OOIR: Observatory of International Research

Papers

(The median citation count of Biodata Mining is 2. 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 2021-08-01 to 2025-08-01.)

Article	Citations
MOCAT: multi-omics integration with auxiliary classifiers enhanced autoencoder	340
Investigating potential drug targets for IgA nephropathy and membranous nephropathy through multi-queue plasma protein analysis: a Mendelian randomization study based on SMR and co-localization analys	278
Correction: Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning	58
Deep joint learning diagnosis of Alzheimer’s disease based on multimodal feature fusion	46
Processing imbalanced medical data at the data level with assisted-reproduction data as an example	45
Transcriptome-based network analysis related to regulatory T cells infiltration identified RCN1 as a potential biomarker for prognosis in clear cell renal cell carcinoma	41
Comparing new tools of artificial intelligence to the authentic intelligence of our global health students	39
Ten simple rules for providing bioinformatics support within a hospital	33
Neural network methods for diagnosing patient conditions from cardiopulmonary exercise testing data	26
Machine learning approaches to identify systemic lupus erythematosus in anti-nuclear antibody-positive patients using genomic data and electronic health records	25
Polygenic risk modeling of tumor stage and survival in bladder cancer	24
Unsupervised clustering based coronary artery segmentation	23
Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient	22
Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning	19
circGPAcorr: an integrative tool for functional annotation of circular RNAs using expression data	19
Detection and classification of long terminal repeat sequences in plant LTR-retrotransposons and their analysis using explainable machine learning	17
Decoding dynamic miRNA:ceRNA interactions unveils therapeutic insights and targets across predominant cancer landscapes	15
The biomedical knowledge graph of symptom phenotype in coronary artery plaque: machine learning-based analysis of real-world clinical data	13
Genetics and precision health: the ecological fallacy and artificial intelligence solutions	13
Supervised multiple kernel learning approaches for multi-omics data integration	11
Comparison of 16S and whole genome dog microbiomes using machine learning	11
Using GPT-4 to write a scientific review article: a pilot evaluation study	10
Gaussian noise up-sampling is better suited than SMOTE and ADASYN for clinical decision making	10
m1A-Ensem: accurate identification of 1-methyladenosine sites through ensemble models	9
Advancing preeclampsia prediction: a tailored machine learning pipeline integrating resampling and ensemble models for handling imbalanced medical data	9

Motif clustering and digital biomarker extraction for free-living physical activity analysis	9
Correction: Motif clustering and digital biomarker extraction for free-living physical activity analysis	9
Assessment of the causal relationship between gut microbiota and cardiovascular diseases: a bidirectional Mendelian randomization analysis	9
From COVID-19 to monkeypox: a novel predictive model for emerging infectious diseases	9
Interpreting drug synergy in breast cancer with deep learning using target-protein inhibition profiles	9
Predictive modeling of ALS progression: an XGBoost approach using clinical features	8
Machine learning models for reinjury risk prediction using cardiopulmonary exercise testing (CPET) data: optimizing athlete recovery	8
Detection of iron deficiency anemia by medical images: a comparative study of machine learning algorithms	8
Effective hybrid feature selection using different bootstrap enhances cancers classification performance	8
Ensemble feature selection and tabular data augmentation with generative adversarial networks to enhance cutaneous melanoma identification and interpretability	8
Saliency-driven explainable deep learning in medical imaging: bridging visual explainability and statistical quantitative analysis	8
Understanding predictions of drug profiles using explainable machine learning models	8
Reference-free phylogeny from sequencing data	8
Disclosing transcriptomics network-based signatures of glioma heterogeneity using sparse methods	8
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation	7
A machine learning approach using conditional normalizing flow to address extreme class imbalance problems in personal health records	7
Open challenges and opportunities in federated foundation models towards biomedical healthcare	7
6mA-StackingCV: an improved stacking ensemble model for predicting DNA N6-methyladenine site	7
An unsupervised image segmentation algorithm for coronary angiography	7
Correction: A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma	6
Deep learning-based Emergency Department In-hospital Cardiac Arrest Score (Deep EDICAS) for early prediction of cardiac arrest and cardiopulmonary resuscitation in the emergency department	6
ChatGPT and large language models in academia: opportunities and challenges	6
Identification of immune-associated biomarkers of diabetes nephropathy tubulointerstitial injury based on machine learning: a bioinformatics multi-chip integrated analysis	6
The Matthews correlation coefficient (MCC) should replace the ROC AUC as the standard metric for assessing binary classification	6
Changing word meanings in biomedical literature reveal pandemics and new technologies	6
Optimizing age-related hearing risk predictions: an advanced machine learning integration with HHIE-S	6
Evaluation of network-guided random forest for disease gene discovery	5
Revealing third-order interactions through the integration of machine learning and entropy methods in genomic studies	5
ScInfoVAE: interpretable dimensional reduction of single cell transcription data with variational autoencoders and extended mutual information regularization	5
MultiChem: predicting chemical properties using multi-view graph attention network	5
TGNet: tensor-based graph convolutional networks for multimodal brain network analysis	5
Network-based multi-omics integrative analysis methods in drug discovery: a systematic review	5
Endoscopy-based IBD identification by a quantized deep learning pipeline	5
A Gated Recurrent Unit based architecture for recognizing ontology concepts from biological literature	5
Construction and application of medication reminder system: intelligent generation of universal medication schedule	5
Machine-learning-based models to predict cardiovascular risk using oculomics and clinic variables in KNHANES	4
Polymorphisms in the mTOR-PI3K-Akt pathway, energy balance-related exposures and colorectal cancer risk in the Netherlands Cohort Study	4
Algorithm-based detection of acute kidney injury according to full KDIGO criteria including urine output following cardiac surgery: a descriptive analysis	4
QIGTD: identifying critical genes in the evolution of lung adenocarcinoma with tensor decomposition	4
Machine Learning Algorithms for understanding the determinants of under-five Mortality	4
A regularized Cox hierarchical model for incorporating annotation information in predictive omic studies	4
Deciphering the tissue-specific functional effect of Alzheimer risk SNPs with deep genome annotation	4
Prediction of MoRFs based on sequence properties and convolutional neural networks	4
Analysis of risk factors progression of preterm delivery using electronic health records	4
Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data	4
The ethics of data mining in healthcare: challenges, frameworks, and future directions	4
Machine learning based study for the classification of Type 2 diabetes mellitus subtypes	4
Enhanced labor pain monitoring using machine learning and ECG waveform analysis for uterine contraction-induced pain	3
Agenda setting for health equity assessment through the lenses of social determinants of health using machine learning approach: a framework and preliminary pilot study	3
PAGER: A novel genotype encoding strategy for modeling deviations from additivity in complex trait association studies	3

