BMC Bioinformatics

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1455
A novel nonparametric computational strategy for identifying differential methylation regions	1046
REDalign: accurate RNA structural alignment using residual encoder-decoder network	300
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	246
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	198
Predictive modeling of gene expression regulation	148
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	130
SALON ontology for the formal description of sequence alignments	103
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	93
Abstraction-based segmental simulation of reaction networks using adaptive memoization	84
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	83
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information	77
airpg: automatically accessing the inverted repeats of archived plastid genomes	77
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	76
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	73
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	70
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	68
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	67
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	65
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	62
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	60
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	59
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	59
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	57
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	55

HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	54
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	53
Multilayer network alignment based on topological assessment via embeddings	52
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	52
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	51
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	50
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	50
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	50
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	50
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	49
A gene based combination test using GWAS summary data	47
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	47
Examination of blood samples using deep learning and mobile microscopy	46
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	46
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	45
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	45
Mabs, a suite of tools for gene-informed genome assembly	44
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon	44
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	43
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	43
Multi-view manifold regularized compact low-rank representation for cancer samples clustering on multi-omics data	42
Deep learning and multi-omics approach to predict drug responses in cancer	42
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	42
Secondary structure specific simpler prediction models for protein backbone angles	41
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	41
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	40
A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells	40
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures	40
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons	38
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	38
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	37
Semantic interoperability: ontological unpacking of a viral conceptual model	37
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	37
A deep learning approach to predict inter-omics interactions in multi-layer networks	37
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	36
BADASS: BActeriocin-Diversity ASsessment Software	36
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	36
False discovery rate estimation using candidate peptides for each spectrum	36
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	35
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	35
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	34
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	34
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	34
INFLECT: an R-package for cytometry cluster evaluation using marker modality	33
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	33
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	32
Identification of fish species through tRNA-based primer design	32
A targeted solution for estimating the cell-type composition of bulk samples	32
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	32
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	31

LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	31
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	31
SVhound: detection of regions that harbor yet undetected structural variation	31
Using empirical biological knowledge to infer regulatory networks from multi-omics data	31
DiseaseNet: a transfer learning approach to noncommunicable disease classification	31
A-Prot: protein structure modeling using MSA transformer	31
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	30
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	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	29
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species	29
Can large language models understand molecules?	29
Evaluation of tree-based statistical learning methods for constructing genetic risk scores	29
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	29
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	28
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions	28
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	28
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	28
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	28
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data	28
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM	28
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	28
A graph neural network framework for mapping histological topology in oral mucosal tissue	28
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	28
HGGA: hierarchical guided genome assembler	28
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	27
Fractal feature selection model for enhancing high-dimensional biological problems	27
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	27
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning	27
Deafness gene screening based on a multilevel cascaded BPNN model	27
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	27
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	27
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	27
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction	27
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	27
Predicting subcellular location of protein with evolution information and sequence-based deep learning	26
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	26
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	26
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	26
Conformal novelty detection for multiple metabolic networks	26
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	26
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	26
Inference of single-cell network using mutual information for scRNA-seq data analysis	26
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	26
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	26
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	25
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	25
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	25
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models	25
FragGeneScanRs: faster gene prediction for short reads	24
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	24
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	24
Classifying chest CT images as COVID-19 positive/negative using a convolutional neural network ensemble model and uniform experimental design method	24
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	24
Reducing Boolean networks with backward equivalence	24
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	24
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	24
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	24
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	23
A tensor-based bi-random walks model for protein function prediction	23
Statistical methods and resources for biomarker discovery using metabolomics	23
SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network	23
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information	23
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	23
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	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
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	22
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	22
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins	22
SwarmTCR: a computational approach to predict the specificity of T cell receptors	22
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	22
Extract antibody and antigen names from biomedical literature	22
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	22
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	22
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	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
Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network	21
DiCleave: a deep learning model for predicting human Dicer cleavage sites	21

Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	21
Rendering protein mutation movies with MutAmore	21
A consensus-based ensemble approach to improve transcriptome assembly	21
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	21
LPMX: a pure rootless composable container system	21
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	21
Wavelet Screening: a novel approach to analyzing GWAS data	21
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	21
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump	21
Ion-pumping microbial rhodopsin protein classification by machine learning approach	21
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	20
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	20
Comparison of sequencing data processing pipelines and application to underrepresented African human populations	20
Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia	20
Taxanorm: a novel taxa-specific normalization approach for microbiome data	20
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	20
Impact of gene annotation choice on the quantification of RNA-seq data	20
GVC: efficient random access compression for gene sequence variations	20
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	19
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	19
An approach for proteins and their encoding genes synonyms integration based on protein ontology	19
ProTaxoVis—protein taxonomic visualisation of presence	19
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	19
Image-centric compression of protein structures improves space savings	19
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	19
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	19
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences	19
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	19
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	19
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
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	18
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions	18
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	18
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	18
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	18
PhenoExam: gene set analyses through integration of different phenotype databases	18
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction	18
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets	18
Comparing neural models for nested and overlapping biomedical event detection	18
Detection of cell markers from single cell RNA-seq with sc2marker	18
SEMgsa: topology-based pathway enrichment analysis with structural equation models	18
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept	18
Optimize data-driven multi-agent simulation for COVID-19 transmission	18
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study	17
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	17
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet	17
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	17
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	17
FindCSV: a long-read based method for detecting complex structural variations	17
Correction: On Bayesian modeling of censored data in JAGS	17
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	17
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification	17
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	17
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	17
Correction to: Mining a stroke knowledge graph from literature	17
Optimizing diabetes classification with a machine learning-based framework	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	16
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery	16
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes	16
Multi-objective data enhancement for deep learning-based ultrasound analysis	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
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	16
MSA: reproducible mutational signature attribution with confidence based on simulations	16
Metacells untangle large and complex single-cell transcriptome networks	16
IMSE: interaction information attention and molecular structure based drug drug interaction extraction	16
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	16
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	16
PRED-LD: efficient imputation of GWAS summary statistics	16
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	16
ProtPlat: an efficient pre-training platform for protein classification based on FastText	16
SNPxE: SNP-environment interaction pattern identifier	16
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures	16
Clustering biological sequences with dynamic sequence similarity threshold	16
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	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
Genealyzer: web application for the analysis and comparison of gene expression data	15
Automatic generation of pseudoknotted RNAs taxonomy	15
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	15
HGDTI: predicting drug–target interaction by using information aggregation based on heterogeneous graph neural network	15
JCBIE: a joint continual learning neural network for biomedical information extraction	15
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	15
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation	15
circGPA: circRNA functional annotation based on probability-generating functions	15
A voting-based machine learning approach for classifying biological and clinical datasets	15
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species	15
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique	15
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction	15
Using individual barcodes to increase quantification power of massively parallel reporter assays	15
CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network	15
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	15
Phylo-rs: an extensible phylogenetic analysis library in rust	15