BMC Bioinformatics

Article	Citations
Moment estimators of relatedness from low-depth whole-genome sequencing data	1216
Hybrid generative adversarial network based on frequency and spatial domain for histopathological image synthesis	847
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	244
Multiview clustering of multi-omics data integration by using a penalty model	187
Constructing multilayer PPI networks based on homologous proteins and integrating multiple PageRank to identify essential proteins	157
ProToDeviseR: an automated protein topology scheme generator	134
Cross-validation for training and testing co-occurrence network inference algorithms	122
Identifying host-specific amino acid signatures for influenza A viruses using an adjusted entropy measure	102
ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition	93
MRI-based brain tumor segmentation using FPGA-accelerated neural network	88
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data	87
llperm: a permutation of regressor residuals test for microbiome data	83
Statistical inference for a quasi birth–death model of RNA transcription	76
Metadag: a web tool to generate and analyse metabolic networks	74
CellMAP: an open-source software tool to batch-process cell topography and stiffness maps collected with an atomic force microscope	71
Instance-level semantic segmentation of nuclei based on multimodal structure encoding	64
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	62
TockyPrep: data preprocessing methods for flow cytometric fluorescent timer analysis	62
Overlapping group screening for detection of gene-environment interactions with application to TCGA high-dimensional survival genomic data	58
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	58
A global $$Anopheles\ gambiae$$ gene co-expression network constructed from hundreds of experimental conditions with missing values	57
Identification and validation of tumor-infiltrating lymphocyte-related prognosis signature for predicting prognosis and immunotherapeutic response in bladder cancer	55
bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data	55
Cancer survival prediction by learning comprehensive deep feature representation for multiple types of genetic data	54
Improvement of variables interpretability in kernel PCA	54

Machine learning techniques on homological persistence features for prostate cancer diagnosis	51
nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs	50
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	49
SNARER: new molecular descriptors for SNARE proteins classification	49
Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction	49
Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone	49
Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning	48
A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches	48
Efficient automatic 3D segmentation of cell nuclei for high-content screening	48
Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP	48
Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches	47
Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing	46
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	43
Supervised promoter recognition: a benchmark framework	43
Deep learning-based classification model for GPR151 activator activity prediction	42
PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data	42
ELIMINATOR: essentiality analysis using multisystem networks and integer programming	42
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis	42
A multimodal deep learning model to infer cell-type-specific functional gene networks	42
Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation	40
Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species	40
Joint deep learning for batch effect removal and classification toward MALDI MS based metabolomics	40
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	39
Symptoms are known by their companies: towards association guided disease diagnosis assistant	39
Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data	39
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	38
Advancing drug–target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining	37
LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification	37
RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics	37
Sketching and sampling approaches for fast and accurate long read classification	37
Development and validation of a coagulation-related genes prognostic model for hepatocellular carcinoma	37
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	37
ACO:lossless quality score compression based on adaptive coding order	37
A systematic comparison of human mitochondrial genome assembly tools	37
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders	36
PIKE-R2P: Protein–protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction	36
MIPPIS: protein–protein interaction site prediction network with multi-information fusion	35
Visualizing the knowledge structure and evolution of bioinformatics	35
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	35
Scalable transcriptomics analysis with Dask: applications in data science and machine learning	35
CirPred, the first structure modeling and linker design system for circularly permuted proteins	35
B-LBConA: a medical entity disambiguation model based on Bio-LinkBERT and context-aware mechanism	35
Novel drug-target interactions via link prediction and network embedding	35
MDFGNN-SMMA: prediction of potential small molecule-miRNA associations based on multi-source data fusion and graph neural networks	34
DeepASDPred: a CNN-LSTM-based deep learning method for Autism spectrum disorders risk RNA identification	34
Concentration optimization of combinatorial drugs using Markov chain-based models	34
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	34
RUBic: rapid unsupervised biclustering	34
BiomiX, a user-friendly bioinformatic tool for democratized analysis and integration of multiomics data	33
Direct coupling analysis and the attention mechanism	32

Conditional similarity triplets enable covariate-informed representations of single-cell data	32
CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity	32
HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer	31
Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks	31
CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs	31
A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers	31
RAE1 is a prognostic biomarker and is correlated with clinicopathological characteristics of patients with hepatocellular carcinoma	31
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	31
CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs	31
Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization	30
Selection of optimal quantile protein biomarkers based on cell-level immunohistochemistry data	30
Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification	30
A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs	29
123VCF: an intuitive and efficient tool for filtering VCF files	29
tRNA-derived fragments as novel potential biomarkers for relapsed/refractory multiple myeloma	29
Evaluation of word embedding models to extract and predict surgical data in breast cancer	29
Hierarchical representation for PPI sites prediction	29
The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data	28
Learning self-supervised molecular representations for drug–drug interaction prediction	28
Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability	28
PredAOT: a computational framework for prediction of acute oral toxicity based on multiple random forest models	28
SpotitPy: a semi-automated tool for object-based co-localization of fluorescent labels in microscopy images	28
Dose–response prediction for in-vitro drug combination datasets: a probabilistic approach	28
SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data	27
Mora: abundance aware metagenomic read re-assignment for disentangling similar strains	27
Sparse sliced inverse regression for high dimensional data analysis	27
Establishment and validation of a predictive model of preeclampsia based on transcriptional signatures of 43 genes in decidua basalis and peripheral blood	26
Cellstitch: 3D cellular anisotropic image segmentation via optimal transport	26
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains	26
scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport	26
Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks	26
Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes	26
A comparison of embedding aggregation strategies in drug–target interaction prediction	26
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach	26
Hierarchical shared transfer learning for biomedical named entity recognition	26
Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique	26
SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications	25
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome	25
Volumetric macromolecule identification in cryo-electron tomograms using capsule networks	25
A protein network refinement method based on module discovery and biological information	25
Correction: Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index	25
Explainable deep drug–target representations for binding affinity prediction	25
Modeling relaxation experiments with a mechanistic model of gene expression	25
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis	25
Using dual-network-analyser for communities detecting in dual networks	25
EnsembleSplice: ensemble deep learning model for splice site prediction	24
Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells	24
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	24
SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions	24
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	24
REDalign: accurate RNA structural alignment using residual encoder-decoder network	24
MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset’s complexity	24
Rapid bacterial identification through volatile organic compound analysis and deep learning	24
RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms	24
Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments	24
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction	23
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization	23
Supervised topological data analysis for MALDI mass spectrometry imaging applications	23
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	23
A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data	23
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences	23
Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks	23
Designing and delivering bioinformatics project-based learning in East Africa	23
A mixed-effects stochastic model reveals clonal dominance in gene therapy safety studies	23
ERStruct: a fast Python package for inferring the number of top principal components from whole genome sequencing data	23
Predicting the pathogenicity of bacterial genomes using widely spread protein families	22
A Poisson reduced-rank regression model for association mapping in sequencing data	22
EasySMPC: a simple but powerful no-code tool for practical secure multiparty computation	22
Distance correlation application to gene co-expression network analysis	22
Correction to: An introduction to new robust linear and monotonic correlation coefficients	22
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding	22
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon	22
Predicting environmentally responsive transgenerational differential DNA methylated regions (epimutations) in the genome using a hybrid deep-machine learning approach	21
Predictive modeling of gene expression regulation	21
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	21
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells	21
SALON ontology for the formal description of sequence alignments	21
gcMECM: graph clustering of mutual exclusivity of cancer mutations	21
Acute stress reduces population-level metabolic and proteomic variation	21
Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy	21

Efficient design of synthetic gene circuits under cell-to-cell variability	21
airpg: automatically accessing the inverted repeats of archived plastid genomes	21
A risk factor attention-based model for cardiovascular disease prediction	21
Graph regularized non-negative matrix factorization with $$L_{2,1}$$ norm regularization terms for drug–target interactions prediction	21
Deep learning and multi-omics approach to predict drug responses in cancer	20
GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data	20
A new method for exploring gene–gene and gene–environment interactions in GWAS with tree ensemble methods and SHAP values	20
Sparse clusterability: testing for cluster structure in high dimensions	20
Predicting biological pathways of chemical compounds with a profile-inspired approach	20
Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques	20
kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes	20
EG-TransUNet: a transformer-based U-Net with enhanced and guided models for biomedical image segmentation	20
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life	20