iGlioSub: an integrative transcriptomic and epigenomic classifier for glioblastoma molecular subtypes	3
Novel digital approaches to the assessment of problematic opioid use	3
subMG automates data submission for metagenomics studies	3
AI as an accelerator for defining new problems that transcends boundaries	3
Comparison of cancer subtype identification methods combined with feature selection methods in omics data analysis	3
Quantum analysis of squiggle data	3
Priority-Elastic net for binary disease outcome prediction based on multi-omics data	3
Electronic medical records imputation by temporal Generative Adversarial Network	3
Enhancing hepatopathy clinical trial efficiency: a secure, large language model-powered pre-screening pipeline	3
Distinct network patterns emerge from Cartesian and XOR epistasis models: a comparative network science analysis	3
Assessing the limitations of relief-based algorithms in detecting higher-order interactions	3
ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data	3
mSRFR: a machine learning model using microalgal signature features for ncRNA classification	3
Towards a potential pan-cancer prognostic signature for gene expression based on probesets and ensemble machine learning	3
Predicting molecular initiating events using chemical target annotations and gene expression	2
Inverse problem for parameters identification in a modified SIRD epidemic model using ensemble neural networks	2
Taxonomy-based data representation for data mining: an example of the magnitude of risk associated with H. pylori infection	2
Prognostic feature based on androgen-responsive genes in bladder cancer and screening for potential targeted drugs	2
Learning the therapeutic targets of acute myeloid leukemia through multiscale human interactome network and community analysis	2
Influenza, dengue and common cold detection using LSTM with fully connected neural network and keywords selection	2
Automated quantitative trait locus analysis (AutoQTL)	2
Overlapping filter bank convolutional neural network for multisubject multicategory motor imagery brain-computer interface	2
Correction: Predictive modeling of ALS progression: an XGBoost approach using clinical features	2
Unsupervised encoding selection through ensemble pruning for biomedical classification	2
iSuc-ChiDT: a computational method for identifying succinylation sites using statistical difference table encoding and the chi-square decision table classifier	2
Can open source large language models be used for tumor documentation in Germany?—An evaluation on urological doctors’ notes	2
Feature graphs for interpretable unsupervised tree ensembles: centrality, interaction, and application in disease subtyping	2
Private pathological assessment via machine learning and homomorphic encryption	2
A deep learning approach for classifying and predicting children's nutritional status in Ethiopia using LSTM-FC neural networks	2
Correction to: iGlioSub: an integrative transcriptomic and epigenomic classifier for glioblastoma molecular subtypes	2
Deep learning-based approaches for multi-omics data integration and analysis	2
Leveraging mixed-effects regression trees for the analysis of high-dimensional longitudinal data to identify the low and high-risk subgroups: simulation study with application to genetic study	2