BMC Bioinformatics

Article	Citations
CellProfiler 4: improvements in speed, utility and usability	914
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads	558
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants	294
So you think you can PLS-DA?	199
Statistical power for cluster analysis	164
TSEBRA: transcript selector for BRAKER	130
Prediction of liquid–liquid phase separating proteins using machine learning	103
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes	100
MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction	94
Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm	90
Evaluation of a decided sample size in machine learning applications	87
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data	86
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models	82
COPLA, a taxonomic classifier of plasmids	78
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules	72
PyClone-VI: scalable inference of clonal population structures using whole genome data	69
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data	68
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes	67
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography	62
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images	62
A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations	57
Correlation AnalyzeR: functional predictions from gene co-expression correlations	55
Selecting single cell clustering parameter values using subsampling-based robustness metrics	54
MiBiOmics: an interactive web application for multi-omics data exploration and integration	54
Hypergraph models of biological networks to identify genes critical to pathogenic viral response	51

Application of network link prediction in drug discovery	51
SAveRUNNER: an R-based tool for drug repurposing	46
SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost	46
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets	45
BugSeq: a highly accurate cloud platform for long-read metagenomic analyses	45
Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides	45
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks	44
IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier	43
Consensus clustering applied to multi-omics disease subtyping	43
Deep learning detection of informative features in tau PET for Alzheimer’s disease classification	42
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data	42
A novel essential protein identification method based on PPI networks and gene expression data	40
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions	40
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing	38
Optimal dimensionality selection for independent component analysis of transcriptomic data	38
Convolutional neural network for automated mass segmentation in mammography	38
TMbed: transmembrane proteins predicted through language model embeddings	38
High expression of cuproptosis-related SLC31A1 gene in relation to unfavorable outcome and deregulated immune cell infiltration in breast cancer: an analysis based on public databases	38
In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform	37
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification	37
Spliceator: multi-species splice site prediction using convolutional neural networks	36
Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms	36
Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data	35
BiGAN: LncRNA-disease association prediction based on bidirectional generative adversarial network	35
Breast cancer prediction with transcriptome profiling using feature selection and machine learning methods	35
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM	35
ElasticBLAST: accelerating sequence search via cloud computing	35
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences	34
High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing	34
PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets	34
Contrastive self-supervised clustering of scRNA-seq data	34
LongStitch: high-quality genome assembly correction and scaffolding using long reads	33
SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures	33
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	32
An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs	31
Design of lung nodules segmentation and recognition algorithm based on deep learning	31
Capsule-LPI: a LncRNA–protein interaction predicting tool based on a capsule network	30
Isabl Platform, a digital biobank for processing multimodal patient data	30
Distance correlation application to gene co-expression network analysis	30
A neural network-based method for polypharmacy side effects prediction	30
Single-cell classification using graph convolutional networks	30
A new method for exploring gene–gene and gene–environment interactions in GWAS with tree ensemble methods and SHAP values	30
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters	30
A base measure of precision for protein stability predictors: structural sensitivity	30
WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis	30
TANTIGEN 2.0: a knowledge base of tumor T cell antigens and epitopes	29
A pipeline for RNA-seq based eQTL analysis with automated quality control procedures	29
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	29
CNN-DDI: a learning-based method for predicting drug–drug interactions using convolution neural networks	29
A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs	28

Popularity and performance of bioinformatics software: the case of gene set analysis	28
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package	28
AttentionDDI: Siamese attention-based deep learning method for drug–drug interaction predictions	27
MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model	27
SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks	27
Hierarchical shared transfer learning for biomedical named entity recognition	27
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning	27
Clinlabomics: leveraging clinical laboratory data by data mining strategies	27
Accurate classification of white blood cells by coupling pre-trained ResNet and DenseNet with SCAM mechanism	26
CoolBox: a flexible toolkit for visual analysis of genomics data	26
MitoTox: a comprehensive mitochondrial toxicity database	26
geneHapR: an R package for gene haplotypic statistics and visualization	26
Asc-Seurat: analytical single-cell Seurat-based web application	26
