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
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	40
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	39
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	36
Biopanning Data Bank 2023: Updating and New Findings	29
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	28
Decoding the Genetic Code: Scientific Exploration of the Telomere-to- Telomere (T2T) Genome	21
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	16
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing in Preimplantation Genetic Testing	14
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	14
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	14
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	12
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	12
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	12
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	11
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	10
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	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
Biomarker Discovery Guided by a Pathway-Masked Phenotype-Specific Network for Pan-Cancer Immunotherapy Responses	10
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	10

EpiSemble: A Novel Ensemble-based Machine-learning Framework for Prediction of DNA N6-methyladenine Sites Using Hybrid Features Selection Approach for Crops	9
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	9
A New Insight into Binning of Metagenomics Data Using Unsupervised Deep Learning Approaches	9
Validating the Distinctiveness of the Omicron Lineage within the SARS-CoV-2 based on Protein Language Models	9
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	9
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	9
Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	9
An Interpretable Explainable Artificial Intelligence Framework for Urinary Cancer Survival Classification using Hybrid Feature Selection and Stacked Ensembles	8
Research on the Mechanism of Traditional Chinese Medicine Treatment for Diseases caused by Human Coronavirus COVID-19	8
Five Years of Gene Networks Modeling in Single-cell RNA-sequencing Studies: Current Approaches and Outstanding Challenges	8
Mapping Drug-gene Interactions to Identify Potential Drug Candidates Targeting Envelope Protein in SARS-CoV-2 Infection	8
Design and In-silico Screening of Short Antimicrobial Peptides (AMPs) as Anti-Tubercular Agents Targeting INHA	8
DEGoldS: A Workflow to Assess the Accuracy of Differential Expression Analysis Pipelines through Gold-standard Construction	7
AttenDRP: A Cross-Attention Network for Cancer Drug Response Prediction by Integrating Multi-Omics Data	7
A Comprehensive Database of Human Transmembrane Protein Mutations	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
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	6
Novel Statistical Approaches for Survival Analysis of RNA-Sequencing Data	6
A Tagging SNP Set Method Based on Network Community Partition of Linkage Disequilibrium and Node Centrality	6
WITHDRAWN: The Significance of Chromosome Conformation Capture in 3D Genome Architecture Comprehension	6
Identification of Key Prognosis-related microRNAs in Early- and Late- Stage Gynecological Cancers Based on TCGA Data	6
ADSVAE: An Adaptive Density-aware Spectral Clustering Method for Multi-omics Data Based on Variational Autoencoder	6
Screening and Identification of Key Genes for Cervical Cancer, Ovarian Cancer and Endometrial Cancer by Combinational Bioinformatic Analysis	6
Intestinal Flora Disease Prediction Based on Global Hybrid Dilated Convolution	6
Differential Gene Expression in Cancer: An Overrated Analysis?	6
Integrated Machine Learning Algorithms for Stratification of Patients with Bladder Cancer	6
LncMiRPath: A Transformer-based Deep Learning Framework for lncRNAs and miRNAs Interaction Prediction	6
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	6
Prediction and Motif Analysis of 2’-O-methylation Using a Hybrid Deep Learning Model from RNA Primary Sequence and Nanopore Signals	6
CNRBind: Small Molecule-RNA Binding Sites Recognition via Site Significant from Nucleotide and Complex Network Information	6
Deep Learning-Based Protein Structure Prediction Integrating Experimental Constraints: Methods and Applications—A Review	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	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
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	5
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	5
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	5
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	5
An End-to-End 3D Graph Neural Network for Predicting Drug-Target-Disease Associations	5
