BMC Bioinformatics

Article	Citations
CellProfiler 4: improvements in speed, utility and usability	652
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads	308
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants	262
PACVr: plastome assembly coverage visualization in R	224
So you think you can PLS-DA?	176
Statistical power for cluster analysis	113
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data	98
TSEBRA: transcript selector for BRAKER	97
DPDDI: a deep predictor for drug-drug interactions	90
Prediction of heart disease and classifiers’ sensitivity analysis	87
Prediction of liquid–liquid phase separating proteins using machine learning	85
MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction	84
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes	80
Graph-based prediction of Protein-protein interactions with attributed signed graph embedding	77
Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm	74
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data	69
Malaria parasite detection in thick blood smear microscopic images using modified YOLOV3 and YOLOV4 models	69
COPLA, a taxonomic classifier of plasmids	66
Conditional permutation importance revisited	64
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules	61
PyClone-VI: scalable inference of clonal population structures using whole genome data	59
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads	57
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes	57
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets	55
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography	54

Broad-coverage biomedical relation extraction with SemRep	54
Amino acid encoding for deep learning applications	54
GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis	54
A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network	50
A representation learning model based on variational inference and graph autoencoder for predicting lncRNA-disease associations	50
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data	50
NBZIMM: negative binomial and zero-inflated mixed models, with application to microbiome/metagenomics data analysis	49
Robust principal component analysis for accurate outlier sample detection in RNA-Seq data	49
Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies	48
Correlation AnalyzeR: functional predictions from gene co-expression correlations	48
MiBiOmics: an interactive web application for multi-omics data exploration and integration	48
CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments	47
VADR: validation and annotation of virus sequence submissions to GenBank	47
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images	47
Selecting single cell clustering parameter values using subsampling-based robustness metrics	47
CosinorPy: a python package for cosinor-based rhythmometry	45
Comparison of smartphone-based retinal imaging systems for diabetic retinopathy detection using deep learning	44
Keras R-CNN: library for cell detection in biological images using deep neural networks	44
SAveRUNNER: an R-based tool for drug repurposing	42
Hypergraph models of biological networks to identify genes critical to pathogenic viral response	42
Application of network link prediction in drug discovery	42
NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization	41
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis	41
SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas	40
Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides	40
Evaluation of a decided sample size in machine learning applications	38
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data	38
Deconvolution of bulk blood eQTL effects into immune cell subpopulations	38
Consensus clustering applied to multi-omics disease subtyping	38
Deep learning detection of informative features in tau PET for Alzheimer’s disease classification	36
In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform	36
BugSeq: a highly accurate cloud platform for long-read metagenomic analyses	36
Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing	36
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks	36
IPCARF: improving lncRNA-disease association prediction using incremental principal component analysis feature selection and a random forest classifier	35
A novel essential protein identification method based on PPI networks and gene expression data	35
Type2 diabetes mellitus prediction using data mining algorithms based on the long-noncoding RNAs expression: a comparison of four data mining approaches	35
SMALF: miRNA-disease associations prediction based on stacked autoencoder and XGBoost	35
IP4M: an integrated platform for mass spectrometry-based metabolomics data mining	34
SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o	34
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification	33
Contrastive self-supervised clustering of scRNA-seq data	33
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions	33
Convolutional neural network for automated mass segmentation in mammography	33
Analysis of genomic and transcriptomic variations as prognostic signature for lung adenocarcinoma	33
Optimal dimensionality selection for independent component analysis of transcriptomic data	32
A preliminary PET radiomics study of brain metastases using a fully automatic segmentation method	32
Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms	32
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM	32
BiGAN: LncRNA-disease association prediction based on bidirectional generative adversarial network	32

Y-LineageTracker: a high-throughput analysis framework for Y-chromosomal next-generation sequencing data	31
High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing	31
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	30
ICEKAT: an interactive online tool for calculating initial rates from continuous enzyme kinetic traces	30
Breast cancer prediction with transcriptome profiling using feature selection and machine learning methods	29
PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets	29
LongStitch: high-quality genome assembly correction and scaffolding using long reads	29
SWnet: a deep learning model for drug response prediction from cancer genomic signatures and compound chemical structures	29
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences	29
A base measure of precision for protein stability predictors: structural sensitivity	28
A new method for exploring gene–gene and gene–environment interactions in GWAS with tree ensemble methods and SHAP values	28
