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 2020-11-01 to 2024-11-01.)

Article	Citations
The Matthews correlation coefficient (MCC) is more reliable than balanced accuracy, bookmaker informedness, and markedness in two-class confusion matrix evaluation	457
ChatGPT and large language models in academia: opportunities and challenges	171
The Matthews correlation coefficient (MCC) should replace the ROC AUC as the standard metric for assessing binary classification	130
Identification of the active substances and mechanisms of ginger for the treatment of colon cancer based on network pharmacology and molecular docking	63
ISLAND: in-silico proteins binding affinity prediction using sequence information	45
Gaussian noise up-sampling is better suited than SMOTE and ADASYN for clinical decision making	33
Exploring active ingredients and function mechanisms of Ephedra-bitter almond for prevention and treatment of Corona virus disease 2019 (COVID-19) based on network pharmacology	32
Indels in SARS-CoV-2 occur at template-switching hotspots	27
Acoustic and language analysis of speech for suicidal ideation among US veterans	27
Evaluation of different approaches for missing data imputation on features associated to genomic data	26
Detection of iron deficiency anemia by medical images: a comparative study of machine learning algorithms	25
A comparison of methods for interpreting random forest models of genetic association in the presence of non-additive interactions	22
Machine Learning Algorithms for understanding the determinants of under-five Mortality	21
Development and validation of a novel blending machine learning model for hospital mortality prediction in ICU patients with Sepsis	19
Benchmarking AutoML frameworks for disease prediction using medical claims	18
LPI-EnEDT: an ensemble framework with extra tree and decision tree classifiers for imbalanced lncRNA-protein interaction data classification	18
A self-inspected adaptive SMOTE algorithm (SASMOTE) for highly imbalanced data classification in healthcare	18
eQTpLot: a user-friendly R package for the visualization of colocalization between eQTL and GWAS signals	15
Prediction of the risk of developing end-stage renal diseases in newly diagnosed type 2 diabetes mellitus using artificial intelligence algorithms	14
Data analytics and clinical feature ranking of medical records of patients with sepsis	13
Influenza, dengue and common cold detection using LSTM with fully connected neural network and keywords selection	12
Feature selection using distributions of orthogonal PLS regression vectors in spectral data	12
Comparative analysis, applications, and interpretation of electronic health record-based stroke phenotyping methods	11
Prediction of short-term mortality in acute heart failure patients using minimal electronic health record data	11
Mechanistic modeling of the SARS-CoV-2 disease map	11

