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 2022-06-01 to 2026-06-01.)

Article	Citations
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	307
CLsquared: A Cleaning and Clustering Tool for Viral Genomic Data	65
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In silico Assessment Steps	46
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	40
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	39
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	36
Biopanning Data Bank 2023: Updating and New Findings	29
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	28
Decoding the Genetic Code: Scientific Exploration of the Telomere-to- Telomere (T2T) Genome	21
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	20
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	17
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	16
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing in Preimplantation Genetic Testing	14
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	14
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	14
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	12
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	12
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	12
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	11
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	10
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	10
Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	10
A Diagnostic Aid Platform to Detect the Transition of Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD)	10
Biomarker Discovery Guided by a Pathway-Masked Phenotype-Specific Network for Pan-Cancer Immunotherapy Responses	10
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	10

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
A New Insight into Binning of Metagenomics Data Using Unsupervised Deep Learning Approaches	9
Validating the Distinctiveness of the Omicron Lineage within the SARS-CoV-2 based on Protein Language Models	9
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	9
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	9
Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	9
An Interpretable Explainable Artificial Intelligence Framework for Urinary Cancer Survival Classification using Hybrid Feature Selection and Stacked Ensembles	8
Research on the Mechanism of Traditional Chinese Medicine Treatment for Diseases caused by Human Coronavirus COVID-19	8
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	8
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	8
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	8
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	7
AttenDRP: A Cross-Attention Network for Cancer Drug Response Prediction by Integrating Multi-Omics Data	7
A Comprehensive Database of Human Transmembrane Protein Mutations	7
Application of Deep Learning Neural Networks in Computer-Aided Drug Discovery: A Review	7
NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins	7
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	6
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	6
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	6
WITHDRAWN: The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	6
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	6
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	6
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	6
Intestinal Flora Disease Prediction Based on Global Hybrid Dilated Convolution	6
Differential Gene Expression in Cancer: An Overrated Analysis?	6
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	6
LncMiRPath: A Transformer-based Deep Learning Framework for lncRNAs and miRNAs Interaction Prediction	6
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	6
Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals	6
CNRBind: Small Molecule-RNA Binding Sites Recognition via Site Significant from Nucleotide and Complex Network Information	6
Deep Learning-Based Protein Structure Prediction Integrating Experimental Constraints: Methods and Applications—A Review	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
scZIGVAE: A Variational Graph Attention Autoencoder Based on the Zero-Inflated Negative Binomial Distribution for Clustering Single-cell RNA-Seq Data	5
AI Data Applications in Drug Design, Development, and Diagnostics: A Comprehensive Approach to Modern Medicine	5
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	5
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	5
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	5
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	5
An End-to-End 3D Graph Neural Network for Predicting Drug-Target-Disease Associations	5
Corrigendum to: An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	5
Analysis of Alternative Splicing Heterogeneity during Early Stages of Mouse Embryonic Development	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
An Effective Method to Identify Cooperation Driver Gene Sets	4
Identifying Biomarkers of Cisplatin Sensitivity in Non-Small Cell Lung Cancer via Comprehensive Integrative Analysis	4
Characterization, Potential Prognostic Value, and Immune Heterogeneity of Cathepsin C in Diffuse Glioma	4
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	4
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	4

Corrigendum to: Elucidating the Functional Role of Predicted miRNAs in Post-Transcriptional Gene Regulation Along with Symbiosis in Medicago truncatula	4
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	4
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	4
Enhancing Drug Peptide Sequence Prediction Using Multi-view Feature Fusion Learning	4
iProm-Yeast: Prediction Tool for Yeast Promoters Based on ML Stacking	4
Integrated Metabolic-related Transcription Factor Protein Activity for Stratification of Breast Cancer with Distinct Clinical Outcomes	4
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	4
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	4
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	4
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	4
MFTP-Tool: A Wide & Deep Learning Framework for Multi-Functional Therapeutic Peptides Prediction	4
Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database	4
TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine	4
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	4
scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data	4
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	4