Current Bioinformatics

Article	Citations
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	307
CLsquared: A Cleaning and Clustering Tool for Viral Genomic Data	65
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In silico Assessment Steps	46
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	40
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	39
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	35
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	27
Biopanning Data Bank 2023: Updating and New Findings	27
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	21
Decoding the Genetic Code: Scientific Exploration of the Telomere-to- Telomere (T2T) Genome	20
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	20
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	17
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	15
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	14
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	14
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	13
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing in Preimplantation Genetic Testing	12
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	11
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	11
Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	10
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	10
Biomarker Discovery Guided by a Pathway-Masked Phenotype-Specific Network for Pan-Cancer Immunotherapy Responses	10
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
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	10

Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	10
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	9
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	9
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	9
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	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
An Interpretable Explainable Artificial Intelligence Framework for Urinary Cancer Survival Classification using Hybrid Feature Selection and Stacked Ensembles	8
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	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
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	7
NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins	7
A Comprehensive Database of Human Transmembrane Protein Mutations	7
Application of Deep Learning Neural Networks in Computer-Aided Drug Discovery: A Review	7
WITHDRAWN: The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	6
CNRBind: Small Molecule-RNA Binding Sites Recognition via Site Significant from Nucleotide and Complex Network Information	6
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	6
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	6
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	6
Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals	6
A Novel Method for Predicting Essential Proteins by Integrating Multidimensional Biological Attribute Information and Topological Properties	6
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	6
AttenDRP: A Cross-Attention Network for Cancer Drug Response Prediction by Integrating Multi-Omics Data	6
Differential Gene Expression in Cancer: An Overrated Analysis?	6
Intestinal Flora Disease Prediction Based on Global Hybrid Dilated Convolution	6
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	6
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	5
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO3) and their Application in Detecting High-Order Breast Cancer Biomarkers	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	5
Deep Learning-Based Protein Structure Prediction Integrating Experimental Constraints: Methods and Applications—A Review	5
LncMiRPath: A Transformer-based Deep Learning Framework for lncRNAs and miRNAs Interaction Prediction	5
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	5
CEGI: Causally Explainable Gene Identification Method for Unveiling Developmental Signatures in Human Prefrontal Cortex	5
Analysis of Alternative Splicing Heterogeneity during Early Stages of Mouse Embryonic Development	5
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	5
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	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
Corrigendum to: An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	5
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	5
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	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	4
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	4
TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine	4