Machine learning approaches for the genomic prediction of rheumatoid arthritis and systemic lupus erythematosus	11
PredictPTB: an interpretable preterm birth prediction model using attention-based recurrent neural networks	10
Machine learning and statistical approaches for classification of risk of coronary artery disease using plasma cytokines	10
LightCUD: a program for diagnosing IBD based on human gut microbiome data	10
Robust and rigorous identification of tissue-specific genes by statistically extending tau score	10
Interpretable recurrent neural network models for dynamic prediction of the extubation failure risk in patients with invasive mechanical ventilation in the intensive care unit	9
Estimating sequencing error rates using families	9
Prediction of synergistic drug combinations using PCA-initialized deep learning	9
Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data	9
COVID-TRACK: world and USA SARS-COV-2 testing and COVID-19 tracking	9
iGlioSub: an integrative transcriptomic and epigenomic classifier for glioblastoma molecular subtypes	8
Privacy-preserving chi-squared test of independence for small samples	8
Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation	8
Prescreening and treatment of aortic dissection through an analysis of infinite-dimension data	6
An efficient computational method for predicting drug-target interactions using weighted extreme learning machine and speed up robot features	6
New neural network classification method for individuals ancestry prediction from SNPs data	6
A prognostic model based on seven immune-related genes predicts the overall survival of patients with hepatocellular carcinoma	6
Identification of natural selection in genomic data with deep convolutional neural network	5
Predicting molecular initiating events using chemical target annotations and gene expression	5
mSRFR: a machine learning model using microalgal signature features for ncRNA classification	5
Probability calibration-based prediction of recurrence rate in patients with diffuse large B-cell lymphoma	5
Comparison of 16S and whole genome dog microbiomes using machine learning	5
RASMA: a reverse search algorithm for mining maximal frequent subgraphs	5
Prediction of MoRFs based on sequence properties and convolutional neural networks	5
Neural network methods for diagnosing patient conditions from cardiopulmonary exercise testing data	5
Genetic risk score for ovarian cancer based on chromosomal-scale length variation	5
Automated quantitative trait locus analysis (AutoQTL)	4
Polygenic risk modeling of tumor stage and survival in bladder cancer	4
Biological knowledge-slanted random forest approach for the classification of calcified aortic valve stenosis	4
Assessment of emerging pretraining strategies in interpretable multimodal deep learning for cancer prognostication	4
A multi-feature hybrid classification data mining technique for human-emotion	4
Single_cell_GRN: gene regulatory network identification based on supervised learning method and Single-cell RNA-seq data	4
Machine-learning based feature selection for a non-invasive breathing change detection	4
Learning and visualizing chronic latent representations using electronic health records	4
An unsupervised image segmentation algorithm for coronary angiography	4
Gene function finding through cross-organism ensemble learning	4
A comparative study on the unified model based multifactor dimensionality reduction methods for identifying gene-gene interactions associated with the survival phenotype	3
Signature literature review reveals AHCY, DPYSL3, and NME1 as the most recurrent prognostic genes for neuroblastoma	3
Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient	3
iU-Net: a hybrid structured network with a novel feature fusion approach for medical image segmentation	3
Performance of model-based multifactor dimensionality reduction methods for epistasis detection by controlling population structure	3
iSuc-ChiDT: a computational method for identifying succinylation sites using statistical difference table encoding and the chi-square decision table classifier	3
Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts	3
Evaluating risk detection methods to uncover ontogenic-mediated adverse drug effect mechanisms in children	3
DeepAutoGlioma: a deep learning autoencoder-based multi-omics data integration and classification tools for glioma subtyping	3
Colorectal cancer subtype identification from differential gene expression levels using minimalist deep learning	3
ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data	3
Machine learning approaches to identify systemic lupus erythematosus in anti-nuclear antibody-positive patients using genomic data and electronic health records	3
The biomedical knowledge graph of symptom phenotype in coronary artery plaque: machine learning-based analysis of real-world clinical data	2
Comparison of cancer subtype identification methods combined with feature selection methods in omics data analysis	2

Ten simple rules for providing bioinformatics support within a hospital	2
A new pipeline for structural characterization and classification of RNA-Seq microbiome data	2
Neural network-based prognostic predictive tool for gastric cardiac cancer: the worldwide retrospective study	2
Assessment of the causal relationship between gut microbiota and cardiovascular diseases: a bidirectional Mendelian randomization analysis	2
Effective hybrid feature selection using different bootstrap enhances cancers classification performance	2
ScInfoVAE: interpretable dimensional reduction of single cell transcription data with variational autoencoders and extended mutual information regularization	2
Towards a potential pan-cancer prognostic signature for gene expression based on probesets and ensemble machine learning	2
Novel digital approaches to the assessment of problematic opioid use	2
Sparse self-attention aggregation networks for neural sequence slice interpolation	2
Development of glaucoma predictive model and risk factors assessment based on supervised models	2
Research agenda for using artificial intelligence in health governance: interpretive scoping review and framework	2
Polymorphisms in the mTOR-PI3K-Akt pathway, energy balance-related exposures and colorectal cancer risk in the Netherlands Cohort Study	2
Bacteria spatial tracking in Urban Park soils with MALDI-TOF Mass Spectrometry and Specific PCR	2
Detecting diseases in medical prescriptions using data mining methods	2
Correction: Confounding of linkage disequilibrium patterns in large scale DNA based gene-gene interaction studies	2
Ten important roles for academic leaders to promote equity, diversity, and inclusion in data science	2
Disclosing transcriptomics network-based signatures of glioma heterogeneity using sparse methods	2
Algorithm-based detection of acute kidney injury according to full KDIGO criteria including urine output following cardiac surgery: a descriptive analysis	2
DASSI: differential architecture search for splice identification from DNA sequences	2