BMC Bioinformatics

Article	Citations
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	1532
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	446
SALON ontology for the formal description of sequence alignments	331
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	162
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	137
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	130
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	119
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	118
A two-phase clustering procedure based on allele specific expression	117
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	116
Machine learning for multi-omics data integration in crop improvement: a systematic review	111
Mabs, a suite of tools for gene-informed genome assembly	102
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	101
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	99
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	95
REDalign: accurate RNA structural alignment using residual encoder-decoder network	92
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	88
Deep learning and multi-omics approach to predict drug responses in cancer	72
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	71
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	71
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	70
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	70
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	67
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	67
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	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
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	65
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	64
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	63
Multilayer network alignment based on topological assessment via embeddings	62
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	62
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	61
A comparative analysis of topological domain callers over RNA-associated interactome	61
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation	60
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	60
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	59
A gene based combination test using GWAS summary data	56
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	54
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	54
Abstraction-based segmental simulation of reaction networks using adaptive memoization	53
SVhound: detection of regions that harbor yet undetected structural variation	52
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	52
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	52
Integration of bulk RNA-seq pipeline metrics for assessing low-quality samples	51
DiseaseNet: a transfer learning approach to noncommunicable disease classification	51
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	51
BADASS: BActeriocin-Diversity ASsessment Software	48
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	48
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	48
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	47
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	46
DHGCMDA: a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction	45
AutoPrompt-SAM3D: integrated generation and selection for SAM2-based 3D medical segmentation	45
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	45
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	45
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	44
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons	44
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	43
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures	43
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	43
False discovery rate estimation using candidate peptides for each spectrum	43
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	43
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	41
Identification of fish species through tRNA-based primer design	41
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	40
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	40
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	40
INFLECT: an R-package for cytometry cluster evaluation using marker modality	39
A graph neural network framework for mapping histological topology in oral mucosal tissue	39
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	39
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	39
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	38
SPAC: a scalable and integrated enterprise platform for single-cell spatial analysis	37
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species	37
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	37

Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	37
A novel modality contribution confidence-enhanced multimodal deep learning framework for multiomics data	37
A novel IVN-entropy based distance-driven MARCOS framework for evaluating and ranking global green hydrogen-producing countries	37
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	36
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	35
Using empirical biological knowledge to infer regulatory networks from multi-omics data	35
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	35
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	35
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	35
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	35
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	34
Semantic interoperability: ontological unpacking of a viral conceptual model	34
Can large language models understand molecules?	34
HGGA: hierarchical guided genome assembler	34
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	34
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	33
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	33
Glucostats: an efficient Python library for glucose time series feature extraction and visual analysis	33
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	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	33
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	32
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	32
Conformal novelty detection for multiple metabolic networks	31
Fractal feature selection model for enhancing high-dimensional biological problems	31
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	31
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	31
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	31
SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network	31
FragGeneScanRs: faster gene prediction for short reads	30
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	30
Inference of single-cell network using mutual information for scRNA-seq data analysis	30
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	30
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	30
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	29
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	29
Reducing Boolean networks with backward equivalence	29
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information	29
A tensor-based bi-random walks model for protein function prediction	29
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	29
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	28
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	28
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	28
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	28
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	28
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	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
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	28
DeShiftNet: a deformable-shifted cross-attention network for lightweight and robust organoid image segmentation	27
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	27
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	27
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	27
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	27
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	27
Extract antibody and antigen names from biomedical literature	26
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	26
ProTaxoVis—protein taxonomic visualisation of presence	26
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets	26
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	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
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	26
Statistical methods and resources for biomarker discovery using metabolomics	26
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	26
GVC: efficient random access compression for gene sequence variations	25
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	25
Adaptive enhancement of chest X-ray images using tissue attenuation and local and global fusion	25
AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions	25
Rendering protein mutation movies with MutAmore	25
Taxanorm: a novel taxa-specific normalization approach for microbiome data	25
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	25
The FBA solution space kernel: introduction and illustrative examples	25
Image-centric compression of protein structures improves space savings	25
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	25
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	25
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	24
Ion-pumping microbial rhodopsin protein classification by machine learning approach	24
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	24
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	24

PhenoExam: gene set analyses through integration of different phenotype databases	24
An approach for proteins and their encoding genes synonyms integration based on protein ontology	24
DiCleave: a deep learning model for predicting human Dicer cleavage sites	24
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	23
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	23
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	23
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	23
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	23
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	23
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	23
Detection of cell markers from single cell RNA-seq with sc2marker	23
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	23
Comparing neural models for nested and overlapping biomedical event detection	23
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	23
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	22
Automatic generation of pseudoknotted RNAs taxonomy	22
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	22
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	22
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	22
DANSE: a pipeline for dynamic modelling of time-series multi-omics data	22
Optimize data-driven multi-agent simulation for COVID-19 transmission	22
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	22
Correction: On Bayesian modeling of censored data in JAGS	22
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions	22
FindCSV: a long-read based method for detecting complex structural variations	22
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	21
MBECS: Microbiome Batch Effects Correction Suite	21
SEMgsa: topology-based pathway enrichment analysis with structural equation models	21
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	21
circGPA: circRNA functional annotation based on probability-generating functions	21
JCBIE: a joint continual learning neural network for biomedical information extraction	21
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	21
KEGG orthology prediction of bacterial proteins using natural language processing	21
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures	21
A voting-based machine learning approach for classifying biological and clinical datasets	21
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	21
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation	21
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App	21
Genealyzer: web application for the analysis and comparison of gene expression data	21
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	21
Multi-objective data enhancement for deep learning-based ultrasound analysis	21
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions	20
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models	20
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations	20
Denoising self-supervised learning for disease-gene association prediction	20
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	20
PRED-LD: efficient imputation of GWAS summary statistics	20
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP	20
Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction	20
Interpretable deep learning methods for multiview learning	20
Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation	20
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	19
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data	19
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	19
ACVI-Med, an open source variant interpretation tool for medical genomics	19
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	19
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants	19
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers	19
Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis	19
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique	19
Metacells untangle large and complex single-cell transcriptome networks	19
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	19
Phylo-rs: an extensible phylogenetic analysis library in rust	19
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	19
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction	19
GGAR: gradient guided adaptive regularization enhances deep learning classification of brassica species using codon usage bias	19
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants	19
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	18
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery	18
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	18
Optimizing diabetes classification with a machine learning-based framework	18
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	18
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species	18
IMSE: interaction information attention and molecular structure based drug drug interaction extraction	18
DCI-SiteDTA: drug-target affinity prediction based on binding sites detection and site-aware dual cross-interaction block	18
Using individual barcodes to increase quantification power of massively parallel reporter assays	18
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	18
DeepBP: Ensemble deep learning strategy for bioactive peptide prediction	17
BioLake: an RNA expression analysis framework for prostate cancer biomarker powered by data lakehouse	17
A novel two-way rebalancing strategy for identifying carbonylation sites	17
Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis	17
M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy	17
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics	17
Drug response prediction using graph representation learning and Laplacian feature selection	17
Control of false discoveries in grouped hypothesis testing for eQTL data	17
Deep learning algorithm reveals two prognostic subtypes in patients with gliomas	17
BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data	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
Parallel multi-swarm cooperative particle swarm optimization for protein–ligand docking and virtual screening	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
SynBioTools: a one-stop facility for searching and selecting synthetic biology tools	17
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters	16
EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning	16