Current Bioinformatics

Article	Citations
Construction and Comprehensive Analysis of a Special Competitive Endogenous RNAs Network to Reveal Potential Prognostic Biomarkers for Endometrial Carcinoma	264
Whole-exome Sequencing of Tumor-only Samples Reveals the Association between Somatic Alterations and Clinical Features in Pancreatic Cancer	73
MDAPlatform: A Component-based Platform for Constructing and Assessing miRNA-disease Association Prediction Methods	51
Identifying Functional Modules Using Energy Minimization with Graph Cuts	47
InConTPSS: Multi-scale Module Based Temporal Convolutional Networks for Accurate Protein Secondary Prediction	38
Integrated Multi-Omics Data Analysis Identifies a Novel Genetics-Risk Gene of IRF4 Associated with Prognosis of Oral Cavity Cancer	32
Bioinformatic Resources for Plant Genomic Research	29
Meet the Editorial Board Member	28
MaxDEL: Accurate and Efficient Calling of Genomic Deletions from Single Molecular Real-time Sequencing Using Integrated Method	28
Acknowledgements to Reviewers	21
A Simple Protein Evolutionary Classification Method Based on the Mutual Relations Between Protein Sequences	21
Meet the Editorial Board Member	20
GenRepAI: Utilizing Artificial Intelligence to Identify Repeats in Genomic Suffix Trees	19
ProtPathDB: A Web-based Resource of Parasite Proteases	18
Association Analysis Between Introns and mRNAs in Caenorhabditis elegans Genes with Different Expression Levels	17
Genome-wide Identification of Differently Expressed lncRNAs, mRNAs, and circRNAs in Patients with Osteoarthritis	16
Comparison of Gene Selection Methods for Clustering Single-cell RNA-seq Data	15
Analyzing Association Between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning	15
AthEDL: Identifying Enhancers in Arabidopsis thaliana Using an Attention-based Deep Learning Method	14
Detecting TYMS Tandem Repeat Polymorphism by the PSSD Method Based on Next-generation Sequencing	12
i4mC-CPXG: A Computational Model for Identifying DNA N4- methylcytosine Sites in Rosaceae Genome Using Novel Encoding Strategy	12
Recent Progress of Deep Learning Methods for RBP Binding Sites Prediction on circRNA	12
Toll-like Receptor 4 Gene Polymorphisms in Chinese Population After Allogeneic Hematopoietic Stem Cell Transplantation	11
Graph Neural Networks in Biomedical Data: A Review	11
A Cross-entropy-based Method for Essential Protein Identification in Yeast Protein-protein Interaction Network	11

Cervical Cancer Metastasis and Recurrence Risk Prediction Based on Deep Convolutional Neural Network	11
Novel Design for Multi-Epitope Vaccines of COVID-19 and Critical In-Silico Assessment Steps	11
Delineating Characteristic Sequence and Structural Features of Precursor and Mature Piwi-interacting RNAs of Epithelial Ovarian Cancer	10
A Comparative Analysis of Biological Data Integration Systems Famous for Data Exploitation and Knowledge Discovery	10
Multimodal Deep Learning for Cancer Survival Prediction: A Review	10
Construction of an Expression Classifier Based on an Immune-related Ten-gene Panel for Rapid Diagnosis of Papillary Thyroid Carcinoma Risks	10
Efficacy Screening of Prospective Anti-allergic Drug Candidates: An In silico Study	10
Prioritizing Cancer lncRNA Modulators via Integrated lncRNA-mRNA Network and Somatic Mutation Data	10
Deep-RPA: Vulnerability Classification of a Genome for CRISPR/Cas9 Off-targets	9
A Systematic Review of the Application of Machine Learning in CpG Island (CGI) Detection and Methylation Prediction	9
Bioinformatics Tools and Databases for Genomics-assisted Breeding and Population Genetics of Plants: A Review	9
Enhancing Drug-Target Binding Affinity Prediction through Deep Learning and Protein Secondary Structure Integration	9
Detection of DNA N6-Methyladenine Modification through SMRT-seq Features and Machine Learning Model	9
Identification of Potential Immune-related Biomarkers in Gastrointestinal Cancers	9
A-RFP: An Adaptive Residue Flexibility Prediction Method Improving Protein-ligand Docking Based on Homologous Proteins	9
