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 2021-12-01 to 2025-12-01.)

Article	Citations
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	303
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	64
CLsquared: A Cleaning and Clustering Tool for Viral Genomic Data	60
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	44
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	43
Biopanning Data Bank 2023: Updating and New Findings	38
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	32
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	22
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	21
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	19
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	19
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	19
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In silico Assessment Steps	18
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	18
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	17
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	17
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	13
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	13
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	12
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	12
CNVviso: Visualisation Solution for Copy Number Variation Data fromUltra-Low Coverage Whole-Genome Sequencing in PreimplantationGenetic Testing	12
Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	11
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	11
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	11
Improved Hybrid Particle Swarm Optimizer with Sine-Cosine Acceleration Coefficients for Transient Electromagnetic Inversion	10

Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	10
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	10
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	10
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	10
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	10
A Diagnostic Aid Platform to Detect the Transition of Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD)	10
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	9
Validating the Distinctiveness of the Omicron Lineage within the SARS-CoV-2 based on Protein Language Models	9
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	9
EpiSemble: A Novel Ensemble-based Machine-learning Framework for Prediction of DNA N6-methyladenine Sites Using Hybrid Features Selection Approach for Crops	8
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	8
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	8
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	8
A New Insight into Binning of Metagenomics Data Using Unsupervised Deep Learning Approaches	8
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	8
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	8
Research on the Mechanism of Traditional Chinese Medicine Treatment for Diseases caused by Human Coronavirus COVID-19	8
WITHDRAWN: The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	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
Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals	7
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	7
Prediction of Drug-target Binding Affinity by An Ensemble Lear ning System with Network Fusion Information	7
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	6
A Novel Method for Predicting Essential Proteins by Integrating Multidimensional Biological Attribute Information and Topological Properties	6
CNRBind: Small Molecule-RNA Binding Sites Recognition via Site Significant from Nucleotide and Complex Network Information	6
Differential Gene Expression in Cancer: An Overrated Analysis?	6
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	6
Corrigendum to: An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	5
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	5
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	5
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	5
AI Data Applications in Drug Design, Development, and Diagnostics: A Comprehensive Approach to Modern Medicine	5
scZIGVAE: A Variational Graph Attention Autoencoder Based on the Zero-Inflated Negative Binomial Distribution for Clustering Single-cell RNA-Seq Data	5
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	5
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	5
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	5
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	5
A Parallel Implementation for Large-Scale TSR-based 3D Structural Comparisons of Protein and Amino Acid	5
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	5
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	5
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	5
Analysis of Alternative Splicing Heterogeneity during Early Stages of Mouse Embryonic Development	5
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	5
MBMM: Moment Estimating Beta Mixture Model-based Clustering Algorithm for m6A Co-methylation Module Mining	5
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	5
Immune-related Gene-based Prognostic Signature for the Risk Stratification Analysis of Breast Cancer	5

Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	4
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	4
CEGI: Causally Explainable Gene Identification Method for Unveiling Developmental Signatures in Human Prefrontal Cortex	4
TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine	4
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	4
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	4
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	4
An End-to-End 3D Graph Neural Network for Predicting Drug-Target-Disease Associations	4
scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data	4
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	4
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO₃) and their Application in Detecting High-Order Breast Cancer Biomarkers	4
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	4
An Effective Method to Identify Cooperation Driver Gene Sets	4
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	4
Identifying Biomarkers of Cisplatin Sensitivity in Non-Small Cell Lung Cancer via Comprehensive Integrative Analysis	4
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	4