BMC Bioinformatics

Papers
(The TQCC of BMC Bioinformatics is 8. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-07-01 to 2025-07-01.)
ArticleCitations
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis1397
A novel nonparametric computational strategy for identifying differential methylation regions983
REDalign: accurate RNA structural alignment using residual encoder-decoder network280
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis233
Employing phylogenetic tree shape statistics to resolve the underlying host population structure188
Predictive modeling of gene expression regulation144
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures127
SALON ontology for the formal description of sequence alignments101
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data95
Abstraction-based segmental simulation of reaction networks using adaptive memoization92
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships83
airpg: automatically accessing the inverted repeats of archived plastid genomes79
rKOMICS: an R package for processing mitochondrial minicircle assemblies in population-scale genome projects74
Correction to: Avian Immunome DB: an example of a user‑friendly interface for extracting genetic information72
A drug repositioning algorithm based on a deep autoencoder and adaptive fusion70
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug–target interactions prediction69
Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response66
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures63
Not seeing the trees for the forest. The impact of neighbours on graph-based configurations in histopathology62
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction62
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice59
Multilayer network alignment based on topological assessment via embeddings58
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers58
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning58
SVDNVLDA: predicting lncRNA-disease associations by Singular Value Decomposition and node2vec57
Prediction of hot spots in protein–DNA binding interfaces based on discrete wavelet transform and wavelet packet transform55
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data52
Enabling personalised disease diagnosis by combining a patient’s time-specific gene expression profile with a biomedical knowledge base51
Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME251
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers51
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins50
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis49
HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets49
A gene based combination test using GWAS summary data48
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells48
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration47
LDAGM: prediction lncRNA-disease asociations by graph convolutional auto-encoder and multilayer perceptron based on multi-view heterogeneous networks46
Examination of blood samples using deep learning and mobile microscopy46
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors46
Mabs, a suite of tools for gene-informed genome assembly45
Deep learning and multi-omics approach to predict drug responses in cancer45
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon45
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens44
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 control44
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform42
Multi-view manifold regularized compact low-rank representation for cancer samples clustering on multi-omics data41
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments41
Secondary structure specific simpler prediction models for protein backbone angles41
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data41
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework41
‘gitana’ (phyloGenetic Imaging Tool for Adjusting Nodes and other Arrangements), a tool for plotting phylogenetic trees into ready-to-publish figures40
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies40
A novel automated image analysis pipeline for quantifying morphological changes to the endoplasmic reticulum in cultured human cells40
MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction39
Can large language models understand molecules?37
A deep learning approach to predict inter-omics interactions in multi-layer networks37
Blastn2dotplots: multiple dot-plot visualizer for genome comparisons37
Fasta2Structure: a user-friendly tool for converting multiple aligned FASTA files to STRUCTURE format36
Ant colony optimization for the identification of dysregulated gene subnetworks from expression data36
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity36
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network35
INFLECT: an R-package for cytometry cluster evaluation using marker modality34
A learning-based method to predict LncRNA-disease associations by combining CNN and ELM34
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples34
A targeted solution for estimating the cell-type composition of bulk samples34
LinG3D: visualizing the spatio-temporal dynamics of clonal evolution34
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects34
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition33
Identification of fish species through tRNA-based primer design33
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites33
SVhound: detection of regions that harbor yet undetected structural variation33
Correction: Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients33
DiseaseNet: a transfer learning approach to noncommunicable disease classification32
Single-cell classification using graph convolutional networks32
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach32
False discovery rate estimation using candidate peptides for each spectrum32
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT32
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates31
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens31
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients31
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species31
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects30
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images30
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages30
A graph neural network framework for mapping histological topology in oral mucosal tissue30
