BMC Bioinformatics

Article	Citations
A novel nonparametric computational strategy for identifying differential methylation regions	1324
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis	379
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis	279
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships	168
SALON ontology for the formal description of sequence alignments	138
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data	120
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction	110
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures	109
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology	105
Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms	101
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers	101
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice	101
A shrinkage-based statistical method for testing group mean differences in quantitative bottom-up proteomics	93
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis	90
DualGCN-GE: integration of spatiotemporal representations from whole-blood expression data with dual-view graph convolution network to identify Parkinson’s disease subtypes	89
Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens	88
Weighted overlapping group lasso for integrating prior network knowledge into gene set analysis	87
REDalign: accurate RNA structural alignment using residual encoder-decoder network	83
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning	76
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base	75
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers	74
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform	74
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration	71
Multilayer network alignment based on topological assessment via embeddings	64
A gene based combination test using GWAS summary data	61

Abstraction-based segmental simulation of reaction networks using adaptive memoization	61
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors	59
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures	56
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks	56
Mabs, a suite of tools for gene-informed genome assembly	56
SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation	55
Examination of blood samples using deep learning and mobile microscopy	54
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction	54
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2	54
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	52
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets	52
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens	51
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform	51
Deep learning and multi-omics approach to predict drug responses in cancer	51
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells	51
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework	50
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins	48
SVhound: detection of regions that harbor yet undetected structural variation	48
A-Prot: protein structure modeling using MSA transformer	46
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples	46
DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit	46
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format	44
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network	44
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens	43
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction	43
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction	43
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network	42
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity	42
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures	41
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites	41
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM	41
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution	41
INFLECT: an R-package for cytometry cluster evaluation using marker modality	41
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies	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 fish species through tRNA-based primer design	39
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images	38
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients	38
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects	38
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons	38
Secondary structure specific simpler prediction models for protein backbone angles	37
Semantic interoperability: ontological unpacking of a viral conceptual model	37
A deep learning approach to predict inter-omics interactions in multi-layer networks	37
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data	37
DiseaseNet: a transfer learning approach to noncommunicable disease classification	36
False discovery rate estimation using candidate peptides for each spectrum	36
A novel modality contribution confidence-enhanced multimodal deep learning framework for multiomics data	35
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins	35
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach	35
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments	35

GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes	34
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT	34
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data	34
BADASS: BActeriocin-Diversity ASsessment Software	33
Using empirical biological knowledge to infer regulatory networks from multi-omics data	33
Evaluation of tree-based statistical learning methods for constructing genetic risk scores	33
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides	33
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition	32
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species	32
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates	32
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages	32
HGGA: hierarchical guided genome assembler	31
Can large language models understand molecules?	31
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data	31
A graph neural network framework for mapping histological topology in oral mucosal tissue	31
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization	31
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects	31
Deafness gene screening based on a multilevel cascaded BPNN model	31
Glucostats: an efficient Python library for glucose time series feature extraction and visual analysis	30
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models	30
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking	30
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space	30
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering	30
BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information	30
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA)	30
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective	29
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions	29
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis	29
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models	29
A tensor-based bi-random walks model for protein function prediction	29
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization	29
Conformal novelty detection for multiple metabolic networks	29
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs	28
Reducing Boolean networks with backward equivalence	28
SaeGraphDTI: drug–target interaction prediction based on sequence attribute extraction and graph neural network	28
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction	28
Combining single-cell ATAC and RNA sequencing for supervised cell annotation	28
ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events	28
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I	28
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction	27
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules	27
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method	27
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime	27
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics	27
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics	27
Inference of single-cell network using mutual information for scRNA-seq data analysis	27
FragGeneScanRs: faster gene prediction for short reads	27
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach	26
Fractal feature selection model for enhancing high-dimensional biological problems	26
A hybrid algorithm for clinical decision support in precision medicine based on machine learning	26
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes	26
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder	26
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer	26
refMLST: reference-based multilocus sequence typing enables universal bacterial typing	26
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts	26
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models	26
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads	25
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements	25
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning	25
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma	25
Statistical methods and resources for biomarker discovery using metabolomics	25
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis	25
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks	24
PhenoExam: gene set analyses through integration of different phenotype databases	24
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example	24
Ion-pumping microbial rhodopsin protein classification by machine learning approach	24
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure	24
ProTaxoVis—protein taxonomic visualisation of presence	24
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences	24
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump	24
An approach for proteins and their encoding genes synonyms integration based on protein ontology	23
Comparing neural models for nested and overlapping biomedical event detection	23
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction	23
Extract antibody and antigen names from biomedical literature	23
Impact of gene annotation choice on the quantification of RNA-seq data	23
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs	23
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology	23
DiCleave: a deep learning model for predicting human Dicer cleavage sites	23
LPMX: a pure rootless composable container system	23
SeqForge: a scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets	23

Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma	22
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences	22
GVC: efficient random access compression for gene sequence variations	22
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches	22
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data	22
Image-centric compression of protein structures improves space savings	22
Taxanorm: a novel taxa-specific normalization approach for microbiome data	22
Rendering protein mutation movies with MutAmore	22
The FBA solution space kernel: introduction and illustrative examples	22
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm	21
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning	21
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models	21
Detection of cell markers from single cell RNA-seq with sc2marker	21
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions	21
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization	21
Protein complexes detection based on node local properties and gene expression in PPI weighted networks	21
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins	21
AlphaFold Database Structure Extractor: a web server and API to download AlphaFold structures using common protein accessions	21
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data	21
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review	20
Optimize data-driven multi-agent simulation for COVID-19 transmission	20
Using individual barcodes to increase quantification power of massively parallel reporter assays	20
Correction: On Bayesian modeling of censored data in JAGS	20
KEGG orthology prediction of bacterial proteins using natural language processing	20
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots	20
FindCSV: a long-read based method for detecting complex structural variations	20
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy	20
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder	20
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values	20
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance	20
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types	20
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions	20
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network	19
Automatic block-wise genotype-phenotype association detection based on hidden Markov model	19
Phylo-rs: an extensible phylogenetic analysis library in rust	19
Optimizing diabetes classification with a machine learning-based framework	19
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models	19
A voting-based machine learning approach for classifying biological and clinical datasets	19
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation	19
Multi-objective data enhancement for deep learning-based ultrasound analysis	19
GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions	19
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data	19
Interpretable deep learning methods for multiview learning	19
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species	18
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures	18
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction	18
PRED-LD: efficient imputation of GWAS summary statistics	18
Denoising self-supervised learning for disease-gene association prediction	18
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest	18
DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations	18
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions	18
Genealyzer: web application for the analysis and comparison of gene expression data	18
MBECS: Microbiome Batch Effects Correction Suite	18
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants	18
Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation	18
circGPA: circRNA functional annotation based on probability-generating functions	18
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest	18
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering	18
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier	18
Automatic generation of pseudoknotted RNAs taxonomy	18
Cancer detection via one-shot learning: integrating gene expression and genomic mutation analysis	18
Graph convolution network based on meta-paths and mutual information for drug-target interaction prediction	18
IMSE: interaction information attention and molecular structure based drug drug interaction extraction	17
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants	17
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation	17
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery	17
SeQual-Stream: approaching stream processing to quality control of NGS datasets	17
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction	17
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App	17
DANSE: a pipeline for dynamic modelling of time-series multi-omics data	17
BarWare: efficient software tools for barcoded single-cell genomics	17
SEMgsa: topology-based pathway enrichment analysis with structural equation models	17
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers	17
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data	17
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP	17
EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning	17
Drug response prediction using graph representation learning and Laplacian feature selection	17
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP	17
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism	17
HGDTI: predicting drug–target interaction by using information aggregation based on heterogeneous graph neural network	17
JCBIE: a joint continual learning neural network for biomedical information extraction	17
ProtPlat: an efficient pre-training platform for protein classification based on FastText	17
Metacells untangle large and complex single-cell transcriptome networks	17
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes	17
Clustering biological sequences with dynamic sequence similarity threshold	17
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction	17
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data	17
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique	17
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics	16
Deep learning algorithm reveals two prognostic subtypes in patients with gliomas	16
expHRD: an individualized, transcriptome-based prediction model for homologous recombination deficiency assessment in cancer	16
An information-theoretic approach to single cell sequencing analysis	16
DeepBP: Ensemble deep learning strategy for bioactive peptide prediction	16
ClearFinder: a Python GUI for annotating cells in cleared mouse brain	16
A novel two-way rebalancing strategy for identifying carbonylation sites	16