Current Bioinformatics

Article	Citations
InConTPSS: Multi-scale Module Based Temporal Convolutional Networks for Accurate Protein Secondary Prediction	287
A Non-invasive Cell-free DNA Diagnosis Method for Hepatocellular Carcinoma Based on Deep Learning	51
Bioinformatic Resources for Plant Genomic Research	42
Optimized Hybrid Deep Learning for Real-Time Pandemic Data Forecasting: Long and Short-Term Perspectives	35
Meet the Editorial Board Member	33
Acknowledgements to Reviewers	32
Meet the Editorial Board Member	28
Identification of Spatial Domains, Spatially Variable Genes, and Genetic Association Studies of Alzheimer Disease with an Autoencoder-based Fuzzy Clustering Algorithm	21
Intersecting Peptidomics and Bioactive Peptides in Drug Therapeutics	19
GB5mCPred: Cross-species 5mc Site Predictor Based on Bootstrap-based Stochastic Gradient Boosting Method for Poaceae	18
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In-Silico Assessment Steps	17
A Comparative Analysis of Biological Data Integration Systems Famous for Data Exploitation and Knowledge Discovery	16
Efficacy Screening of Prospective Anti-allergic Drug Candidates: An In silico Study	15
Deep-RPA: Vulnerability Classification of a Genome for CRISPR/Cas9 Off-targets	14
Detection of DNA N6-Methyladenine Modification through SMRT-seq Features and Machine Learning Model	13
A-RFP: An Adaptive Residue Flexibility Prediction Method Improving Protein-ligand Docking Based on Homologous Proteins	13
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	13
Bioinformatics Tools and Databases for Genomics-assisted Breeding and Population Genetics of Plants: A Review	12
Evaluation of Current Trends in Biomedical Applications Using Soft Computing	11
Prediction of lncRNA-disease Associations Based on Robust Multi-label Learning	10
Detection of Stage-wise Biomarkers in Lung Adenocarcinoma Using Multiplex Analysis	10
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	10
DNA Binding Protein Prediction based on Multi-feature Deep Metatransfer Learning	9
Deep Learning for Clustering Single-cell RNA-seq Data	9
Identification and Analysis of Plant miRNAs: Evolution of In-silico Resources and Future Challenges	9

iTSP-PseAAC: Identifying Tumor Suppressor Proteins by Using Fully Connected Neural Network and PseAAC	9
Intelligent Techniques Analysis for Glycosylation Site Prediction	9
Investigation of LncRNAs Expression as a Potential Biomarker in the Diagnosis and Treatment of Human Brucellosis	9
Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches	8
Evaluating the Reliability of Machine Learning Predictors in m6A-SNP Association Analysis: A Comparative Study Using m6A-QTL Data	8
Biopanning Data Bank 2023: Updating and New Findings	8
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	8
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	8
A Review: Computational Approaches to Design sgRNA of CRISPR-Cas9	8
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	8
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	7
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	7
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	7
Identifying Functional Modules Using Energy Minimization with Graph Cuts	7
Identification of Potential Immune-related Biomarkers in Gastrointestinal Cancers	7
Delineating Characteristic Sequence and Structural Features of Precursor and Mature Piwi-interacting RNAs of Epithelial Ovarian Cancer	7
Prediction of Off-Target Effects in CRISPR/Cas9 System by Ensemble Learning	7
MDAPlatform: A Component-based Platform for Constructing and Assessing miRNA-disease Association Prediction Methods	7
Graph Neural Networks in Biomedical Data: A Review	6
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	6
Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data	6
Construction of an Expression Classifier Based on an Immune-related Ten-gene Panel for Rapid Diagnosis of Papillary Thyroid Carcinoma Risks	6
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	6
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	6
voomSOM: voom-based Self-Organizing Maps for Clustering RNASequencing Data	6
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	6
Diabetes Induced Factors Prediction Based on Various Improved Machine Learning Methods	6
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	6
ProtPathDB: A Web-based Resource of Parasite Proteases	6
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	5
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	5
LPLSG: Prediction of lncRNA-protein Interaction Based on Local Network Structure	5
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	5
Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
Transformer-based Named Entity Recognition for Clinical Cancer Drug Toxicity by Positive-unlabeled Learning and KL Regularizers	5
Comparison of Gene Selection Methods for Clustering Single-cell RNA-seq Data	5
Identification of Membrane Protein Types Based Using Hypergraph Neural Network	5
