BMC Bioinformatics

Article	Citations
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	1572
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	346
SALON ontology for the formal description of sequence alignments	164
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	143
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	135
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	122
REDalign: accurate RNA structural alignment using residual encoder-decoder network	121
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation	120
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	120
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	118
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	110
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	108
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	104
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	99
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	93
Machine learning for multi-omics data integration in crop improvement: a systematic review	89
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	73
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	72
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	72
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	72
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	70
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	69
A two-phase clustering procedure based on allele specific expression	68
Mabs, a suite of tools for gene-informed genome assembly	67
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	66

HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	66
A gene based combination test using GWAS summary data	65
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	63
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	63
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	62
Abstraction-based segmental simulation of reaction networks using adaptive memoization	62
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	61
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	61
A comparative analysis of topological domain callers over RNA-associated interactome	60
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	57
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	56
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	55
Multilayer network alignment based on topological assessment via embeddings	55
Deep learning and multi-omics approach to predict drug responses in cancer	54
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	54
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	53
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	52
SVhound: detection of regions that harbor yet undetected structural variation	51
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	51
A novel modality contribution confidence-enhanced multimodal deep learning framework for multiomics data	50
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	49
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	49
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	49
A novel IVN-entropy based distance-driven MARCOS framework for evaluating and ranking global green hydrogen-producing countries	49
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	49
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	47
INFLECT: an R-package for cytometry cluster evaluation using marker modality	47
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	45
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	45
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	45
SPAC: a scalable and integrated enterprise platform for single-cell spatial analysis	44
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	44
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	44
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	42
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	42
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	41
Semantic interoperability: ontological unpacking of a viral conceptual model	41
False discovery rate estimation using candidate peptides for each spectrum	40
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	40
BADASS: BActeriocin-Diversity ASsessment Software	40
AutoPrompt-SAM3D: integrated generation and selection for SAM2-based 3D medical segmentation	40
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	39
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	39
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	38
Can large language models understand molecules?	38
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	38
DHGCMDA: a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction	38
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	38
Using empirical biological knowledge to infer regulatory networks from multi-omics data	37
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	37

Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	37
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	36
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	36
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	36
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	36
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	35
A graph neural network framework for mapping histological topology in oral mucosal tissue	35
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures	35
Identification of fish species through tRNA-based primer design	35
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	35
Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples	35
DiseaseNet: a transfer learning approach to noncommunicable disease classification	34
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons	34
Glucostats: an efficient Python library for glucose time series feature extraction and visual analysis	33
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	33
Deafness gene screening based on a multilevel cascaded BPNN model	33
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	32
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	32
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	32
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	31
Inference of single-cell network using mutual information for scRNA-seq data analysis	31
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	31
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	31
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	31
SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network	31
Conformal novelty detection for multiple metabolic networks	31
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	31
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	31
Fractal feature selection model for enhancing high-dimensional biological problems	31
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	30
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	30
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	30
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	30
Reducing Boolean networks with backward equivalence	30
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	30
Statistical methods and resources for biomarker discovery using metabolomics	29
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	29
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information	29
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	29
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	29
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	28
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	28
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	28
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	28
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	28
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	28
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	27
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	27
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	27
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	27
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	27
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	27
DeShiftNet: a deformable-shifted cross-attention network for lightweight and robust organoid image segmentation	27
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	27
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets	26
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	26
GVC: efficient random access compression for gene sequence variations	26
Taxanorm: a novel taxa-specific normalization approach for microbiome data	26
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	26
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	26
Rendering protein mutation movies with MutAmore	26
The FBA solution space kernel: introduction and illustrative examples	26
ProTaxoVis—protein taxonomic visualisation of presence	26
Extract antibody and antigen names from biomedical literature	26
Image-centric compression of protein structures improves space savings	26
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	25
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	25
An approach for proteins and their encoding genes synonyms integration based on protein ontology	25
Ion-pumping microbial rhodopsin protein classification by machine learning approach	25
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	25
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	25
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	25
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	25
DiCleave: a deep learning model for predicting human Dicer cleavage sites	25
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	25
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	25
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	25
PhenoExam: gene set analyses through integration of different phenotype databases	25
Detection of cell markers from single cell RNA-seq with sc2marker	25
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	25