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
A Parallel Implementation for Large-Scale TSR-based 3D Structural Comparisons of Protein and Amino Acid	5
CEGI: Causally Explainable Gene Identification Method for Unveiling Developmental Signatures in Human Prefrontal Cortex	5
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	5
An Effective Method to Identify Cooperation Driver Gene Sets	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
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	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
Corrigendum to: Elucidating the Functional Role of Predicted miRNAs in Post-Transcriptional Gene Regulation Along with Symbiosis in Medicago truncatula	4
Prediction of Plant Ubiquitylation Proteins and Sites by Fusing Multiple Features	4
Enhancing Drug Peptide Sequence Prediction Using Multi-view Feature Fusion Learning	4
iProm-Yeast: Prediction Tool for Yeast Promoters Based on ML Stacking	4
Integrated Metabolic-related Transcription Factor Protein Activity for Stratification of Breast Cancer with Distinct Clinical Outcomes	4
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	4
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	4
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	4
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	4
MFTP-Tool: A Wide & Deep Learning Framework for Multi-Functional Therapeutic Peptides Prediction	4
Combining Network-based and Matrix Factorization to Predict Novel Drug-target Interactions: A Case Study Using the Brazilian Natural Chemical Database	4
TCM@MPXV: A Resource for Treating Monkeypox Patients in Traditional Chinese Medicine	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
YADA - Reference Free Deconvolution of RNA Sequencing Data	3
miRNA, siRNA, and lncRNA: Recent Development of Bioinformatics Tools and Databases in Support of Combating Different Diseases	3
Convolutional Neural Networks: A Promising Deep Learning Architecture for Biological Sequence Analysis	3
From Structure to Semantics: Training-Free LLM Guidance for Biomedical Knowledge Graph Fusion	3
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
Novel Gene Signatures for Prostate Cancer Detection: Network Centralitybased Screening with Experimental Validation	3
QLDTI: A Novel Reinforcement Learning-based Prediction Model for Drug-Target Interaction	3
Deep-RPA: Vulnerability Classification of a Genome for CRISPR/Cas9 Off-targets	3
Deep Learning for Clustering Single-cell RNA-seq Data	3
Robust Somatic Copy Number Estimation using Coarse-to-fine Segmentation	3
GAALSMDA: A Graph Attention-based Fusion Network Integrating Dual Attention and BiLSTM for Microbe-Drug Association Prediction	3
iATC-NFMLP: Identifying Classes of Anatomical Therapeutic Chemicals Based on Drug Networks, Fingerprints, and Multilayer Perceptron	3
LO-HDL: A New Method for Prediction of Local Genetic Correlation Based on Maximum Likelihood Estimation	3
Identification and Analysis of Plant miRNAs: Evolution of In-silico Resources and Future Challenges	3
Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data	3
A Pan-cancer Analysis Reveals the Tissue Specificity and Prognostic Impact of Angiogenesis-associated Genes in Human Cancers	3
Acknowledgement to Reviewers	3
O-GlcPRED-Ens: An Ensemble Deep Learning Approach for Predicting O-linked Glycosylation Sites in Proteins	3
Detection of Stage-wise Biomarkers in Lung Adenocarcinoma Using Multiplex Analysis	3
Comparison of Gene Selection Methods for Clustering Single-cell RNA-seq Data	3
i4mC-CPXG: A Computational Model for Identifying DNA N4- methylcytosine Sites in Rosaceae Genome Using Novel Encoding Strategy	3
Identification of Membrane Protein Types Based Using Hypergraph Neural Network	3
Exploring Coding Sequence Length Distributions Across Taxonomic Kingdoms Based on Maximum Information Principle	3
Recommendations for Bioinformatic Tools in lncRNA Research	3
Sia-m7G: Predicting m7G Sites through the Siamese Neural Network with an Attention Mechanism	3
GB5mCPred: Cross-species 5mc Site Predictor Based on Bootstrap-based Stochastic Gradient Boosting Method for Poaceae	3
Exploring the Hepatotoxicity of Drugs through Machine Learning and Network Toxicological Methods	3
Bioinformatics Perspective of Drug Repurposing	3
A Simple and Practical microRNA-based Nomogram to Predict Metastatic HCC	3
BAGT: A Heterogeneous Graph Transformer Framework for Multi-Omics Integration Reveals Key Small RNAs in Rice-Magnaporthe oryzae Interactions	3
Evaluating the Reliability of Machine Learning Predictors in m6A-SNP Association Analysis: A Comparative Study Using m6A-QTL Data	3
A Method of Enhancing Heterogeneous Graph Representation for Predicting the Associations between lncRNAs and Diseases	3