Capsule-LPI: a LncRNA–protein interaction predicting tool based on a capsule network	28
A pipeline for RNA-seq based eQTL analysis with automated quality control procedures	27
TMbed: transmembrane proteins predicted through language model embeddings	27
Single-cell classification using graph convolutional networks	27
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets	26
A rank-based marker selection method for high throughput scRNA-seq data	26
ARTDeco: automatic readthrough transcription detection	26
HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis	26
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	26
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network	26
Spliceator: multi-species splice site prediction using convolutional neural networks	26
Machine learning models predicting multidrug resistant urinary tract infections using “DsaaS”	26
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community	26
Evaluation of variant calling tools for large plant genome re-sequencing	26
Popularity and performance of bioinformatics software: the case of gene set analysis	25
MitoTox: a comprehensive mitochondrial toxicity database	25
Isabl Platform, a digital biobank for processing multimodal patient data	25
Deep learning based DNA:RNA triplex forming potential prediction	25
SNF-NN: computational method to predict drug-disease interactions using similarity network fusion and neural networks	25
Generating realistic null hypothesis of cancer mutational landscapes using SigProfilerSimulator	24
WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis	24
CNN-DDI: a learning-based method for predicting drug–drug interactions using convolution neural networks	23
Comparison of seven in silico tools for evaluating of daphnia and fish acute toxicity: case study on Chinese Priority Controlled Chemicals and new chemicals	23
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning	23
Review of medical image recognition technologies to detect melanomas using neural networks	23
Dysbiosis of the gut microbiome is a risk factor for osteoarthritis in older female adults: a case control study	23
Hierarchical shared transfer learning for biomedical named entity recognition	23
AttentionDDI: Siamese attention-based deep learning method for drug–drug interaction predictions	23
NEDD: a network embedding based method for predicting drug-disease associations	23
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders	23
Performance of Web tools for predicting changes in protein stability caused by mutations	22
CRISPRpred(SEQ): a sequence-based method for sgRNA on target activity prediction using traditional machine learning	22
TANTIGEN 2.0: a knowledge base of tumor T cell antigens and epitopes	22
Automated classification of protein subcellular localization in immunohistochemistry images to reveal biomarkers in colon cancer	22
Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein	22
Auto-HMM-LMF: feature selection based method for prediction of drug response via autoencoder and hidden Markov model	22
A neural network-based method for polypharmacy side effects prediction	22
Accurate classification of white blood cells by coupling pre-trained ResNet and DenseNet with SCAM mechanism	22
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	22
A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs	22
Drug-target interaction prediction using semi-bipartite graph model and deep learning	22
Leveraging TCGA gene expression data to build predictive models for cancer drug response	22
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws	22
The prognostic value of an autophagy-related lncRNA signature in hepatocellular carcinoma	22
Asc-Seurat: analytical single-cell Seurat-based web application	22
ADEPT: a domain independent sequence alignment strategy for gpu architectures	21
PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST	21
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data	21
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes	21
AdmixPipe: population analyses in Admixture for non-model organisms	21
GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data	21
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	21
LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting	21
ATAV: a comprehensive platform for population-scale genomic analyses	21
MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model	21
Biomedical relation extraction via knowledge-enhanced reading comprehension	21
CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures	20
Identifying the sequence specificities of circRNA-binding proteins based on a capsule network architecture	20
Modeling drug mechanism of action with large scale gene-expression profiles using GPAR, an artificial intelligence platform	20
Improving biomedical named entity recognition with syntactic information	20
Deep active learning for classifying cancer pathology reports	20
Simulation study and comparative evaluation of viral contiguous sequence identification tools	20
m5CPred-SVM: a novel method for predicting m5C sites of RNA	20
Design of lung nodules segmentation and recognition algorithm based on deep learning	20
Interpretable prediction of necrotizing enterocolitis from machine learning analysis of premature infant stool microbiota	20
StrongestPath: a Cytoscape application for protein–protein interaction analysis	20
OVarFlow: a resource optimized GATK 4 based Open source Variant calling workFlow	20
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package	20
ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature	20

Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan	20
Matrix factorization with neural network for predicting circRNA-RBP interactions	20
SequelTools: a suite of tools for working with PacBio Sequel raw sequence data	20
An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs	20
Clinlabomics: leveraging clinical laboratory data by data mining strategies	20
Data-based RNA-seq simulations by binomial thinning	19
ElasticBLAST: accelerating sequence search via cloud computing	19
EMU: reconfigurable graphical user interfaces for Micro-Manager	19
A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path	19
scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data	19
Distance correlation application to gene co-expression network analysis	19
Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data	19
Comprehensive host-pathogen protein-protein interaction network analysis	19
CytoTree: an R/Bioconductor package for analysis and visualization of flow and mass cytometry data	19
