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 2021-11-01 to 2025-11-01.)

Article	Citations
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	303
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	64
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	58
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	43
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	41
CLsquared: A Cleaning and Clustering Tool for Viral Genomic Data	38
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	32
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
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	19
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	18
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	17
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	17
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	15
Meet the Editorial Board Member	15
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	14
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	13
CNVviso: Visualisation Solution for Copy Number Variation Data fromUltra-Low Coverage Whole-Genome Sequencing in PreimplantationGenetic Testing	12
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	12
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	12
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	12
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	11
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	11

Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	11
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	10
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	10
A Diagnostic Aid Platform to Detect the Transition of Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD)	9
Improved Hybrid Particle Swarm Optimizer with Sine-Cosine Acceleration Coefficients for Transient Electromagnetic Inversion	9
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	9
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
A New Insight into Binning of Metagenomics Data Using Unsupervised Deep Learning Approaches	9
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	9
Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	9
EpiSemble: A Novel Ensemble-based Machine-learning Framework for Prediction of DNA N6-methyladenine Sites Using Hybrid Features Selection Approach for Crops	9
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	9
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	8
A Comprehensive Database of Human Transmembrane Protein Mutations	8
Application of Deep Learning Neural Networks in Computer-Aided Drug Discovery: A Review	8
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	8
NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins	8
Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals	8
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	8
Prediction of Drug-target Binding Affinity by An Ensemble Lear ning System with Network Fusion Information	8
WITHDRAWN: The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	8
A Novel Method for Predicting Essential Proteins by Integrating Multidimensional Biological Attribute Information and Topological Properties	8
Differential Gene Expression in Cancer: An Overrated Analysis?	7
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	7
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	7
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	7
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	7
CNRBind: Small Molecule-RNA Binding Sites Recognition via Site Significant from Nucleotide and Complex Network Information	7
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	7
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	7
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	6
Corrigendum to: An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	6
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	6
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	6
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	6
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	5
Analysis of Alternative Splicing Heterogeneity during Early Stages of Mouse Embryonic Development	5
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	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
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	5
MBMM: Moment Estimating Beta Mixture Model-based Clustering Algorithm for m6A Co-methylation Module Mining	5
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	5
CEGI: Causally Explainable Gene Identification Method for Unveiling Developmental Signatures in Human Prefrontal Cortex	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	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO₃) and their Application in Detecting High-Order Breast Cancer Biomarkers	5

Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	5
An End-to-End 3D Graph Neural Network for Predicting Drug-Target-Disease Associations	5
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	5
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	4
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	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
scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data	4
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	4
Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database	4
Enhancing Drug Peptide Sequence Prediction Using Multi-view Feature Fusion Learning	4
Integrated Metabolic-related Transcription Factor Protein Activity for Stratification of Breast Cancer with Distinct Clinical Outcomes	4
An Effective Method to Identify Cooperation Driver Gene Sets	4
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	4
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	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
TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine	4
A Parallel Implementation for Large-Scale TSR-based 3D Structural Comparisons of Protein and Amino Acid	4
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	4
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	4
miRNA, siRNA, and lncRNA: Recent Development of Bioinformatics Tools and Databases in Support of Combating Different Diseases	4