Integrating Artificial Intelligence into Neurotherapeutics: A New Frontier in Drug Design and Precision Healthcare	3
Construction of an Expression Classifier Based on an Immune-related Ten-gene Panel for Rapid Diagnosis of Papillary Thyroid Carcinoma Risks	3
Network Propagation-based Identification of Oligometastatic Biomarkers in Metastatic Colorectal Cancer	3
Identifying Diagnostic Biomarkers of Breast Cancer Based on Gene Expression Data and Ensemble Feature Selection	2
Explainable Artificial Intelligence for Protein Function Prediction: A Perspective View	2
Metabolomics: Recent Advances and Future Prospects Unveiled	2
COVID-19 Biomarkers Recognition & Classification Using Intelligent Systems	2
RDR100: A Robust Computational Method for Identification of Krüppel-like Factors	2
Dynamic Multi-Scale Hypergraph Neural Network for Fake Pandemic News Detection in Social Media	2
MSSD: An Efficient Method for Constructing Accurate and Stable Phylogenetic Networks by Merging Subtrees of Equal Depth	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
DCGPert-CDR: A Novel Computational Framework for Cancer Drug Response Prediction Integrating Drug, Cell Line, and Gene Perturbation Features	2
Hybrid Feature Extraction for Breast Cancer Classification Using the Ensemble Residual VGG16 Deep Learning Model	2
BTO-DNA Storage: Efficient and Secure Biotechnology Outsourced DNA Storage System	2
Comprehensive Pan-cancer Gene Signature Assessment through the Implementation of a Cascade Machine Learning System	2
Deep Reinforcement Learning Framework for COVID Therapy: A Research Perspective	2
Nomogram for Prediction of Hepatocellular Carcinoma Prognosis	2
Transformer and Graph Transformer-Based Prediction of Drug-Target Interactions	2
Identification of Mitophagy-Related Genes in Sepsis	2
Genetic Variants of HLA-DRB1 Alleles and the Chance of Developing Rheumatoid Arthritis: Systematic Review and Meta-Analysis	2
ORTRD: A Database for Human Olfactory Receptor and Transcription Factor Interactions	2
Genotype and Phenotype Association Analysis Based on Multi-omics Statistical Data	2
A Deep Learning Method for Identifying G-Protein Coupled Receptors Based on a Feature Pyramid Network and Attention Mechanism	2
NEXT-GEN Medicine: Designing Drugs to Fit Patient Profiles	2
An Analysis of the Interactions between the 5' UTR and Introns in Mitochondrial Ribosomal Protein Genes	2
GenNBPSeq: Online Web Server to Generate Never Born Protein Sequences Using Toeplitz Matrix Approach with Structure Analysis	2
Acknowledgement to Reviewers	2
Structural Biology Meets Biomolecular Networks: The Post-AlphaFold Era	2
Thorough Assessment of Machine Learning Techniques for Predicting Protein-Nucleic Acid Binding Hot Spots	2
IDRnet: A Novel Pixel-enlightened Neural Network for Predicting Protein Subcellular Location Based on Interactive Pointwise Attention	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
Predicting Drug-target Binding Affinity Based on Graph Isomorphism Network and iTransformer	1
Integrative Multi-Omics Approaches for Personalized Medicine and Health	1
Enhancing Microbiome-Based Disease Prediction Through Alpha Diversity Metrics and Heterogeneous Ensemble Learning	1
An Explainable Multichannel Model for COVID-19 Time Series Prediction	1
Prediction of miRNA-disease Associations by Deep Matrix Decomposition Method based on Fused Similarity Information	1
PDTDAHN: Predicting Drug-Target-Disease Associations using a Heterogeneous Network	1
Quality Control of Gene Expression Data Allows Accurate Quantification of Differentially Expressed Biological Pathways	1
Comparative Analysis of Deep Generative Model for Industrial Enzyme Design	1
An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	1
Insights into Co-Expression Network Analysis of MicroProteins and their Target Transcription Factors in Plant Embryo Development	1
Genomic Characterization of Emerging SARS-CoV-2: A Systematic Review	1
A Comparison Analysis for Protein-Protein Interaction Network-Based Methods in Prioritizing Arabidopsis Functional Genes	1
Optimal Feature Non-negative Matrix Factorization (OFNMF) for Enhanced Single-Cell RNA Sequencing Analysis	1
Leveraging Machine Learning to Assess Risk of Type 2 Diabetes and Cardiovascular Diseases in the North Indian Cohort	1
The Immune-based Prognostic Score for the Immunogenomic Landscape Aanalysis and Application of Chemotherapy in Breast Cancer	1
Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis	1
A Comparison of Mutual Information, Linear Models and Deep Learning Networks for Protein Secondary Structure Prediction	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
