BMC Bioinformatics

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1511
A novel nonparametric computational strategy for identifying differential methylation regions	1105
REDalign: accurate RNA structural alignment using residual encoder-decoder network	317
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	253
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	213
Predictive modeling of gene expression regulation	151
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	132
SALON ontology for the formal description of sequence alignments	95
Abstraction-based segmental simulation of reaction networks using adaptive memoization	86
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	86
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information	85
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	85
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	83
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	77
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	73
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	72
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	70
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	69
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	67
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	63
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	62
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	60
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	59
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	59
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	58

CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	57
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	54
Multilayer network alignment based on topological assessment via embeddings	53
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	53
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	53
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	52
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	51
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	50
Mabs, a suite of tools for gene-informed genome assembly	50
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	50
A gene based combination test using GWAS summary data	47
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	46
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	46
Examination of blood samples using deep learning and mobile microscopy	46
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	46
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	46
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	45
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	45
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	45
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	45
Deep learning and multi-omics approach to predict drug responses in cancer	44
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	44
Secondary structure specific simpler prediction models for protein backbone angles	43
Multi-view manifold regularized compact low-rank representation for cancer samples clustering on multi-omics data	43
A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells	42
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures	41
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	41
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	40
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	40
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons	40
Semantic interoperability: ontological unpacking of a viral conceptual model	39
Can large language models understand molecules?	39
False discovery rate estimation using candidate peptides for each spectrum	39
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	38
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species	38
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	38
BADASS: BActeriocin-Diversity ASsessment Software	38
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	36
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	35
Using empirical biological knowledge to infer regulatory networks from multi-omics data	35
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	35
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	34
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM	34
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	33
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	33
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	32
INFLECT: an R-package for cytometry cluster evaluation using marker modality	32
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	32
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	32
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	32

Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	31
Identification of fish species through tRNA-based primer design	31
A targeted solution for estimating the cell-type composition of bulk samples	31
SVhound: detection of regions that harbor yet undetected structural variation	31
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	31
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	31
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	30
DiseaseNet: a transfer learning approach to noncommunicable disease classification	30
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	30
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	30
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	30
A graph neural network framework for mapping histological topology in oral mucosal tissue	29
A-Prot: protein structure modeling using MSA transformer	29
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	29
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	29
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	29
Evaluation of tree-based statistical learning methods for constructing genetic risk scores	29
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	29
A deep learning approach to predict inter-omics interactions in multi-layer networks	28
HGGA: hierarchical guided genome assembler	28
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	28
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions	28
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	28
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	28
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	28
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	28
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	28
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	28
Deafness gene screening based on a multilevel cascaded BPNN model	28
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	27
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	27
Predicting subcellular location of protein with evolution information and sequence-based deep learning	27
Inference of single-cell network using mutual information for scRNA-seq data analysis	27
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	27
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	27
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	27
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	27
Conformal novelty detection for multiple metabolic networks	27
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	27
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	27
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	26
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	26
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models	26
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	26
Reducing Boolean networks with backward equivalence	26
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	25
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	25
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	25
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	25
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information	25
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	25
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	25
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	25
SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network	25
A tensor-based bi-random walks model for protein function prediction	24
FragGeneScanRs: faster gene prediction for short reads	24
Statistical methods and resources for biomarker discovery using metabolomics	24
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	24
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	24
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	24
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction	24
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	24
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	24
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	24
SwarmTCR: a computational approach to predict the specificity of T cell receptors	23
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning	23
Fractal feature selection model for enhancing high-dimensional biological problems	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
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	23
Extract antibody and antigen names from biomedical literature	23
Classifying chest CT images as COVID-19 positive/negative using a convolutional neural network ensemble model and uniform experimental design method	23
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	23
Protein complexes detection based on node local properties and gene expression in PPI weighted networks	23
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	22
Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network	22
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins	22
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	22
LPMX: a pure rootless composable container system	22
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	22

Wavelet Screening: a novel approach to analyzing GWAS data	22
A consensus-based ensemble approach to improve transcriptome assembly	21
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	21
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	21
Ion-pumping microbial rhodopsin protein classification by machine learning approach	21
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	21
DiCleave: a deep learning model for predicting human Dicer cleavage sites	21
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	21
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump	21
Rendering protein mutation movies with MutAmore	21
Comparison of sequencing data processing pipelines and application to underrepresented African human populations	21
Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia	21
Taxanorm: a novel taxa-specific normalization approach for microbiome data	20
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	20
The FBA solution space kernel: introduction and illustrative examples	20
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	20
GVC: efficient random access compression for gene sequence variations	20
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	20
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	20
An approach for proteins and their encoding genes synonyms integration based on protein ontology	19
Image-centric compression of protein structures improves space savings	19
Comparing neural models for nested and overlapping biomedical event detection	19
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	19
ProTaxoVis—protein taxonomic visualisation of presence	19
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	19
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	19
PhenoExam: gene set analyses through integration of different phenotype databases	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
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences	19
Correction to: Mining a stroke knowledge graph from literature	18
Optimize data-driven multi-agent simulation for COVID-19 transmission	18
Detection of cell markers from single cell RNA-seq with sc2marker	18
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	18
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	18
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions	18
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	18
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	18
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	18
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	18
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction	18
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study	18
Correction: On Bayesian modeling of censored data in JAGS	18
Impact of gene annotation choice on the quantification of RNA-seq data	18
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	18
SEMgsa: topology-based pathway enrichment analysis with structural equation models	18
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	18
FindCSV: a long-read based method for detecting complex structural variations	18
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	17
ANINet: a deep neural network for skull ancestry estimation	17
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	17
IMSE: interaction information attention and molecular structure based drug drug interaction extraction	17
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet	17
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	17
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	17
ProtPlat: an efficient pre-training platform for protein classification based on FastText	17
SNPxE: SNP-environment interaction pattern identifier	17
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	17
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	17
MSA: reproducible mutational signature attribution with confidence based on simulations	17
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery	17
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	17
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction	16
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations	16
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants	16
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models	16
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes	16
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	16
Using individual barcodes to increase quantification power of massively parallel reporter assays	16
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App	16
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP	16
KEGG orthology prediction of bacterial proteins using natural language processing	16
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	16
Multi-objective data enhancement for deep learning-based ultrasound analysis	16
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	16
PRED-LD: efficient imputation of GWAS summary statistics	16
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	16
MBECS: Microbiome Batch Effects Correction Suite	16
Genealyzer: web application for the analysis and comparison of gene expression data	16
BarWare: efficient software tools for barcoded single-cell genomics	16
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data	16
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept	16
Metacells untangle large and complex single-cell transcriptome networks	16
Clustering biological sequences with dynamic sequence similarity threshold	16
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	16
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information	16
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	16
Automatic generation of pseudoknotted RNAs taxonomy	16
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	16
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	16
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions	16
Drug response prediction using graph representation learning and Laplacian feature selection	15
HGDTI: predicting drug–target interaction by using information aggregation based on heterogeneous graph neural network	15
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data	15
SeQual-Stream: approaching stream processing to quality control of NGS datasets	15
Using neural networks to support high-quality evidence mapping	15