BMC Bioinformatics

Article	Citations
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	1059
Establishment and validation of a predictive model of preeclampsia based on transcriptional signatures of 43 genes in decidua basalis and peripheral blood	683
IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics	294
MLM-based typographical error correction of unstructured medical texts for named entity recognition	182
Enumeration and comprehensive in-silico modeling of three-helix bundle structures composed of typical αα-hairpins	142
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	121
scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis	115
B-LBConA: a medical entity disambiguation model based on Bio-LinkBERT and context-aware mechanism	110
Cortexa: a comprehensive resource for studying gene expression and alternative splicing in the murine brain	94
MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset’s complexity	90
Performance improvement for a 2D convolutional neural network by using SSC encoding on protein–protein interaction tasks	84
HAVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences	82
Development of the International Classification of Diseases Ontology (ICDO) and its application for COVID-19 diagnostic data analysis	78
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	70
Mixture density networks for the indirect estimation of reference intervals	70
Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments	68
EnsembleSplice: ensemble deep learning model for splice site prediction	68
A mixed-effects stochastic model reveals clonal dominance in gene therapy safety studies	62
Consensus clustering for Bayesian mixture models	60
Predicting biological pathways of chemical compounds with a profile-inspired approach	57
EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA–protein interaction prediction	54
Normalization of gene expression data revisited: the three viewpoints of the transcriptome in human skeletal muscle undergoing load-induced hypertrophy and why they matter	51
Multiview clustering of multi-omics data integration by using a penalty model	51
Assigning protein function from domain-function associations using DomFun	50
Aristotle: stratified causal discovery for omics data	46

gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network	46
DiviK: divisive intelligent K-means for hands-free unsupervised clustering in big biological data	45
InClust+: the deep generative framework with mask modules for multimodal data integration, imputation, and cross-modal generation	45
A comprehensive database for integrated analysis of omics data in autoimmune diseases	45
Using dual-network-analyser for communities detecting in dual networks	44
A Poisson reduced-rank regression model for association mapping in sequencing data	44
Identifying host-specific amino acid signatures for influenza A viruses using an adjusted entropy measure	43
ReRF-Pred: predicting amyloidogenic regions of proteins based on their pseudo amino acid composition and tripeptide composition	42
Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants	42
Volumetric macromolecule identification in cryo-electron tomograms using capsule networks	40
Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life	40
CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides	38
llperm: a permutation of regressor residuals test for microbiome data	38
ERStruct: a fast Python package for inferring the number of top principal components from whole genome sequencing data	38
Acute stress reduces population-level metabolic and proteomic variation	38
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	37
AutoDTI++: deep unsupervised learning for DTI prediction by autoencoders	37
Statistical inference for a quasi birth–death model of RNA transcription	36
GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data	36
Hydropathicity-based prediction of pain-causing NaV1.7 variants	35
SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications	35
Identifying biomarkers for breast cancer by gene regulatory network rewiring	35
Critical assessment of on-premise approaches to scalable genome analysis	34
Fusing graph transformer with multi-aggregate GCN for enhanced drug–disease associations prediction	34
Predicting weighted unobserved nodes in a regulatory network using answer set programming	33
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	33
Overlapping group screening for detection of gene-environment interactions with application to TCGA high-dimensional survival genomic data	32
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	32
A global $$Anopheles\ gambiae$$ gene co-expression network constructed from hundreds of experimental conditions with missing values	31
Pan-genome de Bruijn graph using the bidirectional FM-index	31
Efficient design of synthetic gene circuits under cell-to-cell variability	31
Using machine learning to determine the correlation between physiological and environmental parameters and the induction of acute mountain sickness	31
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	31
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	30
QuickPed: an online tool for drawing pedigrees and analysing relatedness	30
A novel nonparametric computational strategy for identifying differential methylation regions	30
adabmDCA: adaptive Boltzmann machine learning for biological sequences	30
Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements	30
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	30
bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data	30
RNA-clique: a method for computing genetic distances from RNA-seq data	30
Improvement of variables interpretability in kernel PCA	30
Identification and validation of tumor-infiltrating lymphocyte-related prognosis signature for predicting prognosis and immunotherapeutic response in bladder cancer	30
A hierarchical spike-and-slab model for pan-cancer survival using pan-omic data	29
CNN-Siam: multimodal siamese CNN-based deep learning approach for drug‒drug interaction prediction	29
The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data	29
MUREN: a robust and multi-reference approach of RNA-seq transcript normalization	29
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio–temporal architectures of cells	29
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	29
Data-driven biological network alignment that uses topological, sequence, and functional information	28

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone	28
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	28
An uncertainty-based interpretable deep learning framework for predicting breast cancer outcome	28
SNARER: new molecular descriptors for SNARE proteins classification	27
Efficient automatic 3D segmentation of cell nuclei for high-content screening	27