LPLSG: Prediction of lncRNA-protein Interaction Based on Local Network Structure	1
CFCN: An HLA-peptide Prediction Model based on Taylor Extension Theory and Multi-view Learning	1
Drug Repositioning Based on a Multiplex Network by Integrating Disease, Gene, and Drug Information	1
Deep Learning for Aging Research with DNA Methylation	1
EPI-HAN: Identification of Enhancer Promoter Interaction Using Hierarchical Attention Network	1
Hypertension Risk Prediction Based on SNPs by Machine Learning Models	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
FMDVSerPred: A Novel Computational Solution for Foot-and-mouth Disease Virus Classification and Serotype Prediction Prevalent in Asia Using VP1 Nucleotide Sequence Data	1
Screening of Candidate Chemical Regulators for the m 6 A Writer MTA in Arabidopsis	1
Bioinformatics Study of the DNA and RNA Viruses Infecting Plants and Bacteria that Could Potentially Affect Animals and Humans	1
scPPF: Predicting Promoter Fragments in scATAC-seq Based on Transcription Factor Motifs	1
ArtFusionNet: Multilevel Feature Fusion for Emotion Distribution Prediction in Artistic Images	1
dbACP: A Comprehensive Database for Anti-Cancer Peptides	1
Prediction of Drug Bioactivity in Alzheimer’s Disease Using Machine Learning Techniques and Community Networks	1
DeepPTM: Protein Post-translational Modification Prediction from Protein Sequences by Combining Deep Protein Language Model with Vision Transformers	1
Graph-Root: Prediction of Root-Associated Proteins in Maize, Sorghum, And Soybean Based on Graph Convolutional Network and Network Embedding Method	1
An Extended Feature Representation Technique for Predicting Sequenced-based Host-pathogen Protein-protein Interaction	1
A Low Transformed Tubal Rank Tensor Model Using a Spatial-Tubal Constraint for Sample Clustering with Cancer Multi-omics Data	1
DeepEpi: Deep Learning Model for Predicting Gene Expression Regulation Based on Epigenetic Histone Modifications	1
sfMON: Predicting Drug Side Effect Frequencies Based on a Versatile Multi-objective Optimization Network	1
Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches	1
A Novel Mirna-Disease Association Prediction Model Based on an Adaptive Content-Guided Fusion Mechanism and Dilateformer	1
Evaluation of Current Trends in Biomedical Applications Using Soft Computing	1
Single-Cell RNA Sequencing to Identify Natural Killer Cell-Linked Genetic Markers and Regulatory Biomolecules in Coronary Heart Disease	1
ProtPathDB: A Web-based Resource of Parasite Proteases	1
AntiCanNet: A Graph Convolution and Chemical LLM Framework for Predicting Anti-Cancer Small Molecules	1
Deciphering the Influence of Gut Microbiome Disruption on Human Health Through Multi-Algorithm Approaches	1
Predicting the Risk of Breast Cancer Recurrence and Metastasis based on miRNA Expression	1
DS-MCGR: A Dempster-Shafer Combination Method Integrating Molecular Characterization and Graph Representation for Identifying Active Compounds Related to Esophageal Cancer	1
DSAE-Impute: Learning Discriminative Stacked Autoencoders for Imputing Single-cell RNA-seq Data	1
Identification of potential biomarkers in Rheumatoid Arthritis based on DNA methylation and scRNA-Seq	1
Computational Tools for Identifying Cancer Driver Genes and Mutations: A Comprehensive Review	1
A Systematic Review of Medical Expert Systems for Cardiac Arrest Prediction	1
Revealing ANXA6 as a Novel Autophagy-related Target for Pre-eclampsia Based on the Machine Learning	1
A Unified Probabilistic Framework for Modeling and Inferring Spatial Transcriptomic Data	1
Graph Convolution and Attention-Combined Learning for Multi-Type Prediction of miRNA-Disease Associations	1
Artificial Intelligence in Diabetes Mellitus Prediction: Advancements and Challenges - A Review	1
Prediction of Homologous Protein Thermostability at the Single-Cell Level by Incorporating Explicit and Implicit Sequence Features	1
Chronological Order Based Wrapper Technique for Drug-Target Interaction Prediction (CO-WT DTI)	1
CCRMDA: MiRNA-disease Association Prediction Based on Cascade Combination Recommendation Method on a Heterogeneous Network	1
Feature-scML: An Open-source Python Package for the Feature Importance Visualization of Single-Cell Omics with Machine Learning	1
Mining Transcriptional Data for Precision Medicine: Bioinformatics Insights into Inflammatory Bowel Disease	1
scHDR: A Heterogeneous Network Transfer Learning Model for Predicting Single-Cell Drug Responses	1
Advances in Deep Learning Assisted Drug Discovery Methods: A Self-review	1
Transformer-based Named Entity Recognition for Clinical Cancer Drug Toxicity by Positive-unlabeled Learning and KL Regularizers	1
Transcriptomic Profiling of Ganoderic Acid Me-Mediated Prevention of Sendai Virus Infection	1