Integrated Metabolic-related Transcription Factor Protein Activity for Stratification of Breast Cancer with Distinct Clinical Outcomes	4

PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	4
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	4
Corrigendum to: Elucidating the Functional Role of Predicted miRNAs in Post-Transcriptional Gene Regulation Along with Symbiosis in Medicago truncatula	4
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	4
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	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
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	4
Characterization, Potential Prognostic Value, and Immune Heterogeneity of Cathepsin C in Diffuse Glioma	4
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	4
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	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
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	4
An Effective Method to Identify Cooperation Driver Gene Sets	4
Structural and Functional Analyses of SARS COV-2 RNA-dependent RNA Polymerase Protein and Complementary vs. Synthetic Drugs against COVID-19 and the Exploration of Binding Sites for Docking, Molecular	3
Identification of Hub Genes in Neuropathic Pain-induced Depression	3
A Pan-cancer Analysis Reveals the Tissue Specificity and Prognostic Impact of Angiogenesis-associated Genes in Human Cancers	3
Comparison of Gene Selection Methods for Clustering Single-cell RNA-seq Data	3
Exploring Coding Sequence Length Distributions Across Taxonomic Kingdoms Based on Maximum Information Principle	3
Deep Learning for Clustering Single-cell RNA-seq Data	3
A Method of Enhancing Heterogeneous Graph Representation for Predicting the Associations between lncRNAs and Diseases	3
iProm-Yeast: Prediction Tool for Yeast Promoters Based on ML Stacking	3
LO-HDL: A New Method for Prediction of Local Genetic Correlation Based on Maximum Likelihood Estimation	3
Enhancing Drug Peptide Sequence Prediction Using Multi-view Feature Fusion Learning	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
Novel Gene Signatures for Prostate Cancer Detection: Network Centralitybased Screening with Experimental Validation	3
Acknowledgement to Reviewers	3
Identification and Analysis of Plant miRNAs: Evolution of In-silico Resources and Future Challenges	3
Robust Somatic Copy Number Estimation using Coarse-to-fine Segmentation	3
Evaluating the Reliability of Machine Learning Predictors in m6A-SNP Association Analysis: A Comparative Study Using m6A-QTL Data	3
Network Propagation-based Identification of Oligometastatic Biomarkers in Metastatic Colorectal Cancer	3
Detection of Stage-wise Biomarkers in Lung Adenocarcinoma Using Multiplex Analysis	3
Recommendations for Bioinformatic Tools in lncRNA Research	3
Exploring the Hepatotoxicity of Drugs through Machine Learning and Network Toxicological Methods	3
Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database	3
Construction of an Expression Classifier Based on an Immune-related Ten-gene Panel for Rapid Diagnosis of Papillary Thyroid Carcinoma Risks	3
miRNA, siRNA, and lncRNA: Recent Development of Bioinformatics Tools and Databases in Support of Combating Different Diseases	3
Bioinformatics Perspective of Drug Repurposing	3
A Simple and Practical microRNA-based Nomogram to Predict Metastatic HCC	3
QLDTI: A Novel Reinforcement Learning-based Prediction Model for Drug-Target Interaction	3
Integrating Artificial Intelligence into Neurotherapeutics: A New Frontier in Drug Design and Precision Healthcare	3
YADA - Reference Free Deconvolution of RNA Sequencing Data	3
Identification of Membrane Protein Types Based Using Hypergraph Neural Network	3
Convolutional Neural Networks: A Promising Deep Learning Architecture for Biological Sequence Analysis	3
Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data	3
iATC-NFMLP: Identifying Classes of Anatomical Therapeutic Chemicals Based on Drug Networks, Fingerprints, and Multilayer Perceptron	3
GAALSMDA: A Graph Attention-based Fusion Network Integrating Dual Attention and BiLSTM for Microbe-Drug Association Prediction	3
MFTP-Tool: A Wide & Deep Learning Framework for Multi-Functional Therapeutic Peptides Prediction	3
Sia-m7G: Predicting m7G Sites through the Siamese Neural Network with an Attention Mechanism	3
Deep-RPA: Vulnerability Classification of a Genome for CRISPR/Cas9 Off-targets	3
Quality Control of Gene Expression Data Allows Accurate Quantification of Differentially Expressed Biological Pathways	2
Structural Biology Meets Biomolecular Networks: The Post-AlphaFold Era	2
MSSD: An Efficient Method for Constructing Accurate and Stable Phylogenetic Networks by Merging Subtrees of Equal Depth	2