Prediction of lung cancer using gene expression and deep learning with KL divergence gene selection	25
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data	25
Deep learning based DNA:RNA triplex forming potential prediction	25
Performance of Web tools for predicting changes in protein stability caused by mutations	25
Comparison of seven in silico tools for evaluating of daphnia and fish acute toxicity: case study on Chinese Priority Controlled Chemicals and new chemicals	25
Fast activation maximization for molecular sequence design	25
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws	25
Dysbiosis of the gut microbiome is a risk factor for osteoarthritis in older female adults: a case control study	25
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network	25
Comparative evaluation of full-length isoform quantification from RNA-Seq	24
OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow	24
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information	24
Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model	24
ATAV: a comprehensive platform for population-scale genomic analyses	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
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders	24
ideal: an R/Bioconductor package for interactive differential expression analysis	23
The challenges of explainable AI in biomedical data science	23
CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data	23
Benchmark study of feature selection strategies for multi-omics data	23
Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein	23
Biomedical relation extraction via knowledge-enhanced reading comprehension	23
In silico comparative study of SARS-CoV-2 proteins and antigenic proteins in BCG, OPV, MMR and other vaccines: evidence of a possible putative protective effect	22
Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks	22
Root Digger: a root placement program for phylogenetic trees	22
coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies	22
Metacells untangle large and complex single-cell transcriptome networks	22
Development of revised ResNet-50 for diabetic retinopathy detection	22
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma	22
MRI-based brain tumor segmentation using FPGA-accelerated neural network	22
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations	22
GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification	22
Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform	22
EG-TransUNet: a transformer-based U-Net with enhanced and guided models for biomedical image segmentation	22
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes	21
Predicting functions of maize proteins using graph convolutional network	21
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction	21
StrongestPath: a Cytoscape application for protein–protein interaction analysis	21
nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs	21
Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data	21
Improving biomedical named entity recognition with syntactic information	21
In silico design of a multi-epitope vaccine against HPV16/18	21
Prediction of enhancer–promoter interactions using the cross-cell type information and domain adversarial neural network	21
Machine learning-based prediction of survival prognosis in cervical cancer	21
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS	21
Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture	21
Deep active learning for classifying cancer pathology reports	21
A novel method for drug-target interaction prediction based on graph transformers model	21
Simulation study and comparative evaluation of viral contiguous sequence identification tools	21
gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network	20
Current trend and development in bioinformatics research	20
ORFik: a comprehensive R toolkit for the analysis of translation	20
Sfcnn: a novel scoring function based on 3D convolutional neural network for accurate and stable protein–ligand affinity prediction	20
Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images	20
Biological interpretation of deep neural network for phenotype prediction based on gene expression	20
External features enriched model for biomedical question answering	20
Interpretable prediction of necrotizing enterocolitis from machine learning analysis of premature infant stool microbiota	20
FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences	20
Combining sequence and network information to enhance protein–protein interaction prediction	20
Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality	20
Struct2Graph: a graph attention network for structure based predictions of protein–protein interactions	20
Flora Capture: a citizen science application for collecting structured plant observations	20
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	20
The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data	19
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks	19
Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features	19
Combined embedding model for MiRNA-disease association prediction	19

FEGS: a novel feature extraction model for protein sequences and its applications	19
DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing	19
Efficient link prediction in the protein–protein interaction network using topological information in a generative adversarial network machine learning model	19
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	19
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	19
Prediction of unconventional protein secretion by exosomes	19
Prediction of antimicrobial peptides toxicity based on their physico-chemical properties using machine learning techniques	19
Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction	19
Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities	19
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding	18
A multitask transfer learning framework for the prediction of virus-human protein–protein interactions	18
A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application	18
A hierarchical opportunistic screening model for osteoporosis using machine learning applied to clinical data and CT images	18
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA–protein interaction prediction	18
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads	18
CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network	18
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	18