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering	19
External features enriched model for biomedical question answering	18
Predicting MiRNA-disease associations by multiple meta-paths fusion graph embedding model	18
Extending rnaSPAdes functionality for hybrid transcriptome assembly	18
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information	18
Combining sequence and network information to enhance protein–protein interaction prediction	18
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations	18
“METAGENOTE: a simplified web platform for metadata annotation of genomic samples and streamlined submission to NCBI’s sequence read archive”	18
CoolBox: a flexible toolkit for visual analysis of genomics data	18
Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction	18
ideal: an R/Bioconductor package for interactive differential expression analysis	18
Biological interpretation of deep neural network for phenotype prediction based on gene expression	18
Current trend and development in bioinformatics research	18
Prediction of unconventional protein secretion by exosomes	18
Flora Capture: a citizen science application for collecting structured plant observations	18
Toward a more holistic method of genome assembly assessment	18
gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network	18
Root Digger: a root placement program for phylogenetic trees	17
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA–protein interaction prediction	17
PCirc: random forest-based plant circRNA identification software	17
An improved clear cell renal cell carcinoma stage prediction model based on gene sets	17
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters	17
Predicting functions of maize proteins using graph convolutional network	17
In silico design of a multi-epitope vaccine against HPV16/18	17
In silico design of recombinant multi-epitope vaccine against influenza A virus	17
Esmraldi: efficient methods for the fusion of mass spectrometry and magnetic resonance images	17
Machine learning-based prediction of survival prognosis in cervical cancer	17
IDSSIM: an lncRNA functional similarity calculation model based on an improved disease semantic similarity method	17
GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification	17
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	17
Sfcnn: a novel scoring function based on 3D convolutional neural network for accurate and stable protein–ligand affinity prediction	17
Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach	17
Co-AMPpred for in silico-aided predictions of antimicrobial peptides by integrating composition-based features	17
Negative binomial additive model for RNA-Seq data analysis	17
ORFik: a comprehensive R toolkit for the analysis of translation	17
Comparative evaluation of full-length isoform quantification from RNA-Seq	17
The challenges of explainable AI in biomedical data science	17
A data management infrastructure for the integration of imaging and omics data in life sciences	17
Prediction of antimicrobial peptides toxicity based on their physico-chemical properties using machine learning techniques	17
DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing	16
EDLm6APred: ensemble deep learning approach for mRNA m6A site prediction	16
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks	16
FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences	16
MEPHAS: an interactive graphical user interface for medical and pharmaceutical statistical analysis with R and Shiny	16
MRI-based brain tumor segmentation using FPGA-accelerated neural network	16
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network	16
DeeplyEssential: a deep neural network for predicting essential genes in microbes	16
The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data	16
Exploring the dynamics and interplay of human papillomavirus and cervical tumorigenesis by integrating biological data into a mathematical model	16
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding	16
DeepLPI: a multimodal deep learning method for predicting the interactions between lncRNAs and protein isoforms	16
Combined embedding model for MiRNA-disease association prediction	16
Multi-dimensional data integration algorithm based on random walk with restart	16
Fast activation maximization for molecular sequence design	16
FEGS: a novel feature extraction model for protein sequences and its applications	16
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data	16
geneHapR: an R package for gene haplotypic statistics and visualization	16
Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci	16
NormiRazor: tool applying GPU-accelerated computing for determination of internal references in microRNA transcription studies	16
Prediction of lung cancer using gene expression and deep learning with KL divergence gene selection	16
Identification of CD8+ T cell epitopes through proteasome cleavage site predictions	16
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	16
A multitask transfer learning framework for the prediction of virus-human protein–protein interactions	16
Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks	16
R.ROSETTA: an interpretable machine learning framework	15
Using optimal control to understand complex metabolic pathways	15
Identification of early mild cognitive impairment using multi-modal data and graph convolutional networks	15
Concatenation of paired-end reads improves taxonomic classification of amplicons for profiling microbial communities	15
GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences	15
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine	15
Prediction of hot spots in protein–DNA binding interfaces based on supervised isometric feature mapping and extreme gradient boosting	15
A novel method for drug-target interaction prediction based on graph transformers model	15
DRPnet: automated particle picking in cryo-electron micrographs using deep regression	15
Prediction of enhancer–promoter interactions using the cross-cell type information and domain adversarial neural network	15
BioRel: towards large-scale biomedical relation extraction	15
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides	15
DSCMF: prediction of LncRNA-disease associations based on dual sparse collaborative matrix factorization	15
Super.FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data	15
CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis	15
DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning	15
nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs	15