Multi-granularity transformer contrastive learning and feature reconstruction for prediction of disease-related miRNAs	24
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	24
Comparing neural models for nested and overlapping biomedical event detection	24
BIOWATCH: a R shiny application for the detection of species of interest in metabarcoding datasets	24
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	24
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	24
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	23
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	23
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	23
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	23
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	23
AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions	23
A two-stage sperm holomorphological analysis method based on multi-output network construction	23
Adaptive enhancement of chest X-ray images using tissue attenuation and local and global fusion	23
FindCSV: a long-read based method for detecting complex structural variations	22
PRED-LD: efficient imputation of GWAS summary statistics	22
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures	22
Interpretable deep learning methods for multiview learning	22
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	22
Optimize data-driven multi-agent simulation for COVID-19 transmission	22
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	22
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	22
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	21
A voting-based machine learning approach for classifying biological and clinical datasets	21
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	21
JCBIE: a joint continual learning neural network for biomedical information extraction	21
KEGG orthology prediction of bacterial proteins using natural language processing	21
Genealyzer: web application for the analysis and comparison of gene expression data	21
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants	21
Multi-objective data enhancement for deep learning-based ultrasound analysis	21
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP	21
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	21
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	21
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App	21
Phylo-rs: an extensible phylogenetic analysis library in rust	21
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	21
SEMgsa: topology-based pathway enrichment analysis with structural equation models	21
Correction: On Bayesian modeling of censored data in JAGS	21
Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis	21
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	20
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models	20
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	20
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation	20
ACVI-Med, an open source variant interpretation tool for medical genomics	20
circGPA: circRNA functional annotation based on probability-generating functions	20
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	20
Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation	20
MBECS: Microbiome Batch Effects Correction Suite	20
Metacells untangle large and complex single-cell transcriptome networks	20
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	20
DANSE: a pipeline for dynamic modelling of time-series multi-omics data	20
Automatic generation of pseudoknotted RNAs taxonomy	19
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants	19
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	19
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations	19
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction	19
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions	19
IMSE: interaction information attention and molecular structure based drug drug interaction extraction	19
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers	19
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	19
Using individual barcodes to increase quantification power of massively parallel reporter assays	19
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	19
Optimizing diabetes classification with a machine learning-based framework	18
Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction	18
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions	18
Drug response prediction using graph representation learning and Laplacian feature selection	18
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery	18
DCI-SiteDTA: drug-target affinity prediction based on binding sites detection and site-aware dual cross-interaction block	18
Denoising self-supervised learning for disease-gene association prediction	18
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	18
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	18
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species	18
GGAR: gradient guided adaptive regularization enhances deep learning classification of brassica species using codon usage bias	18
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	18
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	18
ClearFinder: a Python GUI for annotating cells in cleared mouse brain	17
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics	17
ASV portal: an interface to DNA-based biodiversity data in the Living Atlas	17
A novel two-way rebalancing strategy for identifying carbonylation sites	17
A MATLAB-based app to improve LC–MS/MS data analysis for N-linked glycan peak identification	17
Multi-task genomic prediction using gated residual variable selection neural networks	17
EasyKASP: a simple and fast tool for KASP primer design	17
cnnLSV: detecting structural variants by encoding long-read alignment information and convolutional neural network	17
SeQual-Stream: approaching stream processing to quality control of NGS datasets	17
BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data	17
Practical application of a Bayesian network approach to poultry epigenetics and stress	17
An information-theoretic approach to single cell sequencing analysis	17
ASET: an end-to-end pipeline for quantification and visualization of allele specific expression	17
Prediction of disease-related miRNAs by voting with multiple classifiers	17
Control of false discoveries in grouped hypothesis testing for eQTL data	17
SynBioTools: a one-stop facility for searching and selecting synthetic biology tools	17
M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy	17
Slideflow: deep learning for digital histopathology with real-time whole-slide visualization	16
Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis	16
Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution	16