OOIR: Observatory of International Research

Papers

(The TQCC of Current Bioinformatics is 3. 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 2021-06-01 to 2025-06-01.)

Article	Citations
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	294
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In-Silico Assessment Steps	58
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	42
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	37
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	37
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	32
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	28
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
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	20
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	20
Biopanning Data Bank 2023: Updating and New Findings	19
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	17
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing and Preimplantation Genetic Testing	17
Meet the Editorial Board Member	16
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	15
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	13
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	13
The Prospect of Bioactive Peptide Research: A Review on Databases and Tools	12
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	11
Deep Learning in Disease Diagnosis: Models and Datasets	10
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	10
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	10
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	10
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	10

Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	9
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	9
Improved Hybrid Particle Swarm Optimizer with Sine-Cosine Acceleration Coefficients for Transient Electromagnetic Inversion	9
Effective Classification of Melting Curve in Real-time PCR Based on Dynamic Filter-based Convolutional Neural Network	9
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	9
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	9
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	8
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	8
Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	8
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	8
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	8
Validating the Distinctiveness of the Omicron Lineage within the SARS-CoV-2 based on Protein Language Models	8
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	8
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	8
EpiSemble: A Novel Ensemble-based Machine-learning Framework for Prediction of DNA N6-methyladenine Sites Using Hybrid Features Selection Approach for Crops	8
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	8
Prediction of Drug-target Binding Affinity by An Ensemble Lear ning System with Network Fusion Information	7
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	7
Meet the Editorial Board Member	7
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	7
Application of Deep Learning Neural Networks in Computer-Aided Drug Discovery: A Review	7
Research on the Mechanism of Traditional Chinese Medicine Treatment for Diseases caused by Human Coronavirus COVID-19	7
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	7
NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins	7
Differential Gene Expression in Cancer: An Overrated Analysis?	6
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	6
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	6
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	6
A Novel Method for Predicting Essential Proteins by Integrating Multidimensional Biological Attribute Information and Topological Properties	6
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	6
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	6
The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	6
Delineating Characteristic Sequence and Structural Features of Precursor and Mature Piwi-interacting RNAs of Epithelial Ovarian Cancer	6
Meet the Section Editor	6
Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals	6
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	6
HAMP: A Knowledge-base of Antimicrobial Peptides from Human Microbiome	6
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	6
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
Analysis of Alternative Splicing Heterogeneity during Early Stages of Mouse Embryonic Development	5
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	5
Scaling Method for Batch Effect Correction of Gene Expression Data Based on Spectral Clustering	5
Potentiality of Risk SNPs Identification Based on GSP Theory	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
scZIGVAE: A Variational Graph Attention Autoencoder Based on the Zero-Inflated Negative Binomial Distribution for Clustering Single-cell RNA-Seq Data	5
SNPs of Metabolic Syndrome are Associated with Benign Prostatic Hyperplasia Development and Progression in Chinese Population	5
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO₃) and their Application in Detecting High-Order Breast Cancer Biomarkers	5
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	5

MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	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
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	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	4
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	4
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	4
An Effective Method to Identify Cooperation Driver Gene Sets	4
Artificial Neural Network Models for Coronary Artery Disease	4
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	4
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	4
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	4
scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data	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
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	4
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	4
Machine Learning and Deep Learning Strategies in Drug Repositioning	3
Screening Differential Hub Genes Related with the Hypoglycemic Effect of Quercetin Through Data Mining	3
i4mC-CPXG: A Computational Model for Identifying DNA N4- methylcytosine Sites in Rosaceae Genome Using Novel Encoding Strategy	3
GB5mCPred: Cross-species 5mc Site Predictor Based on Bootstrap-based Stochastic Gradient Boosting Method for Poaceae	3
Recommendations for Bioinformatic Tools in lncRNA Research	3
A Method of Enhancing Heterogeneous Graph Representation for Predicting the Associations between lncRNAs and Diseases	3
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	3
miRNA, siRNA, and lncRNA: Recent Development of Bioinformatics Tools and Databases in Support of Combating Different Diseases	3
iProm-Yeast: Prediction Tool for Yeast Promoters Based on ML Stacking	3
Colorectal Cancer Classification and Survival Analysis Based on an Integrated RNA and DNA Molecular Signature	3
CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction, Detection, and Overcoming Strategies	3
Exploring the Hepatotoxicity of Drugs through Machine Learning and Network Toxicological Methods	3
Identification and Analysis of Plant miRNAs: Evolution of In-silico Resources and Future Challenges	3
Construction of an Expression Classifier Based on an Immune-related Ten-gene Panel for Rapid Diagnosis of Papillary Thyroid Carcinoma Risks	3
Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data	3
Convolutional Neural Networks: A Promising Deep Learning Architecture for Biological Sequence Analysis	3
Enhancing Drug Peptide Sequence Prediction Using Multi-view Feature Fusion Learning	3
Network Propagation-based Identification of Oligometastatic Biomarkers in Metastatic Colorectal Cancer	3
iAnt: Combination of Convolutional Neural Network and Random Forest Models Using PSSM and BERT Features to Identify Antioxidant Proteins	3
Exploring Coding Sequence Length Distributions Across Taxonomic Kingdoms Based on Maximum Information Principle	3
Characterization, Potential Prognostic Value, and Immune Heterogeneity of Cathepsin C in Diffuse Glioma	3
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	3
Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database	3
Detection of Hepatitis B Virus-associated Hepatocellular Carcinoma Disease Using Hybrid Hierarchical k-Means Clustering and SVM Algorithm	3
MDAPlatform: A Component-based Platform for Constructing and Assessing miRNA-disease Association Prediction Methods	3
QLDTI: A Novel Reinforcement Learning-based Prediction Model for Drug-Target Interaction	3
Meet the Editorial Board Member	3
Robust Somatic Copy Number Estimation using Coarse-to-fine Segmentation	3
YADA - Reference Free Deconvolution of RNA Sequencing Data	3
Evaluating the Reliability of Machine Learning Predictors in m6A-SNP Association Analysis: A Comparative Study Using m6A-QTL Data	3
iATC-NFMLP: Identifying Classes of Anatomical Therapeutic Chemicals Based on Drug Networks, Fingerprints, and Multilayer Perceptron	3
Sia-m7G: Predicting m7G Sites through the Siamese Neural Network with an Attention Mechanism	3
MFTP-Tool: A Wide & Deep Learning Framework for Multi-Functional Therapeutic Peptides Prediction	3
Identifying Biomarkers of Cisplatin Sensitivity in Non-Small Cell Lung Cancer via Comprehensive Integrative Analysis	3