OOIR: Observatory of International Research

Papers

(The TQCC of Current Bioinformatics is 3. 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 2021-04-01 to 2025-04-01.)

Article	Citations
InConTPSS: Multi-scale Module Based Temporal Convolutional Networks for Accurate Protein Secondary Prediction	287
A Non-invasive Cell-free DNA Diagnosis Method for Hepatocellular Carcinoma Based on Deep Learning	51
Bioinformatic Resources for Plant Genomic Research	42
Optimized Hybrid Deep Learning for Real-Time Pandemic Data Forecasting: Long and Short-Term Perspectives	35
Meet the Editorial Board Member	33
Acknowledgements to Reviewers	32
Meet the Editorial Board Member	28
Identification of Spatial Domains, Spatially Variable Genes, and Genetic Association Studies of Alzheimer Disease with an Autoencoder-based Fuzzy Clustering Algorithm	21
Intersecting Peptidomics and Bioactive Peptides in Drug Therapeutics	19
GB5mCPred: Cross-species 5mc Site Predictor Based on Bootstrap-based Stochastic Gradient Boosting Method for Poaceae	18
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In-Silico Assessment Steps	17
A Comparative Analysis of Biological Data Integration Systems Famous for Data Exploitation and Knowledge Discovery	16
Efficacy Screening of Prospective Anti-allergic Drug Candidates: An In silico Study	15
Deep-RPA: Vulnerability Classification of a Genome for CRISPR/Cas9 Off-targets	14
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	13
Detection of DNA N6-Methyladenine Modification through SMRT-seq Features and Machine Learning Model	13
A-RFP: An Adaptive Residue Flexibility Prediction Method Improving Protein-ligand Docking Based on Homologous Proteins	13
Bioinformatics Tools and Databases for Genomics-assisted Breeding and Population Genetics of Plants: A Review	12
Evaluation of Current Trends in Biomedical Applications Using Soft Computing	11
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	10
Prediction of lncRNA-disease Associations Based on Robust Multi-label Learning	10
Detection of Stage-wise Biomarkers in Lung Adenocarcinoma Using Multiplex Analysis	10
Intelligent Techniques Analysis for Glycosylation Site Prediction	9
Investigation of LncRNAs Expression as a Potential Biomarker in the Diagnosis and Treatment of Human Brucellosis	9
DNA Binding Protein Prediction based on Multi-feature Deep Metatransfer Learning	9

Deep Learning for Clustering Single-cell RNA-seq Data	9
Identification and Analysis of Plant miRNAs: Evolution of In-silico Resources and Future Challenges	9
iTSP-PseAAC: Identifying Tumor Suppressor Proteins by Using Fully Connected Neural Network and PseAAC	9
A Review: Computational Approaches to Design sgRNA of CRISPR-Cas9	8
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	8
Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches	8
Evaluating the Reliability of Machine Learning Predictors in m6A-SNP Association Analysis: A Comparative Study Using m6A-QTL Data	8
Biopanning Data Bank 2023: Updating and New Findings	8
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	8
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	8
Delineating Characteristic Sequence and Structural Features of Precursor and Mature Piwi-interacting RNAs of Epithelial Ovarian Cancer	7
Prediction of Off-Target Effects in CRISPR/Cas9 System by Ensemble Learning	7
MDAPlatform: A Component-based Platform for Constructing and Assessing miRNA-disease Association Prediction Methods	7
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	7
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	7
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	7
Identifying Functional Modules Using Energy Minimization with Graph Cuts	7
Identification of Potential Immune-related Biomarkers in Gastrointestinal Cancers	7
Diabetes Induced Factors Prediction Based on Various Improved Machine Learning Methods	6
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	6
ProtPathDB: A Web-based Resource of Parasite Proteases	6
Graph Neural Networks in Biomedical Data: A Review	6
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	6
Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data	6
Construction of an Expression Classifier Based on an Immune-related Ten-gene Panel for Rapid Diagnosis of Papillary Thyroid Carcinoma Risks	6
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	6
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	6
voomSOM: voom-based Self-Organizing Maps for Clustering RNASequencing Data	6
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	6
Advanced Multivariable Statistical Analysis Interactive Tool for Handling Missing Data and Confounding Covariates for Label-free LC-MS Proteomics Experiments	5
i4mC-CPXG: A Computational Model for Identifying DNA N4- methylcytosine Sites in Rosaceae Genome Using Novel Encoding Strategy	5
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	5
A Systematic Review of the Application of Machine Learning in CpG Island (CGI) Detection and Methylation Prediction	5
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	5
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	5
LPLSG: Prediction of lncRNA-protein Interaction Based on Local Network Structure	5
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
Transformer-based Named Entity Recognition for Clinical Cancer Drug Toxicity by Positive-unlabeled Learning and KL Regularizers	5
Comparison of Gene Selection Methods for Clustering Single-cell RNA-seq Data	5
Identification of Membrane Protein Types Based Using Hypergraph Neural Network	5
Development and Study of a Knowledge Graph for Retrieving the Relationship Between BVDV and Related Genes	5
iPSI(2L)-EDL: a Two-layer Predictor for Identifying Promoters and their Types based on Ensemble Deep Learning	5
Meet the Editorial Board Member	4
Inferring the Functional Effect of Gene-body H3K79me2 Signals in Normal Samples on Gene Expression Changes: A Potential Susceptibility Marker in Chronic Myelogenous Leukemia	4
Cervical Cancer Metastasis and Recurrence Risk Prediction Based on Deep Convolutional Neural Network	4
Long Non-coding RNAs in Heart Failure: A Deep Belief Network Based Cluster Analysis	4
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing and Preimplantation Genetic Testing	4
QLDTI: A Novel Reinforcement Learning-based Prediction Model for Drug-Target Interaction	4
NLP-MeTaxa: A Natural Language Processing Approach for Metagenomic Taxonomic Binning Based on Deep Learning	4