Distance correlation application to gene co-expression network analysis	27
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor	27
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	27
Using flux theory in dynamic omics data sets to identify differentially changing signals using DPoP	26
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation	26
scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data	26
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	26
Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks	26
Supervised promoter recognition: a benchmark framework	25
Pre-capture multiplexing provides additional power to detect copy number variation in exome sequencing	25
A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study	25
Supervised topological data analysis for MALDI mass spectrometry imaging applications	25
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	25
SAPFIR: A webserver for the identification of alternative protein features	25
CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter	25
Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs	24
Risk prediction for dermatomyositis-associated hepatocellular carcinoma	24
ELIMINATOR: essentiality analysis using multisystem networks and integer programming	24
Deep learning-based classification model for GPR151 activator activity prediction	24
PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data	24
Boosting tissue-specific prediction of active cis-regulatory regions through deep learning and Bayesian optimization techniques	24
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS	24
A multimodal deep learning model to infer cell-type-specific functional gene networks	24
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon	23
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis	23
Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting	23
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	23
PIKE-R2P: Protein–protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction	23
Proteome-wide analysis of Coxiella burnetii for conserved T-cell epitopes with presentation across multiple host species	22
Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation	22
BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations	22
Gene regulatory network inference based on a nonhomogeneous dynamic Bayesian network model with an improved Markov Monte Carlo sampling	22
Simultant: simultaneous curve fitting of functions and differential equations using analytical gradient calculations	22
Discovery of moiety preference by Shapley value in protein kinase family using random forest models	22
Bayesian inference for identifying tumour-specific cancer dependencies through integration of ex-vivo drug response assays and drug-protein profiling	22
Fast and accurate genome-wide predictions and structural modeling of protein–protein interactions using Galaxy	22
aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights	22
PIGNON: a protein–protein interaction-guided functional enrichment analysis for quantitative proteomics	22
Joint deep learning for batch effect removal and classification toward MALDI MS based metabolomics	22
Ideal adaptive control in biological systems: an analysis of $$\mathbb {P}$$-invariance and dynamical compensation properties	22
MetaTron: advancing biomedical annotation empowering relation annotation and collaboration	22
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	21
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments	21
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”	21
IndelsRNAmute: predicting deleterious multiple point substitutions and indels mutations	21
topr: an R package for viewing and annotating genetic association results	21
Symptoms are known by their companies: towards association guided disease diagnosis assistant	21
SALON ontology for the formal description of sequence alignments	21
EG-TransUNet: a transformer-based U-Net with enhanced and guided models for biomedical image segmentation	21
Shrinkage estimation of gene interaction networks in single-cell RNA sequencing data	21
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	21
Multilayer network alignment based on topological assessment via embeddings	21
Dualmarker: a flexible toolset for exploratory analysis of combinatorial dual biomarkers for clinical efficacy	21
DGDTA: dynamic graph attention network for predicting drug–target binding affinity	21
Prediction of the effects of small molecules on the gut microbiome using machine learning method integrating with optimal molecular features	20
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	20
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	20
CarSite-II: an integrated classification algorithm for identifying carbonylated sites based on K-means similarity-based undersampling and synthetic minority oversampling techniques	20
trioPhaser: using Mendelian inheritance logic to improve genomic phasing of trios	20
End-to-end learning for compound activity prediction based on binding pocket information	20
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information	20
RankCompV3: a differential expression analysis algorithm based on relative expression orderings and applications in single-cell RNA transcriptomics	20
Tpgen: a language model for stable protein design with a specific topology structure	20
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’	20
Predictive modeling of gene expression regulation	20
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	20
Pattern recognition of topologically associating domains using deep learning	20
scDIOR: single cell RNA-seq data IO software	20
A systematic comparison of human mitochondrial genome assembly tools	19
Contrastive self-supervised clustering of scRNA-seq data	19
ACO:lossless quality score compression based on adaptive coding order	19
MADGAN: unsupervised medical anomaly detection GAN using multiple adjacent brain MRI slice reconstruction	19
Development and validation of a coagulation-related genes prognostic model for hepatocellular carcinoma	19
Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis	19
Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS	19

CNN-based two-branch multi-scale feature extraction network for retrosynthesis prediction	19
LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification	19
Weighted minimum feedback vertex sets and implementation in human cancer genes detection	19
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	18
Sketching and sampling approaches for fast and accurate long read classification	18
A graph-based algorithm for detecting rigid domains in protein structures	18
PCirc: random forest-based plant circRNA identification software	18
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata	18
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	18