Diabetes Induced Factors Prediction Based on Various Improved Machine Learning Methods	9
QLDTI: A Novel Reinforcement Learning-based Prediction Model for Drug-Target Interaction	8
Identification of Membrane Protein Types Based Using Hypergraph Neural Network	8
Early Prediction of Malignant Mesothelioma: An Approach Towards Non-invasive Method	8
Evaluation of Current Trends in Biomedical Applications Using Soft Computing	8
LPLSG: Prediction of lncRNA-protein Interaction Based on Local Network Structure	8
Inferring the Functional Effect of Gene-body H3K79me2 Signals in Normal Samples on Gene Expression Changes: A Potential Susceptibility Marker in Chronic Myelogenous Leukemia	8
Prediction of Off-Target Effects in CRISPR/Cas9 System by Ensemble Learning	7
iTSP-PseAAC: Identifying Tumor Suppressor Proteins by Using Fully Connected Neural Network and PseAAC	7
Prediction of lncRNA-disease Associations Based on Robust Multi-label Learning	7
Translation of Circular RNAs: Functions of Translated Products and Related Bioinformatics Approaches	7
Deep Learning for Clustering Single-cell RNA-seq Data	7
Intelligent Techniques Analysis for Glycosylation Site Prediction	7
Biomarkers Identification of Hepatocellular Carcinoma Based on Multiomics Data Integration and Graph-embedded Deep Neural Network	7
Multivariate Information Fusion for Identifying Antifungal Peptides with Hilbert-Schmidt Independence Criterion	7
DNA Binding Protein Prediction based on Multi-feature Deep Metatransfer Learning	7
Investigation of LncRNAs Expression as a Potential Biomarker in the Diagnosis and Treatment of Human Brucellosis	7
Detection of Stage-wise Biomarkers in Lung Adenocarcinoma Using Multiplex Analysis	7
DILI-Stk: An Ensemble Model for the Prediction of Drug-induced Liver Injury of Drug Candidates	6
Development and Study of a Knowledge Graph for Retrieving the Relationship Between BVDV and Related Genes	6
iPSI(2L)-EDL: a Two-layer Predictor for Identifying Promoters and their Types based on Ensemble Deep Learning	6
NLP-MeTaxa: A Natural Language Processing Approach for Metagenomic Taxonomic Binning Based on Deep Learning	6
Identification and Analysis of Plant miRNAs: Evolution of In-silico Resources and Future Challenges	6
Evaluating the Reliability of Machine Learning Predictors in m6A-SNP Association Analysis: A Comparative Study Using m6A-QTL Data	6
Bioluminescent Proteins Prediction with Voting Strategy	6
A Review: Computational Approaches to Design sgRNA of CRISPR-Cas9	6
Decoding the Genetic Code: Scientific Exploration of the Telomere-totelomere (T2T) Genome	6
A Skin Cancer Detector Based on Transfer Learning and Feature Fusion	6
Advanced Multivariable Statistical Analysis Interactive Tool for Handling Missing Data and Confounding Covariates for Label-free LC-MS Proteomics Experiments	5
Optimized Hybrid Deep Learning for Real-Time Pandemic Data Forecasting: Long and Short-Term Perspectives	5
Transformer-based Named Entity Recognition for Clinical Cancer Drug Toxicity by Positive-unlabeled Learning and KL Regularizers	5
Robust Transcription Factor Binding Site Prediction Using Deep Neural Networks	5
A Novel Feature Selection Method Based on MRMR and Enhanced Flower Pollination Algorithm for High Dimensional Biomedical Data	5
Meet the Editorial Board Member	5
Identification of Spatial Domains, Spatially Variable Genes, and Genetic Association Studies of Alzheimer Disease with an Autoencoder-based Fuzzy Clustering Algorithm	5

Inferring Gene Regulatory Networks from Single-Cell Time-Course Data Based on Temporal Convolutional Networks	5
GB5mCPred: Cross-species 5mc Site Predictor Based on Bootstrap-based Stochastic Gradient Boosting Method for Poaceae	5
Toxicity Prediction for Immune Thrombocytopenia Caused by Drugs Based on Logistic Regression with Feature Importance	5
A Pan-cancer Analysis Reveals the Tissue Specificity and Prognostic Impact of Angiogenesis-associated Genes in Human Cancers	5
Intersecting Peptidomics and Bioactive Peptides in Drug Therapeutics	5
PredART: Uncertainty-quantified Machine Learning Prediction of Androgen Receptor Agonists Overcoming Imbalanced Dataset	5