BADASS: BActeriocin-Diversity ASsessment Software30
Using empirical biological knowledge to infer regulatory networks from multi-omics data29
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data29
A-Prot: protein structure modeling using MSA transformer29
Semantic interoperability: ontological unpacking of a viral conceptual model29
Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions28
CCL-DTI: contributing the contrastive loss in drug–target interaction prediction28
GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes28
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins28
Web-based LinRegPCR: application for the visualization and analysis of (RT)-qPCR amplification and melting data28
The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes28
UniAMP: enhancing AMP prediction using deep neural networks with inferred information of peptides28
Evaluation of tree-based statistical learning methods for constructing genetic risk scores28
HGGA: hierarchical guided genome assembler28
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network28
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer27
A clustering procedure for three-way RNA sequencing data using data transformations and matrix-variate Gaussian mixture models27
Conformal novelty detection for multiple metabolic networks27
Deafness gene screening based on a multilevel cascaded BPNN model27
Prediction of mutation-induced protein stability changes based on the geometric representations learned by a self-supervised method27
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma27
Combining single-cell ATAC and RNA sequencing for supervised cell annotation27
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime27
Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking27
A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions27
MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization27
Predicting subcellular location of protein with evolution information and sequence-based deep learning26
Piikun: an information theoretic toolkit for analysis and visualization of species delimitation metric space26
A seed expansion-based method to identify essential proteins by integrating protein–protein interaction sub-networks and multiple biological characteristics26
Informeasure: an R/bioconductor package for quantifying nonlinear dependence between variables in biological networks from an information theory perspective26
Classifying chest CT images as COVID-19 positive/negative using a convolutional neural network ensemble model and uniform experimental design method26
Inference of single-cell network using mutual information for scRNA-seq data analysis26
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models25
A hybrid algorithm for clinical decision support in precision medicine based on machine learning25
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 events25
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models25
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization25
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads25
A tensor-based bi-random walks model for protein function prediction25
MHESMMR: a multilevel model for predicting the regulation of miRNAs expression by small molecules25
Statistical methods and resources for biomarker discovery using metabolomics24
Development of a TSR-based method for understanding structural relationships of cofactors and local environments in photosystem I24
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics24
FragGeneScanRs: faster gene prediction for short reads24
Reducing Boolean networks with backward equivalence24
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction24
GSAMDA: a computational model for predicting potential microbe–drug associations based on graph attention network and sparse autoencoder24
SwarmTCR: a computational approach to predict the specificity of T cell receptors24
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering24
Fractal feature selection model for enhancing high-dimensional biological problems23
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis23
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs23
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts23
Classification of age-related macular degeneration using convolutional-neural-network-based transfer learning23
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction23
Probabilistic quotient’s work and pharmacokinetics’ contribution: countering size effect in metabolic time series measurements23
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis23
refMLST: reference-based multilocus sequence typing enables universal bacterial typing23
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach23
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins22
Wavelet Screening: a novel approach to analyzing GWAS data22
Extract antibody and antigen names from biomedical literature22
A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology22
Data-driven discovery of chemotactic migration of bacteria via coordinate-invariant machine learning22
Protein complexes detection based on node local properties and gene expression in PPI weighted networks22
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches22
LOCC: a novel visualization and scoring of cutoffs for continuous variables with hepatocellular carcinoma prognosis as an example21
Rendering protein mutation movies with MutAmore21
Using entropy-driven amplifier circuit response to build nonlinear model under the influence of Lévy jump21
Comparative analysis of aneurysm subtypes associated genes based on protein–protein interaction network21
A consensus-based ensemble approach to improve transcriptome assembly21
Closha 2.0: a bio-workflow design system for massive genome data analysis on high performance cluster infrastructure21
LPMX: a pure rootless composable container system21
DiCleave: a deep learning model for predicting human Dicer cleavage sites21
Ion-pumping microbial rhodopsin protein classification by machine learning approach21
Impact of gene annotation choice on the quantification of RNA-seq data20
Goistrat: gene-of-interest-based sample stratification for the evaluation of functional differences20
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction20
Comparison of sequencing data processing pipelines and application to underrepresented African human populations20
