BMC Bioinformatics

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1333
A novel nonparametric computational strategy for identifying differential methylation regions	940
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	268
REDalign: accurate RNA structural alignment using residual encoder-decoder network	218
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	176
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	139
Predictive modeling of gene expression regulation	127
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	100
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	95
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	90
SALON ontology for the formal description of sequence alignments	79
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	77
Abstraction-based segmental simulation of reaction networks using adaptive memoization	71
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	66
airpg: automatically accessing the inverted repeats of archived plastid genomes	65
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	65
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information	62
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	60
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	60
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	58
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	57
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	55
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	55
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	55
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	53

PIGNON: a protein–protein interaction-guided functional enrichment analysis for quantitative proteomics	51
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	50
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	49
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	49
Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images	48
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	47
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	47
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	46
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	45
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	44
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	44
A gene based combination test using GWAS summary data	44
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	44
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon	43
Examination of blood samples using deep learning and mobile microscopy	43
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	43
Multilayer network alignment based on topological assessment via embeddings	43
Deep learning and multi-omics approach to predict drug responses in cancer	42
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	42
Mabs, a suite of tools for gene-informed genome assembly	41
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	40
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	40
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	40
Improving the recall of biomedical named entity recognition with label re-correction and knowledge distillation	39
DiseaseNet: a transfer learning approach to noncommunicable disease classification	39
False discovery rate estimation using candidate peptides for each spectrum	39
Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis	39
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	38
Secondary structure specific simpler prediction models for protein backbone angles	38
Multi-view manifold regularized compact low-rank representation for cancer samples clustering on multi-omics data	38
Evaluation of tree-based statistical learning methods for constructing genetic risk scores	37
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	37
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	36
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	36
Forecasting the spread of COVID-19 using LSTM network	35
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	35
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	35
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	35
A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells	35
A-Prot: protein structure modeling using MSA transformer	34
BADASS: BActeriocin-Diversity ASsessment Software	34
Semantic interoperability: ontological unpacking of a viral conceptual model	34
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	34
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	33
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	33
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	33
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	32
INFLECT: an R-package for cytometry cluster evaluation using marker modality	31
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	31
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	31

VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	31
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	31
A targeted solution for estimating the cell-type composition of bulk samples	30
Identification of fish species through tRNA-based primer design	30
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	30
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM	30
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	30
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	30
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	30
SVhound: detection of regions that harbor yet undetected structural variation	30
Using empirical biological knowledge to infer regulatory networks from multi-omics data	29
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	29
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	29
Can large language models understand molecules?	28
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data	28
A deep learning approach to predict inter-omics interactions in multi-layer networks	28
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	28
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions	28
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species	28
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	28
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	28
A graph neural network framework for mapping histological topology in oral mucosal tissue	28
Single-cell classification using graph convolutional networks	28
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	28
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	28
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	28
Deafness gene screening based on a multilevel cascaded BPNN model	27
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	27
HGGA: hierarchical guided genome assembler	27
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	26
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	26
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	26
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	26
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	26
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	26
StrongestPath: a Cytoscape application for protein–protein interaction analysis	26
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning	26
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	26
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	26
Conformal novelty detection for multiple metabolic networks	25
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	25
Predicting subcellular location of protein with evolution information and sequence-based deep learning	25
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	25
Inference of single-cell network using mutual information for scRNA-seq data analysis	25
Classifying chest CT images as COVID-19 positive/negative using a convolutional neural network ensemble model and uniform experimental design method	25
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	25
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	25
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	25
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	24
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	24
A tensor-based bi-random walks model for protein function prediction	24
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models	24
SwarmTCR: a computational approach to predict the specificity of T cell receptors	24
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	24
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	24
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	24
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	24
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	24
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	24
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	24
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	24
Reducing Boolean networks with backward equivalence	24
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction	23
FragGeneScanRs: faster gene prediction for short reads	23
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	23
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	23
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	23
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	23
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	23
Fractal feature selection model for enhancing high-dimensional biological problems	23
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	23
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	23
Statistical methods and resources for biomarker discovery using metabolomics	23
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	22
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins	22
Taxanorm: a novel taxa-specific normalization approach for microbiome data	22
Extract antibody and antigen names from biomedical literature	22
Protein complexes detection based on node local properties and gene expression in PPI weighted networks	22
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	22
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	22

A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	22
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	22
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	22
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences	21
A consensus-based ensemble approach to improve transcriptome assembly	21
Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development	21
LPMX: a pure rootless composable container system	21
Wavelet Screening: a novel approach to analyzing GWAS data	21
DiCleave: a deep learning model for predicting human Dicer cleavage sites	21
Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network	21
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	21
Rendering protein mutation movies with MutAmore	21
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	20
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	20
Comparison of sequencing data processing pipelines and application to underrepresented African human populations	20
Ion-pumping microbial rhodopsin protein classification by machine learning approach	20
Correction to: Impact of concurrency on the performance of a whole exome sequencing pipeline	20
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	20
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	20
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump	20
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	19
Comparing neural models for nested and overlapping biomedical event detection	19
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	19
ProTaxoVis—protein taxonomic visualisation of presence	19
An approach for proteins and their encoding genes synonyms integration based on protein ontology	19
PhenoExam: gene set analyses through integration of different phenotype databases	19
Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia	19
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	19
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	19
Impact of gene annotation choice on the quantification of RNA-seq data	19
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	19
GVC: efficient random access compression for gene sequence variations	19
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	19
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	19
Image-centric compression of protein structures improves space savings	19
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	18
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	18
Optimize data-driven multi-agent simulation for COVID-19 transmission	18
SEMgsa: topology-based pathway enrichment analysis with structural equation models	18
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	18
Multi-objective data enhancement for deep learning-based ultrasound analysis	18
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions	18
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	18
Detection of cell markers from single cell RNA-seq with sc2marker	18
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	18
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	17
Automatic generation of pseudoknotted RNAs taxonomy	17
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept	17
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study	17
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization	17
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	17
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	17
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	17
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	17
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	17
FindCSV: a long-read based method for detecting complex structural variations	17
Correction to: Mining a stroke knowledge graph from literature	17
Correction to: Moonlighting protein prediction using physico‑chemical and evolutional properties via machine learning methods	17
PDBeCIF: an open-source mmCIF/CIF parsing and processing package	17
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	17
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction	17
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets	17
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	17
Correction: On Bayesian modeling of censored data in JAGS	17
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet	17
ANINet: a deep neural network for skull ancestry estimation	16
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations	16
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	16
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species	16
Metacells untangle large and complex single-cell transcriptome networks	16
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	16
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures	16
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes	16
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	16
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	16
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	16
BarWare: efficient software tools for barcoded single-cell genomics	16
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP	16
PRED-LD: efficient imputation of GWAS summary statistics	16
Optimizing diabetes classification with a machine learning-based framework	16
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	16
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	16
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants	16
Interpretable deep learning methods for multiview learning	16
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification	16
IMSE: interaction information attention and molecular structure based drug drug interaction extraction	16
MBECS: Microbiome Batch Effects Correction Suite	16
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique	16
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	15
Genealyzer: web application for the analysis and comparison of gene expression data	15
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App	15
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions	15
Using individual barcodes to increase quantification power of massively parallel reporter assays	15
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	15
circGPA: circRNA functional annotation based on probability-generating functions	15