Network Subgraph-based Method: Alignment-free Technique for Molecular Network Analysis	5
voomSOM: voom-based Self-Organizing Maps for Clustering RNASequencing Data	5
Decoding Seven Basic Odors by Investigating Pharmacophores and Molecular Features of Odorants	5
Biopanning Data Bank 2023: Updating and New Findings	5
A Review of DNA Data Storage Technologies Based on Biomolecules	5
Virtual Screening of Acetylcholinesterase Inhibitors Based on Machine Learning Combined with Molecule Docking Methods	4
Extracting Gradual Rules to Reveal Regulation Between Genes	4
SNPs of Metabolic Syndrome are Associated with Benign Prostatic Hyperplasia Development and Progression in Chinese Population	4
Continual Cough: Experience and Lessons from a Case of Bronchial Adenoid Cystic Carcinoma	4
Advances in Peptide/Protein Structure Prediction Tools and their Relevance for Structural Biology in the Last Decade	4
Scaling Method for Batch Effect Correction of Gene Expression Data Based on Spectral Clustering	4
Construction of Anatomical Structure-specific Developmental Dynamic Networks for Human Brain on Multiple Omics Levels	4
Multi-label Learning for the Diagnosis of Cancer and Identification of Novel Biomarkers with High-throughput Omics	4
An Efficient Multiple Kernel Support Vector Regression Model for Assessing Dry Weight of Hemodialysis Patients	4
Withdrawal Notice: Identification of Five Hub Genes Associated with Progression Development and Prognosis of Lung Adenocarcinoma Identified by Co-expression Analysis	4
SpBLRSR: Schatten p-norm Constrained Bounded Low-rank Subspace Recovery for Predicting N7-methylguanosine (m7G)-disease Associations	4
Machine Learning Applications in the Study of Parkinson’s Disease: A Systematic Review	4
Long Non-coding RNAs in Heart Failure: A Deep Belief Network Based Cluster Analysis	4
Artificial Intelligence in Diabetes Mellitus Prediction: Advancements and Challenges - A Review	4
TumorDet: A Breast Tumor Detection Model Based on Transfer Learning and ShuffleNet	4
Meet the Section Editor	4
Potentiality of Risk SNPs Identification Based on GSP Theory	4
A Simple and Practical microRNA-based Nomogram to Predict Metastatic HCC	4
Screening Analysis of Predictive Markers for Cytokine Release Syndrome Risk in CAR-T Cell Therapy	4
Identifying Critical States of Hepatocellular Carcinoma Based on Single- Sample Dynamic Network Biomarkers Combined with Simulated Annealing Algorithm	3
A Novel Machine-learning Model to Classify Schizophrenia Using Methylation Data Based on Gene Expression	3
Transcriptome Analysis Reveals Possible Virulence Factors of Paragonimus proliferus	3
Deep Learning in Disease Diagnosis: Models and Datasets	3
Explainable Artificial Intelligence for Protein Function Prediction: A Perspective View	3
Expression Profiles and Bioinformatics Analysis of Full-length circRNA Isoforms in Gliomas	3
PKE-Ubsite: A Ubiquitylation Site Predictor for Plants Based on Multiple Encoders and Ensemble Deep Learning Framework	3
CLPr_in_ML: Cleft Lip and Palate Reconstructed Features with Machine Learning	3
Precision Medicine on Chronic Disease Based on Bioinformatics and Computational Biology	3
Multinomial Logistic Regression with Adaptive Regularization for Cancer Subtype Classification via Multi-omics Data	3
Hybrid Feature Extraction for Breast Cancer Classification Using the Ensemble Residual VGG16 Deep Learning Model	3
Analysis of the Salivary Microbiome in the Periodontal Disease Patients with Hypertension and Non-hypertension	3
Acknowledgement to Reviewers	3
A Deep Learning Method for Identifying G-Protein Coupled Receptors based on a Feature Pyramid Network and Attention Mechanism	3
Predicting Interactions Between Pathogen and Human Proteins Based on the Relation Between Sequence Length and Amino Acid Composition	3
BDselect: A Package for k-mer Selection Based on the Binomial Distribution	3
Novel Gene Signatures for Prostate Cancer Detection: Network Centralitybased Screening with Experimental Validation	3