Development and Study of a Knowledge Graph for Retrieving the Relationship Between BVDV and Related Genes	5
iPSI(2L)-EDL: a Two-layer Predictor for Identifying Promoters and their Types based on Ensemble Deep Learning	5
Advanced Multivariable Statistical Analysis Interactive Tool for Handling Missing Data and Confounding Covariates for Label-free LC-MS Proteomics Experiments	5
i4mC-CPXG: A Computational Model for Identifying DNA N4- methylcytosine Sites in Rosaceae Genome Using Novel Encoding Strategy	5
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	5
A Systematic Review of the Application of Machine Learning in CpG Island (CGI) Detection and Methylation Prediction	5
QLDTI: A Novel Reinforcement Learning-based Prediction Model for Drug-Target Interaction	4
NLP-MeTaxa: A Natural Language Processing Approach for Metagenomic Taxonomic Binning Based on Deep Learning	4
Predicting Distant Metastatic Sites in Cancer Using miRNA and mRNA Expression Data	4
Artificial Intelligence in Diabetes Mellitus Prediction: Advancements and Challenges - A Review	4
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	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	4
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	4

Withdrawal Notice: Identification of Five Hub Genes Associated with Progression Development and Prognosis of Lung Adenocarcinoma Identified by Co-expression Analysis	4
Meet the Editorial Board Member	4
Inferring the Functional Effect of Gene-body H3K79me2 Signals in Normal Samples on Gene Expression Changes: A Potential Susceptibility Marker in Chronic Myelogenous Leukemia	4
Cervical Cancer Metastasis and Recurrence Risk Prediction Based on Deep Convolutional Neural Network	4
Long Non-coding RNAs in Heart Failure: A Deep Belief Network Based Cluster Analysis	4
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing and Preimplantation Genetic Testing	4
An Analysis of the Interactions between the 5' UTR and Introns in Mitochondrial Ribosomal Protein Genes	3
Continual Cough: Experience and Lessons from a Case of Bronchial Adenoid Cystic Carcinoma	3
Discovering Microbe-disease Associations with Weighted Graph Convolution Networks and Taxonomy Common Tree	3
Comparative Analysis of Deep Generative Model for Industrial Enzyme Design	3
Analysis of Novel Variants Associated with Three Human Ovarian Cancer Cell Lines	3
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	3
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	3
Predicting Interactions Between Pathogen and Human Proteins Based on the Relation Between Sequence Length and Amino Acid Composition	3
CLPr_in_ML: Cleft Lip and Palate Reconstructed Features with Machine Learning	3
Immune-related Gene-based Prognostic Signature for the Risk Stratification Analysis of Breast Cancer	3
Meet the Section Editor	3
Hybrid Feature Extraction for Breast Cancer Classification Using the Ensemble Residual VGG16 Deep Learning Model	3
Prediction of Drug Pathway-based Disease Classes using Multiple Properties of Drugs	3
Bioinformatics Perspective of Drug Repurposing	3
A Deep Learning Method for Identifying G-Protein Coupled Receptors based on a Feature Pyramid Network and Attention Mechanism	3
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	3
SNPs of Metabolic Syndrome are Associated with Benign Prostatic Hyperplasia Development and Progression in Chinese Population	3
scZIGVAE: A Variational Graph Attention Autoencoder Based on the Zero-Inflated Negative Binomial Distribution for Clustering Single-cell RNA-Seq Data	3
Precision Medicine on Chronic Disease Based on Bioinformatics and Computational Biology	3
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	3
Screening Analysis of Predictive Markers for Cytokine Release Syndrome Risk in CAR-T Cell Therapy	3
NEXT-GEN Medicine: Designing Drugs to Fit Patient Profiles	3
Acknowledgement to Reviewers	3
Potentiality of Risk SNPs Identification Based on GSP Theory	3
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	3
An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	3
Predicting COVID-19 Severity Integrating RNA-Seq Data Using Machine Learning Techniques	2
Bioinformatics Study of the DNA and RNA Viruses Infecting Plants and Bacteria that Could Potentially Affect Animals and Humans	2
Construction of Anatomical Structure-specific Developmental Dynamic Networks for Human Brain on Multiple Omics Levels	2
Scaling Method for Batch Effect Correction of Gene Expression Data Based on Spectral Clustering	2
DMR_Kmeans: Identifying Differentially Methylated Regions Based on k-means Clustering and Read Methylation Haplotype Filtering	2
An Iterative Model for Identifying Essential Proteins Based on the Whole Process Network of Protein Evolution	2
NeuMF: Predicting Anti-cancer Drug Response Through a Neural Matrix Factorization Model	2
A Machine Learning Perspective on DNA and RNA G-quadruplexes	2
A Pan-cancer Analysis Reveals the Tissue Specificity and Prognostic Impact of Angiogenesis-associated Genes in Human Cancers	2
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	2
