BMC Bioinformatics

Article	Citations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	1276
A novel nonparametric computational strategy for identifying differential methylation regions	890
Examination of blood samples using deep learning and mobile microscopy	258
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	203
REDalign: accurate RNA structural alignment using residual encoder-decoder network	164
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	135
Employing phylogenetic tree shape statistics to resolve the underlying host population structure	123
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	97
Predictive modeling of gene expression regulation	90
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	88
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	76
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	74
SALON ontology for the formal description of sequence alignments	69
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	67
Abstraction-based segmental simulation of reaction networks using adaptive memoization	63
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	60
airpg: automatically accessing the inverted repeats of archived plastid genomes	60
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon	59
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects	58
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information	57
Mabs, a suite of tools for gene-informed genome assembly	54
A gene based combination test using GWAS summary data	54
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	53
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion	53
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	53

Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	52
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response	49
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	49
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	48
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	48
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	48
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	47
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	47
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	47
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	46
PIGNON: a protein–protein interaction-guided functional enrichment analysis for quantitative proteomics	45
Deep learning and multi-omics approach to predict drug responses in cancer	44
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	44
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	44
Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images	43
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec	43
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	41
Multilayer network alignment based on topological assessment via embeddings	41
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	41
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	40
GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package	40
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	39
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	39
DiseaseNet: a transfer learning approach to noncommunicable disease classification	38
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	38
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	38
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	38
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	38
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	38
Improving the recall of biomedical named entity recognition with label re-correction and knowledge distillation	38
Uncovering the roles of microRNAs/lncRNAs in characterising breast cancer subtypes and prognosis	38
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	37
Can large language models understand molecules?	37
A graph neural network framework for mapping histological topology in oral mucosal tissue	37
False discovery rate estimation using candidate peptides for each spectrum	37
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	36
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	36
Multi-view manifold regularized compact low-rank representation for cancer samples clustering on multi-omics data	36
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	35
Single-cell classification using graph convolutional networks	35
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	35
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	34
Secondary structure specific simpler prediction models for protein backbone angles	34
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	34
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	34
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species	34
Evaluation of tree-based statistical learning methods for constructing genetic risk scores	34
Semantic interoperability: ontological unpacking of a viral conceptual model	34
A deep learning approach to predict inter-omics interactions in multi-layer networks	33
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	33

CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	33
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	33
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	32
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	32
A-Prot: protein structure modeling using MSA transformer	32
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	32
A targeted solution for estimating the cell-type composition of bulk samples	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
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM	31
INFLECT: an R-package for cytometry cluster evaluation using marker modality	31
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	30
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	30
Identification of fish species through tRNA-based primer design	29
SVhound: detection of regions that harbor yet undetected structural variation	29
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	29
Using empirical biological knowledge to infer regulatory networks from multi-omics data	28
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	28
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	28
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	28
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	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
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data	28
A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells	28
BADASS: BActeriocin-Diversity ASsessment Software	27
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction	27
Deafness gene screening based on a multilevel cascaded BPNN model	27
Forecasting the spread of COVID-19 using LSTM network	27
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	27
Reducing Boolean networks with backward equivalence	27
HGGA: hierarchical guided genome assembler	27
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	27
Statistical methods and resources for biomarker discovery using metabolomics	27
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	27
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	26
Super.FELT: supervised feature extraction learning using triplet loss for drug response prediction with multi-omics data	26
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	26
StrongestPath: a Cytoscape application for protein–protein interaction analysis	26
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	25
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	25
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	25
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning	25
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	25
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	25
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	25
An effective method to resolve ambiguous bisulfite-treated reads	25
FragGeneScanRs: faster gene prediction for short reads	25
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	24
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	24
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	24
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	24
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	24
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	24
Inference of single-cell network using mutual information for scRNA-seq data analysis	24
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	24
Conformal novelty detection for multiple metabolic networks	24
SwarmTCR: a computational approach to predict the specificity of T cell receptors	24
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	24
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	23
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	23
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	23
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	23
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models	23
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	23
Predicting subcellular location of protein with evolution information and sequence-based deep learning	23
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	23
A tensor-based bi-random walks model for protein function prediction	23
Classifying chest CT images as COVID-19 positive/negative using a convolutional neural network ensemble model and uniform experimental design method	23
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	22
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	22
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	22
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	22
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	22
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	22
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	22
Protein complexes detection based on node local properties and gene expression in PPI weighted networks	22
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	22
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	22
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	22