Predicting Distant Metastatic Sites in Cancer Using miRNA and mRNA Expression Data	4
Artificial Intelligence in Diabetes Mellitus Prediction: Advancements and Challenges - A Review	4
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	4
Structural and Functional Analyses of SARS COV-2 RNA-dependent RNA Polymerase Protein and Complementary vs. Synthetic Drugs against COVID-19 and the Exploration of Binding Sites for Docking, Molecular	4
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	4
Withdrawal Notice: Identification of Five Hub Genes Associated with Progression Development and Prognosis of Lung Adenocarcinoma Identified by Co-expression Analysis	4
Meet the Section Editor	3
scZIGVAE: A Variational Graph Attention Autoencoder Based on the Zero-Inflated Negative Binomial Distribution for Clustering Single-cell RNA-Seq Data	3
Prediction of Drug Pathway-based Disease Classes using Multiple Properties of Drugs	3
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	3
Bioinformatics Perspective of Drug Repurposing	3
A Deep Learning Method for Identifying G-Protein Coupled Receptors based on a Feature Pyramid Network and Attention Mechanism	3
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	3
SNPs of Metabolic Syndrome are Associated with Benign Prostatic Hyperplasia Development and Progression in Chinese Population	3
Precision Medicine on Chronic Disease Based on Bioinformatics and Computational Biology	3
Screening Analysis of Predictive Markers for Cytokine Release Syndrome Risk in CAR-T Cell Therapy	3
An Analysis of the Interactions between the 5' UTR and Introns in Mitochondrial Ribosomal Protein Genes	3
NEXT-GEN Medicine: Designing Drugs to Fit Patient Profiles	3
Discovering Microbe-disease Associations with Weighted Graph Convolution Networks and Taxonomy Common Tree	3
Acknowledgement to Reviewers	3
Potentiality of Risk SNPs Identification Based on GSP Theory	3
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	3
An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	3
Continual Cough: Experience and Lessons from a Case of Bronchial Adenoid Cystic Carcinoma	3
CLPr_in_ML: Cleft Lip and Palate Reconstructed Features with Machine Learning	3
Comparative Analysis of Deep Generative Model for Industrial Enzyme Design	3
Immune-related Gene-based Prognostic Signature for the Risk Stratification Analysis of Breast Cancer	3
Analysis of Novel Variants Associated with Three Human Ovarian Cancer Cell Lines	3
Hybrid Feature Extraction for Breast Cancer Classification Using the Ensemble Residual VGG16 Deep Learning Model	3
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	3
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	3
Predicting Interactions Between Pathogen and Human Proteins Based on the Relation Between Sequence Length and Amino Acid Composition	3