple classifiers	17
Deep learning algorithm reveals two prognostic subtypes in patients with gliomas	17
EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning	17
Efficient and interpretable DNA/RNA representation using Komlós–Hadamard transforms	17
Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution	17
Accelign: a GPU-based library for accelerating pairwise sequence alignment	17
Galba: genome annotation with miniprot and AUGUSTUS	17
HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer	16
MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network	16
DeepBP: Ensemble deep learning strategy for bioactive peptide prediction	16