KATZNCP: a miRNA–disease association prediction model integrating KATZ algorithm and network consistency projection	20
PDA-PRGCN: identification of Piwi-interacting RNA-disease associations through subgraph projection and residual scaling-based feature augmentation	20
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	20
PIGNON: a protein–protein interaction-guided functional enrichment analysis for quantitative proteomics	20
In silico drug repositioning using deep learning and comprehensive similarity measures	20
Predicting weighted unobserved nodes in a regulatory network using answer set programming	19
Reply: Correspondence on NanoVar’s performance outlined by Jiang T. et al. in ‘Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation’	19
MTG-Link: leveraging barcode information from linked-reads to assemble specific loci	19
CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques	19
Normalization of gene expression data revisited: the three viewpoints of the transcriptome in human skeletal muscle undergoing load-induced hypertrophy and why they matter	19
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information	19
Velo-Predictor: an ensemble learning pipeline for RNA velocity prediction	19
Optimizing biomedical information retrieval with a keyword frequency-driven prompt enhancement strategy	19
Prediction of the effects of small molecules on the gut microbiome using machine learning method integrating with optimal molecular features	19
Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization	19
Correspondence on NanoVar’s performance outlined by Jiang T. et al. in “Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation”	19
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	19
xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes	19
Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis	18
DI2: prior-free and multi-item discretization of biological data and its applications	18
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments	18
Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data	18
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation	18
Quantitative prediction model for affinity of drug–target interactions based on molecular vibrations and overall system of ligand-receptor	18
nPoRe: n-polymer realigner for improved pileup-based variant calling	18
Estimating colocalization probability from limited summary statistics	18
Integrated structure-based protein interface prediction	18
Abstraction-based segmental simulation of reaction networks using adaptive memoization	18
Mabs, a suite of tools for gene-informed genome assembly	18
CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter	18
Pan-genome de Bruijn graph using the bidirectional FM-index	17
A novel nonparametric computational strategy for identifying differential methylation regions	17
Clinlabomics: leveraging clinical laboratory data by data mining strategies	17
Correction: Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly	17
ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications	17
Tpgen: a language model for stable protein design with a specific topology structure	17
Examination of blood samples using deep learning and mobile microscopy	17
adabmDCA: adaptive Boltzmann machine learning for biological sequences	17
InClust+: the deep generative framework with mask modules for multimodal data integration, imputation, and cross-modal generation	17
IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics	17
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations	17
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	17
Predicting lncRNA–protein interactions through deep learning framework employing multiple features and random forest algorithm	17
Correction: Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data	17
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions	17
CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides	17
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	17
A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns	17
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	17
Ideal adaptive control in biological systems: an analysis of $$\mathbb {P}$$-invariance and dynamical compensation properties	17
PxBLAT: an efficient python binding library for BLAT	16
RNA-clique: a method for computing genetic distances from RNA-seq data	16
A comprehensive database for integrated analysis of omics data in autoimmune diseases	16
MetaTron: advancing biomedical annotation empowering relation annotation and collaboration	16
gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network	16
CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes	16
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information	16
Benchmarking robustness of deep neural networks in semantic segmentation of fluorescence microscopy images	16
Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants	16
Identifying biomarkers for breast cancer by gene regulatory network rewiring	16
LinkedImm: a linked data graph database for integrating immunological data	16
DeSP: a systematic DNA storage error simulation pipeline	16
QuickPed: an online tool for drawing pedigrees and analysing relatedness	16
Mixture density networks for the indirect estimation of reference intervals	16
Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers	16
A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study	16
DiviK: divisive intelligent K-means for hands-free unsupervised clustering in big biological data	16
Multiblock variable influence on orthogonal projections (MB-VIOP) for enhanced interpretation of total, global, local and unique variations in OnPLS models	15
Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs	15
End-to-end learning for compound activity prediction based on binding pocket information	15
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	15
Completing a genomic characterisation of microscopic tumour samples with copy number	15
Critical assessment of on-premise approaches to scalable genome analysis	15
Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly	15
Classifying microscopic images as acute lymphoblastic leukemia by Resnet ensemble model and Taguchi method	15
Discovery of moiety preference by Shapley value in protein kinase family using random forest models	15
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	15
Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma	15
scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data	15
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	15
scDIOR: single cell RNA-seq data IO software	15
PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data	15