BMC Bioinformatics

Article	Citations
A novel nonparametric computational strategy for identifying differential methylation regions	1294
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	361
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	263
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	162
SALON ontology for the formal description of sequence alignments	136
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	113
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	105
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	100
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	99
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	98
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	97
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	97
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	89
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	87
REDalign: accurate RNA structural alignment using residual encoder-decoder network	86
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	84
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	83
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	76
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	73
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	71
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	69
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	69
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	67
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	64
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	60

SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	58
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	58
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	55
Multilayer network alignment based on topological assessment via embeddings	55
A gene based combination test using GWAS summary data	54
Abstraction-based segmental simulation of reaction networks using adaptive memoization	54
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	53
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	53
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	52
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data	52
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	50
Mabs, a suite of tools for gene-informed genome assembly	50
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	50
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	50
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	50
Examination of blood samples using deep learning and mobile microscopy	48
Deep learning and multi-omics approach to predict drug responses in cancer	47
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	46
SVhound: detection of regions that harbor yet undetected structural variation	45
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	45
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	45
BADASS: BActeriocin-Diversity ASsessment Software	44
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures	43
INFLECT: an R-package for cytometry cluster evaluation using marker modality	41
Multi-view manifold regularized compact low-rank representation for cancer samples clustering on multi-omics data	41
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	41
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients	41
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	41
Identification of fish species through tRNA-based primer design	40
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	40
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	40
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	39
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	39
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons	39
A novel modality contribution confidence-enhanced multimodal deep learning framework for multiomics data	38
DiseaseNet: a transfer learning approach to noncommunicable disease classification	38
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	38
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM	38
False discovery rate estimation using candidate peptides for each spectrum	38
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	37
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	37
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	37
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	36
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	36
Secondary structure specific simpler prediction models for protein backbone angles	36
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	36
A-Prot: protein structure modeling using MSA transformer	36
Semantic interoperability: ontological unpacking of a viral conceptual model	35
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	35
Using empirical biological knowledge to infer regulatory networks from multi-omics data	35

CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	35
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	34
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species	34
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	34
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	34
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	33
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	33
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	32
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	32
A graph neural network framework for mapping histological topology in oral mucosal tissue	32
A deep learning approach to predict inter-omics interactions in multi-layer networks	32
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	31
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	31
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	31
Can large language models understand molecules?	31
HGGA: hierarchical guided genome assembler	30
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	30
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	30
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	30
Evaluation of tree-based statistical learning methods for constructing genetic risk scores	30
Deafness gene screening based on a multilevel cascaded BPNN model	30
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	29
Conformal novelty detection for multiple metabolic networks	29
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	29
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	29
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	29
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	29
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	29
A tensor-based bi-random walks model for protein function prediction	29
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	29
Glucostats: an efficient Python library for glucose time series feature extraction and visual analysis	29
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	29
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	28
SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network	28
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information	28
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	28
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	28
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	28
Reducing Boolean networks with backward equivalence	28
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	28
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	27
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	27
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	27
Statistical methods and resources for biomarker discovery using metabolomics	27
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models	27
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	26
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	26
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	25
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	25
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	25
FragGeneScanRs: faster gene prediction for short reads	25
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	25
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction	25
Extract antibody and antigen names from biomedical literature	24
Inference of single-cell network using mutual information for scRNA-seq data analysis	24
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	24
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	24
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	24
Fractal feature selection model for enhancing high-dimensional biological problems	24
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	24
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	24
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	24
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	24
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	23
DiCleave: a deep learning model for predicting human Dicer cleavage sites	23
Ion-pumping microbial rhodopsin protein classification by machine learning approach	23
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	23
Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network	23
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump	23
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	23
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences	23
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	23
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	23
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins	23
PhenoExam: gene set analyses through integration of different phenotype databases	23
ProTaxoVis—protein taxonomic visualisation of presence	23
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	22
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	22
An approach for proteins and their encoding genes synonyms integration based on protein ontology	22
Comparing neural models for nested and overlapping biomedical event detection	22

Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	22
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	22
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	22
Impact of gene annotation choice on the quantification of RNA-seq data	21
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	21
Taxanorm: a novel taxa-specific normalization approach for microbiome data	21
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	21
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	21
Rendering protein mutation movies with MutAmore	21
GVC: efficient random access compression for gene sequence variations	21
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets	21
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	21
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	21
Image-centric compression of protein structures improves space savings	21
LPMX: a pure rootless composable container system	21
Protein complexes detection based on node local properties and gene expression in PPI weighted networks	20
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	20
Detection of cell markers from single cell RNA-seq with sc2marker	20
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	20
The FBA solution space kernel: introduction and illustrative examples	20
AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions	20
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	20
Optimize data-driven multi-agent simulation for COVID-19 transmission	20
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	20
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	20
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	20
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	19
Interpretable deep learning methods for multiview learning	19
FindCSV: a long-read based method for detecting complex structural variations	19
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	19
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations	19
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers	19
Correction: On Bayesian modeling of censored data in JAGS	19
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	19
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	19
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	19
Correction to: Mining a stroke knowledge graph from literature	19
Using individual barcodes to increase quantification power of massively parallel reporter assays	19
KEGG orthology prediction of bacterial proteins using natural language processing	18
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	18
A voting-based machine learning approach for classifying biological and clinical datasets	18
Clustering biological sequences with dynamic sequence similarity threshold	18
Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation	18
MBECS: Microbiome Batch Effects Correction Suite	18
SEMgsa: topology-based pathway enrichment analysis with structural equation models	18
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	18
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	18
Multi-objective data enhancement for deep learning-based ultrasound analysis	18
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants	18
Denoising self-supervised learning for disease-gene association prediction	18
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique	18
PRED-LD: efficient imputation of GWAS summary statistics	18
Automatic generation of pseudoknotted RNAs taxonomy	18
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions	18
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	18
circGPA: circRNA functional annotation based on probability-generating functions	18
Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis	18
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	18
Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction	18
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data	17
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants	17
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction	17
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet	17
ProtPlat: an efficient pre-training platform for protein classification based on FastText	17
Phylo-rs: an extensible phylogenetic analysis library in rust	17
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	17
Metacells untangle large and complex single-cell transcriptome networks	17
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models	17
BarWare: efficient software tools for barcoded single-cell genomics	17
Genealyzer: web application for the analysis and comparison of gene expression data	17
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	17
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App	17
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	17
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	17
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	17
HGDTI: predicting drug–target interaction by using information aggregation based on heterogeneous graph neural network	17
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	17
JCBIE: a joint continual learning neural network for biomedical information extraction	17
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	17
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP	17
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation	16
Prediction of disease-related miRNAs by voting with multiple classifiers	16
Control of false discoveries in grouped hypothesis testing for eQTL data	16
Practical application of a Bayesian network approach to poultry epigenetics and stress	16
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data	16
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species	16
Drug response prediction using graph representation learning and Laplacian feature selection	16
Scellpam: an R package/C++ library to perform parallel partitioning around medoids on scRNAseq data sets	16
DMoVGPE: predicting gut microbial associated metabolites profiles with deep mixture of variational Gaussian Process experts	16
Multi-task genomic prediction using gated residual variable selection neural networks	16
Optimizing diabetes classification with a machine learning-based framework	16
SeQual-Stream: approaching stream processing to quality control of NGS datasets	16
BioLake: an RNA expression analysis framework for prostate cancer biomarker powered by data lakehouse	16
cnnLSV: detecting structural variants by encoding long-read alignment information and convolutional neural network	16
Parallel multi-swarm cooperative particle swarm optimization for protein–ligand docking and virtual screening	16