Learning self-supervised molecular representations for drug–drug interaction prediction	18
kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes	18
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	18
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	18
MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data	18
Concentration optimization of combinatorial drugs using Markov chain-based models	18
Lantern: an integrative repository of functional annotations for lncRNAs in the human genome	18
RUBic: rapid unsupervised biclustering	18
DI2: prior-free and multi-item discretization of biological data and its applications	18
Exploration of chemical space with partial labeled noisy student self-training and self-supervised graph embedding	18
Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images	17
Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning	17
LinkedImm: a linked data graph database for integrating immunological data	17
CrisprVi: a software for visualizing and analyzing CRISPR sequences of prokaryotes	17
gcMECM: graph clustering of mutual exclusivity of cancer mutations	17
In silico drug repositioning based on the integration of chemical, genomic and pharmacological spaces	17
A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches	17
CMIC: an efficient quality score compressor with random access functionality	17
Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks	17
Noisecut: a python package for noise-tolerant classification of binary data using prior knowledge integration and max-cut solutions	17
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization	17
Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers	17
Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches	17
Selection of optimal quantile protein biomarkers based on cell-level immunohistochemistry data	16
RAE1 is a prognostic biomarker and is correlated with clinicopathological characteristics of patients with hepatocellular carcinoma	16
Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization	16
nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs	16
tRNA-derived fragments as novel potential biomarkers for relapsed/refractory multiple myeloma	16
CircNetVis: an interactive web application for visualizing interaction networks of circular RNAs	16
CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs	16
A machine learning framework that integrates multi-omics data predicts cancer-related LncRNAs	16
Quantitative prediction model for affinity of drug–target interactions based on molecular vibrations and overall system of ligand-receptor	16
Moment estimators of relatedness from low-depth whole-genome sequencing data	16
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	16
Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein	16
Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification	16
Evaluation of word embedding models to extract and predict surgical data in breast cancer	16
A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data	16
Asc-Seurat: analytical single-cell Seurat-based web application	15
Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes	15
MTG-Link: leveraging barcode information from linked-reads to assemble specific loci	15
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions	15
scEGOT: single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport	15
Mora: abundance aware metagenomic read re-assignment for disentangling similar strains	15
Hierarchical representation for PPI sites prediction	15
Integrated structure-based protein interface prediction	15
Examination of blood samples using deep learning and mobile microscopy	15
A risk factor attention-based model for cardiovascular disease prediction	15
tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R	15
Mabs, a suite of tools for gene-informed genome assembly	15
Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells	15
SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data	15
Multiblock variable influence on orthogonal projections (MB-VIOP) for enhanced interpretation of total, global, local and unique variations in OnPLS models	15
PWN: enhanced random walk on a warped network for disease target prioritization	15
123VCF: an intuitive and efficient tool for filtering VCF files	15
Explainable deep drug–target representations for binding affinity prediction	15
SCOUR: a stepwise machine learning framework for predicting metabolite-dependent regulatory interactions	15
Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers	15
PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data	15
Sparse sliced inverse regression for high dimensional data analysis	15
Detecting genomic deletions from high-throughput sequence data with unsupervised learning	15
vcf2fhir: a utility to convert VCF files into HL7 FHIR format for genomics-EHR integration	15
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	15
Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line	15
Dyport: dynamic importance-based biomedical hypothesis generation benchmarking technique	14
Cellstitch: 3D cellular anisotropic image segmentation via optimal transport	14
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data	14
In silico drug repositioning using deep learning and comprehensive similarity measures	14
xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes	14
Multi-dimensional data integration algorithm based on random walk with restart	14
NeuronBridge: an intuitive web application for neuronal morphology search across large data sets	14
Robust optimization of convolutional neural networks with a uniform experiment design method: a case of phonocardiogram testing in patients with heart diseases	14
A comparison of embedding aggregation strategies in drug–target interaction prediction	14
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	14
Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes	14
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	14
KATZNCP: a miRNA–disease association prediction model integrating KATZ algorithm and network consistency projection	14
PopMLvis: a tool for analysis and visualization of population structure using genotype data from genome-wide association studies	14
Polynomial superlevel set representation of the multistationarity region of chemical reaction networks	14
Cellograph: a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks	14
nPoRe: n-polymer realigner for improved pileup-based variant calling	14
PangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains	14
Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data	14
MSPCD: predicting circRNA-disease associations via integrating multi-source data and hierarchical neural network	14
Modeling relaxation experiments with a mechanistic model of gene expression	13
DrGA: cancer driver gene analysis in a simpler manner	13