IDRnet: A Novel Pixel-enlightened Neural Network for Predicting Protein Subcellular Location Based on Interactive Pointwise Attention	2
Comprehensive Pan-cancer Gene Signature Assessment through the Implementation of a Cascade Machine Learning System	2
DCGPert-CDR: A Novel Computational Framework for Cancer Drug Response Prediction Integrating Drug, Cell Line, and Gene Perturbation Features	2
A Deep Learning Method for Identifying G-Protein Coupled Receptors Based on a Feature Pyramid Network and Attention Mechanism	2
BTO-DNA Storage: Efficient and Secure Biotechnology Outsourced DNA Storage System	2
COVID-19 Biomarkers Recognition & Classification Using Intelligent Systems	2
Thorough Assessment of Machine Learning Techniques for Predicting Protein-Nucleic Acid Binding Hot Spots	2
Prediction of miRNA-disease Associations by Deep Matrix Decomposition Method based on Fused Similarity Information	2
RDR100: A Robust Computational Method for Identification of Krüppel-like Factors	2
Acknowledgement to Reviewers	2
Non-small Cell Lung Cancer Survival Estimation Through Multi-omic Two-layer SVM: A Multi-omics and Multi-Sources Integrative Model	2
Integrated Pipelines for Inferring Gene Regulatory Networks from Single-Cell Data	2
Metabolomics: Recent Advances and Future Prospects Unveiled	2
An Analysis of the Interactions between the 5' UTR and Introns in Mitochondrial Ribosomal Protein Genes	2
NEXT-GEN Medicine: Designing Drugs to Fit Patient Profiles	2
Identifying Diagnostic Biomarkers of Breast Cancer Based on Gene Expression Data and Ensemble Feature Selection	2
Deep Reinforcement Learning Framework for COVID Therapy: A Research Perspective	2
Screening of Candidate Chemical Regulators for the m 6 A Writer MTA in Arabidopsis	2
Identification of Mitophagy-Related Genes in Sepsis	2
Dynamic Multi-Scale Hypergraph Neural Network for Fake Pandemic News Detection in Social Media	2
Genetic Variants of HLA-DRB1 Alleles and the Chance of Developing Rheumatoid Arthritis: Systematic Review and Meta-Analysis	2
Genotype and Phenotype Association Analysis Based on Multi-omics Statistical Data	2
A Novel Multitask Association Analysis Model with Deep Self-reconstruction for Diagnosis of Alzheimer’s Disease	2
A graph-based multilevel property extraction network for predicting protein drug target binding affinity	2
Hybrid Feature Extraction for Breast Cancer Classification Using the Ensemble Residual VGG16 Deep Learning Model	2

Explainable Artificial Intelligence for Protein Function Prediction: A Perspective View	2
GenNBPSeq: Online Web Server to Generate Never Born Protein Sequences Using Toeplitz Matrix Approach with Structure Analysis	2
Transformer and Graph Transformer-Based Prediction of Drug-Target Interactions	2
An Explainable Multichannel Model for COVID-19 Time Series Prediction	1
Advances in Deep Learning Assisted Drug Discovery Methods: A Self-review	1
Comparative Analysis of Deep Generative Model for Industrial Enzyme Design	1
Graph-Root: Prediction of Root-Associated Proteins in Maize, Sorghum, And Soybean Based on Graph Convolutional Network and Network Embedding Method	1
Interplay of miRNA-TF-Gene Through a Novel Six-node Feed-forward Loop Identified Inflammatory Genes as Key Regulators in Type-2 Diabetes	1
DeepEpi: Deep Learning Model for Predicting Gene Expression Regulation Based on Epigenetic Histone Modifications	1
Integration of Artificial Intelligence, Machine Learning and Deep Learning Techniques in Genomics: Review on Computational Perspectives for NGS Analysis of DNA and RNA Seq Data	1
DSAE-Impute: Learning Discriminative Stacked Autoencoders for Imputing Single-cell RNA-seq Data	1
Drug Repositioning Based on a Multiplex Network by Integrating Disease, Gene, and Drug Information	1
Predicting the Risk of Breast Cancer Recurrence and Metastasis based on miRNA Expression	1
A Systematic Review of Medical Expert Systems for Cardiac Arrest Prediction	1
scPPF: Predicting Promoter Fragments in scATAC-seq Based on Transcription Factor Motifs	1
Enhancing Microbiome-Based Disease Prediction Through Alpha Diversity Metrics and Heterogeneous Ensemble Learning	1
The Immune-based Prognostic Score for the Immunogenomic Landscape Aanalysis and Application of Chemotherapy in Breast Cancer	1
Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches	1
CCRMDA: MiRNA-disease Association Prediction Based on Cascade Combination Recommendation Method on a Heterogeneous Network	1
scHDR: A Heterogeneous Network Transfer Learning Model for Predicting Single-Cell Drug Responses	1
FMDVSerPred: A Novel Computational Solution for Foot-and-mouth Disease Virus Classification and Serotype Prediction Prevalent in Asia Using VP1 Nucleotide Sequence Data	1