Extract antibody and antigen names from biomedical literature	22
Fractal feature selection model for enhancing high-dimensional biological problems	22
Taxanorm: a novel taxa-specific normalization approach for microbiome data	21
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	21
Wavelet Screening: a novel approach to analyzing GWAS data	21
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	21
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets	21
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins	21
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	21
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences	21
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	21
GVC: efficient random access compression for gene sequence variations	21
Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network	21
LPMX: a pure rootless composable container system	21
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	20
A consensus-based ensemble approach to improve transcriptome assembly	20
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump	20
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	20
Ion-pumping microbial rhodopsin protein classification by machine learning approach	20
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides	20
DiCleave: a deep learning model for predicting human Dicer cleavage sites	20
Correction to: Impact of concurrency on the performance of a whole exome sequencing pipeline	20
Detection of cell markers from single cell RNA-seq with sc2marker	20
Comparison of sequencing data processing pipelines and application to underrepresented African human populations	20
Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development	20
Rendering protein mutation movies with MutAmore	20
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	20
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	20
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	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
Image-centric compression of protein structures improves space savings	19
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	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
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	19
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	19
A voting-based machine learning approach for classifying biological and clinical datasets	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
PhenoExam: gene set analyses through integration of different phenotype databases	19
Bioinformatics screening of biomarkers related to liver cancer	19
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	19
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	19
Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia	19
Impact of gene annotation choice on the quantification of RNA-seq data	19
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	18
Multi-objective data enhancement for deep learning-based ultrasound analysis	18
SEMgsa: topology-based pathway enrichment analysis with structural equation models	18
SNPxE: SNP-environment interaction pattern identifier	18
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	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
Optimize data-driven multi-agent simulation for COVID-19 transmission	18
circGPA: circRNA functional annotation based on probability-generating functions	18
KEGG orthology prediction of bacterial proteins using natural language processing	18
Automatic generation of pseudoknotted RNAs taxonomy	18
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction	17
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	17
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study	17
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	17
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	17
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information	17
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	17
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	17
JCBIE: a joint continual learning neural network for biomedical information extraction	17
Correction: On Bayesian modeling of censored data in JAGS	17
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets	17
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept	17
ProtPlat: an efficient pre-training platform for protein classification based on FastText	17
FindCSV: a long-read based method for detecting complex structural variations	17
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization	17
CRPGCN: predicting circRNA-disease associations using graph convolutional network based on heterogeneous network	17
PRED-LD: efficient imputation of GWAS summary statistics	16
Using individual barcodes to increase quantification power of massively parallel reporter assays	16
Correction to: Moonlighting protein prediction using physico‑chemical and evolutional properties via machine learning methods	16
PDBeCIF: an open-source mmCIF/CIF parsing and processing package	16
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	16
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	16
ANINet: a deep neural network for skull ancestry estimation	16
MBECS: Microbiome Batch Effects Correction Suite	16
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	16
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet	16
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	16
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes	16
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	16
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures	16
Correction to: Mining a stroke knowledge graph from literature	16
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	16
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique	16
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	16
Genealyzer: web application for the analysis and comparison of gene expression data	16
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery	15
Optimizing diabetes classification with a machine learning-based framework	15
HGDTI: predicting drug–target interaction by using information aggregation based on heterogeneous graph neural network	15
GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification	15