Novel Gene Signatures for Prostate Cancer Detection: Network Centralitybased Screening with Experimental Validation	2
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	2
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	2
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	2
Analysis of the Salivary Microbiome in the Periodontal Disease Patients with Hypertension and Non-hypertension	2
SpBLRSR: Schatten p-norm Constrained Bounded Low-rank Subspace Recovery for Predicting N7-methylguanosine (m7G)-disease Associations	2
Integration of Multi-Omics Data Using Probabilistic Graph Models and External Knowledge	2
Identifying Critical States of Hepatocellular Carcinoma Based on Single- Sample Dynamic Network Biomarkers Combined with Simulated Annealing Algorithm	2
Advances in Peptide/Protein Structure Prediction Tools and their Relevance for Structural Biology in the Last Decade	2
Virtual Screening of Acetylcholinesterase Inhibitors Based on Machine Learning Combined with Molecule Docking Methods	2
MBMM: Moment Estimating Beta Mixture Model-based Clustering Algorithm for m6A Co-methylation Module Mining	2
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	2
SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	2
Identifying Diagnostic Biomarkers of Breast Cancer Based on Gene Expression Data and Ensemble Feature Selection	2
COL1A1 as a Potential Prognostic Marker and Therapeutic Target in Non-small Cell Lung Cancer	2
Identification of Hub Genes in Neuropathic Pain-induced Depression	2
Improved Hybrid Particle Swarm Optimizer with Sine-Cosine Acceleration Coefficients for Transient Electromagnetic Inversion	2
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	2
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	2
Identification of Key Histone Modifications and Hub Genes for Colorectal Cancer Metastasis	2
Explainable Artificial Intelligence for Protein Function Prediction: A Perspective View	2
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	2
Tensor Decomposition Based on Global Features and Sparse Structure for Analyzing Cancer Multiomics Data	2
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	2
Expression Profiles and Bioinformatics Analysis of Full-length circRNA Isoforms in Gliomas	2
The Prospect of Bioactive Peptide Research: A Review on Databases and Tools	2
A Simple and Practical microRNA-based Nomogram to Predict Metastatic HCC	2
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO3) and their Application in Detecting High-Order Breast Cancer Biomarkers	2
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	2
Possibilities and Limitations of CNV Interpretation Software and Algorithms in Homo Sapiens	2
Predicting Herb-disease Associations Through Graph Convolutional Network	2
Identification of Potential Inhibitors Against SARS-CoV-2 Using Computational Drug Repurposing Study	2
A Unified Probabilistic Framework for Modeling and Inferring Spatial Transcriptomic Data	2
DSAE-Impute: Learning Discriminative Stacked Autoencoders for Imputing Single-cell RNA-seq Data	2
DeepPTM: Protein Post-translational Modification Prediction from Protein Sequences by Combining Deep Protein Language Model with Vision Transformers	2
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	2
A Novel Feature Selection Method Based on MRMR and Enhanced Flower Pollination Algorithm for High Dimensional Biomedical Data	2
A Review of DNA Data Storage Technologies Based on Biomolecules	2

Deep Learning in Disease Diagnosis: Models and Datasets	2
Predicting the Risk of Breast Cancer Recurrence and Metastasis based on miRNA Expression	1
Genome-wide Characterization Deciphers Distinct Properties of Aquaporins in Six Phytophthora Species	1
A Comparison Analysis for Protein-Protein Interaction Network-Based Methods in Prioritizing Arabidopsis Functional Genes	1
An Overview of Spatial Transcriptomics Methodologies in Traversing the Biological System	1
DSPE: An End-to-End Drug Synergy Combination Prediction Algorithm for Echinococcosis	1
Effect of Various Sequence Descriptors in Predicting Human Proteinprotein Interactions Using ANN-based Prediction Models	1
Enhanced Moth-flame Optimizer with Quasi-Reflection and Refraction Learning with Application to Image Segmentation and Medical Diagnosis	1
A Low Transformed Tubal Rank Tensor Model Using a Spatial-Tubal Constraint for Sample Clustering with Cancer Multi-omics Data	1
ConvChrome: Predicting Gene Expression Based on Histone Modifications Using Deep Learning Techniques	1
Development of Machine Learning Based Blood-brain Barrier Permeability Prediction Models Using Physicochemical Properties, MACCS and Substructure Fingerprints	1
Investigating Full-Length circRNA Transcripts to Reveal circRNAMediated Regulation of Competing Endogenous RNAs in Gastric Cancer	1
Automatic Detection of Standard Planes in Fetal Ultrasound Images based on Convolutional Neural Networks and Ensemble Learning	1
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	1