Chronological Order Based Wrapper Technique for Drug-Target Interaction Prediction (CO-WT DTI)	1
Revealing ANXA6 as a Novel Autophagy-related Target for Pre-eclampsia Based on the Machine Learning	1
A Combined Feature Screening Approach of Random Forest and Filterbased Methods for Ultra-high Dimensional Data	1
A Unified Probabilistic Framework for Modeling and Inferring Spatial Transcriptomic Data	1
Insights into Co-Expression Network Analysis of MicroProteins and their Target Transcription Factors in Plant Embryo Development	1
Mining Transcriptional Data for Precision Medicine: Bioinformatics Insights into Inflammatory Bowel Disease	1
ArtFusionNet: Multilevel Feature Fusion for Emotion Distribution Prediction in Artistic Images	1
A Machine Learning Perspective on DNA and RNA G-quadruplexes	1
sfMON: Predicting Drug Side Effect Frequencies Based on a Versatile Multi-objective Optimization Network	1
Transformer-based Named Entity Recognition for Clinical Cancer Drug Toxicity by Positive-unlabeled Learning and KL Regularizers	1
Prediction of Homologous Protein Thermostability at the Single-Cell Level by Incorporating Explicit and Implicit Sequence Features	1
Computational Tools for Identifying Cancer Driver Genes and Mutations: A Comprehensive Review	1
Predicting Drug-target Binding Affinity Based on Graph Isomorphism Network and iTransformer	1
Leveraging Machine Learning to Assess Risk of Type 2 Diabetes and Cardiovascular Diseases in the North Indian Cohort	1
DS-MCGR: A Dempster-Shafer Combination Method Integrating Molecular Characterization and Graph Representation for Identifying Active Compounds Related to Esophageal Cancer	1
Hypertension Risk Prediction Based on SNPs by Machine Learning Models	1
Integrative Multi-Omics Approaches for Personalized Medicine and Health	1
DeepPTM: Protein Post-translational Modification Prediction from Protein Sequences by Combining Deep Protein Language Model with Vision Transformers	1
An Extended Feature Representation Technique for Predicting Sequenced-based Host-pathogen Protein-protein Interaction	1
Transcriptomic Profiling of Ganoderic Acid Me-Mediated Prevention of Sendai Virus Infection	1
Graph Convolutional Neural Network with Multi-Layer Attention Mechanism for Predicting Potential Microbe-Disease Associations	1
A Novel Mirna-Disease Association Prediction Model Based on an Adaptive Content-Guided Fusion Mechanism and Dilateformer	1
Single-Cell RNA Sequencing to Identify Natural Killer Cell-Linked Genetic Markers and Regulatory Biomolecules in Coronary Heart Disease	1
LPLSG: Prediction of lncRNA-protein Interaction Based on Local Network Structure	1
A Comparison Analysis for Protein-Protein Interaction Network-Based Methods in Prioritizing Arabidopsis Functional Genes	1
CFCN: An HLA-peptide Prediction Model based on Taylor Extension Theory and Multi-view Learning	1
An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	1
A Low Transformed Tubal Rank Tensor Model Using a Spatial-Tubal Constraint for Sample Clustering with Cancer Multi-omics Data	1
Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis	1
Analysis of Novel Variants Associated with Three Human Ovarian Cancer Cell Lines	1
Prediction of Drug Bioactivity in Alzheimer’s Disease Using Machine Learning Techniques and Community Networks	1
Genomic Characterization of Emerging SARS-CoV-2: A Systematic Review	1
Optimal Feature Non-negative Matrix Factorization (OFNMF) for Enhanced Single-Cell RNA Sequencing Analysis	1
Bioinformatics Study of the DNA and RNA Viruses Infecting Plants and Bacteria that Could Potentially Affect Animals and Humans	1
EPI-HAN: Identification of Enhancer Promoter Interaction Using Hierarchical Attention Network	1
Nomogram for Prediction of Hepatocellular Carcinoma Prognosis	1
Identification of potential biomarkers in Rheumatoid Arthritis based on DNA methylation and scRNA-Seq	1
Artificial Intelligence in Diabetes Mellitus Prediction: Advancements and Challenges - A Review	1
Feature-scML: An Open-source Python Package for the Feature Importance Visualization of Single-Cell Omics with Machine Learning	1
A Comparison of Mutual Information, Linear Models and Deep Learning Networks for Protein Secondary Structure Prediction	1
ProtPathDB: A Web-based Resource of Parasite Proteases	1
Deep Learning for Aging Research with DNA Methylation	1
Improved Hybrid Approach for Enhancing Protein-Coding Regions Identification in DNA Sequences	1
Graph Convolution and Attention-Combined Learning for Multi-Type Prediction of miRNA-Disease Associations	1
PDTDAHN: Predicting Drug-Target-Disease Associations using a Heterogeneous Network	1
Evaluation of Current Trends in Biomedical Applications Using Soft Computing	1