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

Article	Citations
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	303
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	64
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	60
CLsquared: A Cleaning and Clustering Tool for Viral Genomic Data	46
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	43
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In silico Assessment Steps	38
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	32
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	24
Biopanning Data Bank 2023: Updating and New Findings	22
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	21
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	21
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	21
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	19
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	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	15
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	14
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	13
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	12
CNVviso: Visualisation Solution for Copy Number Variation Data fromUltra-Low Coverage Whole-Genome Sequencing in PreimplantationGenetic Testing	12
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	12
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	12
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	11
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	11
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	11

Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	11
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
Improved Hybrid Particle Swarm Optimizer with Sine-Cosine Acceleration Coefficients for Transient Electromagnetic Inversion	10
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	10
Validating the Distinctiveness of the Omicron Lineage within the SARS-CoV-2 based on Protein Language Models	9
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	9
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	9
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	9
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	9
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	8
EpiSemble: A Novel Ensemble-based Machine-learning Framework for Prediction of DNA N6-methyladenine Sites Using Hybrid Features Selection Approach for Crops	8
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	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
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	8
Research on the Mechanism of Traditional Chinese Medicine Treatment for Diseases caused by Human Coronavirus COVID-19	8
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	7
WITHDRAWN: The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	7
A Comprehensive Database of Human Transmembrane Protein Mutations	7
A Novel Method for Predicting Essential Proteins by Integrating Multidimensional Biological Attribute Information and Topological Properties	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
CNRBind: Small Molecule-RNA Binding Sites Recognition via Site Significant from Nucleotide and Complex Network Information	6
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	6
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	6
Differential Gene Expression in Cancer: An Overrated Analysis?	6
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	6
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
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	5
scZIGVAE: A Variational Graph Attention Autoencoder Based on the Zero-Inflated Negative Binomial Distribution for Clustering Single-cell RNA-Seq Data	5
CEGI: Causally Explainable Gene Identification Method for Unveiling Developmental Signatures in Human Prefrontal Cortex	5
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	5
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	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
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
An End-to-End 3D Graph Neural Network for Predicting Drug-Target-Disease Associations	5
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	5
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	5
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	5
Immune-related Gene-based Prognostic Signature for the Risk Stratification Analysis of Breast Cancer	5
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	5
AI Data Applications in Drug Design, Development, and Diagnostics: A Comprehensive Approach to Modern Medicine	5
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	4
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	4

An Effective Method to Identify Cooperation Driver Gene Sets	4
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO₃) and their Application in Detecting High-Order Breast Cancer Biomarkers	4
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	4
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	4
Identifying Biomarkers of Cisplatin Sensitivity in Non-Small Cell Lung Cancer via Comprehensive Integrative Analysis	4
Integrated Metabolic-related Transcription Factor Protein Activity for Stratification of Breast Cancer with Distinct Clinical Outcomes	4
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	4
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	4
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	4
TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine	4
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	4
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	4
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	4
scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data	4