GVNNVAE: A Novel Microbe-Drug Association Prediction Model based on an Improved Graph Neural Network and the Variational Auto-Encoder	1
GenNBPSeq: Online Web Server to Generate Never Born Protein Sequences Using Toeplitz Matrix Approach with Structure Analysis	1
Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	1
In silico Study of Clinical Prognosis Associated MicroRNAs for Patients with Metastasis in Clear Cell Renal Carcinoma	1
Modeling Hereditary Disease Behavior Using an Innovative Similarity Criterion and Ensemble Clustering	1
Genotype and Phenotype Association Analysis Based on Multi-omics Statistical Data	1
Representation Learning of Biological Concepts: A Systematic Review	1
CCRMDA: MiRNA-disease Association Prediction Based on Cascade Combination Recommendation Method on a Heterogeneous Network	1
A Novel Multitask Association Analysis Model with Deep Selfreconstruction for Diagnosis of Alzheimer’s Disease	1
A Path-based Method for Identification of Protein Phenotypic Annotations	1
Artificial Neural Network Models for Coronary Artery Disease	1
A Network-Based Method for the Detection of Cancer Driver Genes in Transcriptional Regulatory Networks Using the Structural Analysis of Weighted Regulatory Interactions	1
Prediction of Drug Bioactivity in Alzheimer’s Disease Using Machine Learning Techniques and Community Networks	1
PDTDAHN: Predicting Drug-Target-Disease Associations using a Heterogeneous Network	1
Deep Learning for Aging Research with DNA Methylation	1
Rank Matrix Approach for Endometriosis: Integrating Data and Constructing Diagnostic Models	1
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	1
A Novel Method for Mining Regulatory sRNAs Related to Rice Resistance Against Blast Fungus from Multi-Omics Data	1
Genetic Variants of HLA-DRB1 Alleles and the Chance of Developing Rheumatoid Arthritis: Systematic Review and Meta-Analysis	1
Effective Classification of Melting Curve in Real-time PCR Based on Dynamic Filter-based Convolutional Neural Network	1
Exploiting Gene Expression Signatures in Breast Cancer Cell Lines to Unveil Novel Drug Candidates and Synergistic Combinations	1
Drug Design and Disease Diagnosis: The Potential of Deep Learning Models in Biology	1
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	1
Withdrawal Notice: Identifying Genetic Related Neuroimaging Biomarkers of Alzheimer's Disease via Diagnosis-Guided Group Sparse Multitask Learning Method	1
New Method for Sequence Similarity Analysis Based on the Position and Frequency of Statistically Significant Repeats	1
PSO-ELM with Modified Acceleration Coefficients for Classifying the Active Compound	1
An Automated Model for Target Protein Prediction in PPI	1
A Novel Natural Graph for Efficient Clustering of Virus Genome Sequences	1
Revealing ANXA6 as a Novel Autophagy-related Target for Pre-eclampsia Based on the Machine Learning	1
Multi-channel Partial Graph Integration Learning of Partial Multi-omics Data for Cancer Subtyping	1
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	1
Structural Biology Meets Biomolecular Networks: The Post-AlphaFold Era	1
Promising Novel Biomarkers and Candidate Drugs or Herbs in Osteoarthritis: Evidence from Bioinformatics Analysis of High‐throughput Data	1
Metabolomics: Recent Advances and Future Prospects Unveiled	1
Identification of Biomarkers and Functional Modules from Genomic Data in Stage-wise Breast Cancer	1
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	1
Recent Advances in the Phylogenetic Analysis to Study Rumen Microbiome	1
Highly Accurate Gene Essentiality Prediction with W-Nucleotide Z Curve Features and Feature Selection Technique in Saccharomyces cerevisiae	1
Insights into Co-Expression Network Analysis of MicroProteins and their Target Transcription Factors in Plant Embryo Development	1
M-CAMPTM: A Cloud-based Web Platform with a Novel Approach for Species-level Classification of 16S rRNA Microbiome Sequences	1
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	1
Prediction of Super-enhancers Based on Mean-shift Undersampling	1
A graph-based multilevel property extraction network for predicting protein drug target binding affinity	1
MGCN-PolyA: An Integrated Computational Framework for Predicting Poly(A) Signals with Multiscale-gated Convolutional Networks	1
Identifying Pathological Myopia Associated Genes with A Random Walk-Based Method in Protein-Protein Interaction Network	1
Identification of Disease-specific Single Amino Acid Polymorphisms Using a Simple Random Forest at Protein-level	1
A Roadmap to Sequence Assembly Evaluation Tools	1
An Explainable Multichannel Model for COVID-19 Time Series Prediction	1
Meet the Editorial Board Member	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
Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	1
Graph-Root: Prediction of Root-Associated Proteins in Maize, Sorghum, And Soybean Based on Graph Convolutional Network and Network Embedding Method	1
Identification of Risk Molecular Subtype of Colon Cancer with Lymphovascular Invasion	1