Machine learning to reveal an astute risk predictive framework for Gynecologic Cancer and its impact on women psychology: Bangladeshi perspective	18
Inferring time-dependent population growth rates in cell cultures undergoing adaptation	18
SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing	18
Predicting miRNA-disease associations based on graph attention network with multi-source information	18
PCirc: random forest-based plant circRNA identification software	18
Graph embeddings on gene ontology annotations for protein–protein interaction prediction	18
Multi-type feature fusion based on graph neural network for drug-drug interaction prediction	18
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data	18
Identification of early mild cognitive impairment using multi-modal data and graph convolutional networks	18
MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanism	18
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases	18
Identification of CD8+ T cell epitopes through proteasome cleavage site predictions	18
A diabetes prediction model based on Boruta feature selection and ensemble learning	18
A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data	18
RNA secondary structure prediction with convolutional neural networks	18
GeneralizedDTA: combining pre-training and multi-task learning to predict drug-target binding affinity for unknown drug discovery	18
TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification	18
In silico design of recombinant multi-epitope vaccine against influenza A virus	18
AMPDeep: hemolytic activity prediction of antimicrobial peptides using transfer learning	17
EDLm6APred: ensemble deep learning approach for mRNA m6A site prediction	17
DRPnet: automated particle picking in cryo-electron micrographs using deep regression	17
Multi-dimensional data integration algorithm based on random walk with restart	17
Novel deep learning-based transcriptome data analysis for drug-drug interaction prediction with an application in diabetes	17
EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends	17
DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization	17
Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system	17
Putative markers for the detection of early-stage bladder cancer selected by urine metabolomics	17
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms	17
A data management infrastructure for the integration of imaging and omics data in life sciences	17
DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning	17
Algorithm for DNA sequence assembly by quantum annealing	16
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species	16
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides	16
An efficient ensemble method for missing value imputation in microarray gene expression data	16
R.ROSETTA: an interpretable machine learning framework	16
LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification	16
Prediction and prioritization of autism-associated long non-coding RNAs using gene expression and sequence features	16
Multiple-testing correction in metabolome-wide association studies	16
Predicting circRNA-drug sensitivity associations via graph attention auto-encoder	16
miTAR: a hybrid deep learning-based approach for predicting miRNA targets	16
CytoGLMM: conditional differential analysis for flow and mass cytometry experiments	16
RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data	16
Euclidean distance-optimized data transformation for cluster analysis in biomedical data (EDOtrans)	16
Deepstacked-AVPs: predicting antiviral peptides using tri-segment evolutionary profile and word embedding based multi-perspective features with deep stacking model	16
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine	16
Comparison of five supervised feature selection algorithms leading to top features and gene signatures from multi-omics data in cancer	16
Reproducibility of mass spectrometry based metabolomics data	16
CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis	16
Consensus clustering for Bayesian mixture models	16
Non-small-cell lung cancer classification via RNA-Seq and histology imaging probability fusion	15
Learning curves for drug response prediction in cancer cell lines	15
Protein–protein interaction prediction based on ordinal regression and recurrent convolutional neural networks	15
Double matrix completion for circRNA-disease association prediction	15
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets	15
m7GDisAI: N7-methylguanosine (m7G) sites and diseases associations inference based on heterogeneous network	15
Forecasting the spread of COVID-19 using LSTM network	15
pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science	15
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes	15
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts	15
Leveraging pre-trained language models for mining microbiome-disease relationships	15
DePolymerase Predictor (DePP): a machine learning tool for the targeted identification of phage depolymerases	15
An effective drug-disease associations prediction model based on graphic representation learning over multi-biomolecular network	15
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	15
Super.FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data	15
EMDLP: Ensemble multiscale deep learning model for RNA methylation site prediction	15
A comprehensive database for integrated analysis of omics data in autoimmune diseases	15
Refactoring and performance analysis of the main CNN architectures: using false negative rate minimization to solve the clinical images melanoma detection problem	15
In-silico design of an immunoinformatics based multi-epitope vaccine against Leishmania donovani	15
scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data	15
METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs	15
Deep learning for cancer type classification and driver gene identification	15
moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks	15
Analysis of single-cell RNA sequencing data based on autoencoders	15
General deep learning model for detecting diabetic retinopathy	15
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	15
BioRel: towards large-scale biomedical relation extraction	15
A novel miRNA-based classification model of risks and stages for clear cell renal cell carcinoma patients	14
Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers	14