Bayesian variable selection for high-dimensional data with an ordinal response: identifying genes associated with prognostic risk group in acute myeloid leukemia20
Taxanorm: a novel taxa-specific normalization approach for microbiome data20
Detection of cell markers from single cell RNA-seq with sc2marker20
Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks20
GVC: efficient random access compression for gene sequence variations20
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review20
Dual-approach co-expression analysis framework (D-CAF) enables identification of novel circadian co-regulation from multi-omic timeseries data20
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions19
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization19
ProTaxoVis—protein taxonomic visualisation of presence19
PhenoExam: gene set analyses through integration of different phenotype databases19
Comparing neural models for nested and overlapping biomedical event detection19
DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs19
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma19
LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences19
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models19
Image-centric compression of protein structures improves space savings19
An approach for proteins and their encoding genes synonyms integration based on protein ontology19
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data19
GKLOMLI: a link prediction model for inferring miRNA–lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm18
Multi-objective data enhancement for deep learning-based ultrasound analysis18
A multilayer dynamic perturbation analysis method for predicting ligand–protein interactions18
Optimize data-driven multi-agent simulation for COVID-19 transmission18
scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder18
Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values18
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction18
Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning18
MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots18
SEMgsa: topology-based pathway enrichment analysis with structural equation models18
Finding functional associations between prokaryotic virus orthologous groups: a proof of concept18
Correction: On Bayesian modeling of censored data in JAGS17
Correction to: Moonlighting protein prediction using physico‑chemical and evolutional properties via machine learning methods17
PDBeCIF: an open-source mmCIF/CIF parsing and processing package17
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering17
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types17
FindCSV: a long-read based method for detecting complex structural variations17
Correction to: ncDLRES: a novel method for non‑coding RNAs family prediction based on dynamic LSTM and ResNet17
MFCADTI: improving drug-target interaction prediction by integrating multiple feature through cross attention mechanism17
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets17
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization17
Correction to: Mining a stroke knowledge graph from literature17
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction17
CDPMF-DDA: contrastive deep probabilistic matrix factorization for drug-disease association prediction17
shinyCurves, a shiny web application to analyse multisource qPCR amplification data: a COVID-19 case study17
ANINet: a deep neural network for skull ancestry estimation16
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions16
LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA–protein interaction identification16
AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance16
KEGG orthology prediction of bacterial proteins using natural language processing16
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers16
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes16
The effect of data balancing approaches on the prediction of metabolic syndrome using non-invasive parameters based on random forest16
PRED-LD: efficient imputation of GWAS summary statistics16
Prediction of vancomycin initial dosage using artificial intelligence models applying ensemble strategy16
Optimizing diabetes classification with a machine learning-based framework16
A voting-based machine learning approach for classifying biological and clinical datasets16
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data16
C-ziptf: stable tensor factorization for zero-inflated multi-dimensional genomics data16
GAT-LI: a graph attention network based learning and interpreting method for functional brain network classification16
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest16
M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures16
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes16
An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models16
CNVizard—a lightweight streamlit application for an interactive analysis of copy number variants16
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data16
BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network16
HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation15
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP15
Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation15
circGPA: circRNA functional annotation based on probability-generating functions15
SNPxE: SNP-environment interaction pattern identifier15
Interpretable deep learning methods for multiview learning15
Genealyzer: web application for the analysis and comparison of gene expression data15
ProtPlat: an efficient pre-training platform for protein classification based on FastText15
Computational application of internationally harmonized defined approaches to skin sensitization: DASS App15
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction15
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP15
Automatic generation of pseudoknotted RNAs taxonomy15
Clustering biological sequences with dynamic sequence similarity threshold15
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery15
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier15
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information15
HGDTI: predicting drug–target interaction by using information aggregation based on heterogeneous graph neural network15
MBECS: Microbiome Batch Effects Correction Suite15
Using individual barcodes to increase quantification power of massively parallel reporter assays15
0.05647611618042