OOIR: Observatory of International Research

Papers

(The TQCC of Current Bioinformatics is 4. 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
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In-Silico Assessment Steps	299
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	58
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	58
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	43
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	38
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	37
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	32
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	28
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	22
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	21
Biopanning Data Bank 2023: Updating and New Findings	21
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	19
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing and Preimplantation Genetic Testing	18
Meet the Editorial Board Member	17
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	16
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	15
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	15
The Prospect of Bioactive Peptide Research: A Review on Databases and Tools	14
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	13
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	12
Deep Learning in Disease Diagnosis: Models and Datasets	11
Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	11
Effective Classification of Melting Curve in Real-time PCR Based on Dynamic Filter-based Convolutional Neural Network	11
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	11
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	11

Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	11
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	10
Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	10
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	10
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	10
Validating the Distinctiveness of the Omicron Lineage within the SARS-CoV-2 based on Protein Language Models	9
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	9
Improved Hybrid Particle Swarm Optimizer with Sine-Cosine Acceleration Coefficients for Transient Electromagnetic Inversion	9
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	9
EpiSemble: A Novel Ensemble-based Machine-learning Framework for Prediction of DNA N6-methyladenine Sites Using Hybrid Features Selection Approach for Crops	9
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	9
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	9
Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals	8
Meet the Editorial Board Member	8
Application of Deep Learning Neural Networks in Computer-Aided Drug Discovery: A Review	8
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	8
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	8
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	8
Research on the Mechanism of Traditional Chinese Medicine Treatment for Diseases caused by Human Coronavirus COVID-19	8
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	8
Meet the Section Editor	8
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	8
Prediction of Drug-target Binding Affinity by An Ensemble Lear ning System with Network Fusion Information	8
NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins	8
WITHDRAWN: The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	7
HAMP: A Knowledge-base of Antimicrobial Peptides from Human Microbiome	7
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	7
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	7
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	7
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	7
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	7
Delineating Characteristic Sequence and Structural Features of Precursor and Mature Piwi-interacting RNAs of Epithelial Ovarian Cancer	7
A Novel Method for Predicting Essential Proteins by Integrating Multidimensional Biological Attribute Information and Topological Properties	7
CNRBind: Small Molecule-RNA Binding Sites Recognition via Site Significant from Nucleotide and Complex Network Information	7
Differential Gene Expression in Cancer: An Overrated Analysis?	7
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	7
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	6
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	6
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	6
Potentiality of Risk SNPs Identification Based on GSP Theory	6
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	6
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	6
MBMM: Moment Estimating Beta Mixture Model-based Clustering Algorithm for m6A Co-methylation Module Mining	6
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	6
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	6
Analysis of Alternative Splicing Heterogeneity during Early Stages of Mouse Embryonic Development	6
Corrigendum to: An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	6
Scaling Method for Batch Effect Correction of Gene Expression Data Based on Spectral Clustering	5
SNPs of Metabolic Syndrome are Associated with Benign Prostatic Hyperplasia Development and Progression in Chinese Population	5
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	5

Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	5
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	5
An Effective Method to Identify Cooperation Driver Gene Sets	5
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	5
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO₃) and their Application in Detecting High-Order Breast Cancer Biomarkers	5
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	5
Immune-related Gene-based Prognostic Signature for the Risk Stratification Analysis of Breast Cancer	5
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	5
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	5
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	5
scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data	5
A Parallel Implementation for Large-Scale TSR-based 3D Structural Comparisons of Protein and Amino Acid	5
CEGI: Causally Explainable Gene Identification Method for Unveiling Developmental Signatures in Human Prefrontal Cortex	5
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	5
Artificial Neural Network Models for Coronary Artery Disease	5
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	5
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	5
Sia-m7G: Predicting m7G Sites through the Siamese Neural Network with an Attention Mechanism	4
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	4
Characterization, Potential Prognostic Value, and Immune Heterogeneity of Cathepsin C in Diffuse Glioma	4
MFTP-Tool: A Wide & Deep Learning Framework for Multi-Functional Therapeutic Peptides Prediction	4
Colorectal Cancer Classification and Survival Analysis Based on an Integrated RNA and DNA Molecular Signature	4
YADA - Reference Free Deconvolution of RNA Sequencing Data	4
Screening Differential Hub Genes Related with the Hypoglycemic Effect of Quercetin Through Data Mining	4
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	4
TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine	4
Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database	4
iAnt: Combination of Convolutional Neural Network and Random Forest Models Using PSSM and BERT Features to Identify Antioxidant Proteins	4
Exploring the Hepatotoxicity of Drugs through Machine Learning and Network Toxicological Methods	4
Exploring Coding Sequence Length Distributions Across Taxonomic Kingdoms Based on Maximum Information Principle	4
Identifying Biomarkers of Cisplatin Sensitivity in Non-Small Cell Lung Cancer via Comprehensive Integrative Analysis	4
iProm-Yeast: Prediction Tool for Yeast Promoters Based on ML Stacking	4
Enhancing Drug Peptide Sequence Prediction Using Multi-view Feature Fusion Learning	4
miRNA, siRNA, and lncRNA: Recent Development of Bioinformatics Tools and Databases in Support of Combating Different Diseases	4
iATC-NFMLP: Identifying Classes of Anatomical Therapeutic Chemicals Based on Drug Networks, Fingerprints, and Multilayer Perceptron	4
CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction, Detection, and Overcoming Strategies	4