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 2021-05-01 to 2025-05-01.)

Article	Citations
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	291
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	58
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	42
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In-Silico Assessment Steps	36
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	34
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	32
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	28
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	21
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	19
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	19
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	18
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	18
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing and Preimplantation Genetic Testing	17
Deep Learning in Disease Diagnosis: Models and Datasets	16
Meet the Editorial Board Member	16
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	15
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	13
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	13
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	11
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	10
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	10
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	10
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	10
The Prospect of Bioactive Peptide Research: A Review on Databases and Tools	10
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	9

Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	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
Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	9
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	9
Validating the Distinctiveness of the Omicron Lineage within the SARS-CoV-2 based on Protein Language Models	8
EpiSemble: A Novel Ensemble-based Machine-learning Framework for Prediction of DNA N6-methyladenine Sites Using Hybrid Features Selection Approach for Crops	8
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	8
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	8
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	8
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	8
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	8
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	8
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	8
Application of Deep Learning Neural Networks in Computer-Aided Drug Discovery: A Review	7
Meet the Editorial Board Member	7
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	7
NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins	7
Research on the Mechanism of Traditional Chinese Medicine Treatment for Diseases caused by Human Coronavirus COVID-19	7
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	7
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	7
Prediction of Drug-target Binding Affinity by An Ensemble Lear ning System with Network Fusion Information	7
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	6
Differential Gene Expression in Cancer: An Overrated Analysis?	6
A Novel Method for Predicting Essential Proteins by Integrating Multidimensional Biological Attribute Information and Topological Properties	6
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	6
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	6
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	6
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	6
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	6
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	6
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	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
HAMP: A Knowledge-base of Antimicrobial Peptides from Human Microbiome	6
The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	6
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	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
Scaling Method for Batch Effect Correction of Gene Expression Data Based on Spectral Clustering	5
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	5
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	5
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	5
SNPs of Metabolic Syndrome are Associated with Benign Prostatic Hyperplasia Development and Progression in Chinese Population	5
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	5
Delineating Characteristic Sequence and Structural Features of Precursor and Mature Piwi-interacting RNAs of Epithelial Ovarian Cancer	5
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	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

Potentiality of Risk SNPs Identification Based on GSP Theory	5
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	5
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
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	4
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	4
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	4
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	4
Immune-related Gene-based Prognostic Signature for the Risk Stratification Analysis of Breast Cancer	4
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	4
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO₃) and their Application in Detecting High-Order Breast Cancer Biomarkers	4
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	4
Artificial Neural Network Models for Coronary Artery Disease	4
An Effective Method to Identify Cooperation Driver Gene Sets	4
Sia-m7G: Predicting m7G Sites through the Siamese Neural Network with an Attention Mechanism	3
Enhancing Drug Peptide Sequence Prediction Using Multi-view Feature Fusion Learning	3
Robust Somatic Copy Number Estimation using Coarse-to-fine Segmentation	3
Convolutional Neural Networks: A Promising Deep Learning Architecture for Biological Sequence Analysis	3
CRISPR/ Cas9 Off-targets: Computational Analysis of Causes, Prediction, Detection, and Overcoming Strategies	3
Detection of Hepatitis B Virus-associated Hepatocellular Carcinoma Disease Using Hybrid Hierarchical k-Means Clustering and SVM Algorithm	3
iAnt: Combination of Convolutional Neural Network and Random Forest Models Using PSSM and BERT Features to Identify Antioxidant Proteins	3
Colorectal Cancer Classification and Survival Analysis Based on an Integrated RNA and DNA Molecular Signature	3
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	3
iATC-NFMLP: Identifying Classes of Anatomical Therapeutic Chemicals Based on Drug Networks, Fingerprints, and Multilayer Perceptron	3
Exploring the Hepatotoxicity of Drugs through Machine Learning and Network Toxicological Methods	3
Detection of Stage-wise Biomarkers in Lung Adenocarcinoma Using Multiplex Analysis	3
A Method of Enhancing Heterogeneous Graph Representation for Predicting the Associations between lncRNAs and Diseases	3
Screening Differential Hub Genes Related with the Hypoglycemic Effect of Quercetin Through Data Mining	3
Exploring Coding Sequence Length Distributions Across Taxonomic Kingdoms Based on Maximum Information Principle	3
scTSSR-D: Gene Expression Recovery by Two-side Self-Representation and Dropout Information for scRNA-seq Data	3
Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database	3
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	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
YADA - Reference Free Deconvolution of RNA Sequencing Data	3
Meet the Editorial Board Member	3
Network Propagation-based Identification of Oligometastatic Biomarkers in Metastatic Colorectal Cancer	3
Machine Learning and Deep Learning Strategies in Drug Repositioning	3
Recommendations for Bioinformatic Tools in lncRNA Research	3
MFTP-Tool: A Wide & Deep Learning Framework for Multi-Functional Therapeutic Peptides Prediction	3
Characterization, Potential Prognostic Value, and Immune Heterogeneity of Cathepsin C in Diffuse Glioma	3
iProm-Yeast: Prediction Tool for Yeast Promoters Based on ML Stacking	3
Identifying Biomarkers of Cisplatin Sensitivity in Non-Small Cell Lung Cancer via Comprehensive Integrative Analysis	3