Analysis of Novel Variants Associated with Three Human Ovarian Cancer Cell Lines	3
A Machine Learning-based Self-risk Assessment Technique for Cervical Cancer	3
Identification of Hub Genes in Neuropathic Pain-induced Depression	3
Tensor Decomposition Based on Global Features and Sparse Structure for Analyzing Cancer Multiomics Data	3
An Exploratory Review on Recent Computational Approaches Devised for MiRNA Disease Association Prediction	3
Identification of Potential Inhibitors Against SARS-CoV-2 Using Computational Drug Repurposing Study	2
MBMM: Moment Estimating Beta Mixture Model-based Clustering Algorithm for m6A Co-methylation Module Mining	2
An Iterative Model for Identifying Essential Proteins Based on the Whole Process Network of Protein Evolution	2
Discovering Microbe-disease Associations with Weighted Graph Convolution Networks and Taxonomy Common Tree	2
Representation Learning of Biological Concepts: A Systematic Review	2
DMR_Kmeans: Identifying Differentially Methylated Regions Based on k-means Clustering and Read Methylation Haplotype Filtering	2
NEXT-GEN Medicine: Designing Drugs to Fit Patient Profiles	2
A Parallel Implementation for Large-Scale TSR-based 3D Structural Comparisons of Protein and Amino Acid	2
P4PC: A Portal for Bioinformatics Resources of piRNAs and circRNAs	2
Construction of Network Biomarkers Using Inter-Feature Correlation Coefficients (FeCO3) and their Application in Detecting High-Order Breast Cancer Biomarkers	2
A Deep Neural Network Model with Attribute Network Representation for lncRNA-Protein Interaction Prediction	2
CNVviso: Visualisation Solution for Copy Number Variation Data from Ultra-Low Coverage Whole-Genome Sequencing and Preimplantation Genetic Testing	2
Predicting Distant Metastatic Sites in Cancer Using miRNA and mRNA Expression Data	2
Bioinformatics Study of the DNA and RNA Viruses Infecting Plants and Bacteria that Could Potentially Affect Animals and Humans	2
Integration of Multi-Omics Data Using Probabilistic Graph Models and External Knowledge	2
Predicting COVID-19 Severity Integrating RNA-Seq Data Using Machine Learning Techniques	2
Protein Secondary Structure Prediction Using Character Bi-gram Embedding and Bi-LSTM	2
Possibilities and Limitations of CNV Interpretation Software and Algorithms in Homo Sapiens	2
Stacking-Kcr: A Stacking Model for Predicting the Crotonylation Sites of Lysine by Fusing Serial and Automatic Encoder	2
Highly Accurate Gene Essentiality Prediction with W-Nucleotide Z Curve Features and Feature Selection Technique in Saccharomyces cerevisiae	2
Full-length PacBio Amplicon Sequencing to Unveil RNA Editing Sites	2
Prediction of Drug Pathway-based Disease Classes using Multiple Properties of Drugs	2
Bioinformatics Perspective of Drug Repurposing	2
Predicting the Risk of Breast Cancer Recurrence and Metastasis based on miRNA Expression	2
The Prospect of Bioactive Peptide Research: A Review on Databases and Tools	2
Drug-target Interaction Prediction By Combining Transformer and Graph Neural Networks	2
Identifying Diagnostic Biomarkers of Breast Cancer Based on Gene Expression Data and Ensemble Feature Selection	2
CCRMDA: MiRNA-disease Association Prediction Based on Cascade Combination Recommendation Method on a Heterogeneous Network	2

SNP-based Computational Analysis Reveals Recombination-associated Genome Evolution in Humans	2
scSDSC: Self-supervised Deep Subspace Clustering for scRNA-seq Data	2
Mathematical Modelling and Bioinformatics Analyses of Drug Resistance for Cancer Treatment	2
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	2
Revealing ANXA6 as a Novel Autophagy-related Target for Pre-eclampsia Based on the Machine Learning	2
Application of Improved Support Vector Machine for Pulmonary Syndrome Exposure with Computer Vision Measures	2
Improved Hybrid Particle Swarm Optimizer with Sine-Cosine Acceleration Coefficients for Transient Electromagnetic Inversion	2
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework	2
DeepPTM: Protein Post-translational Modification Prediction from Protein Sequences by Combining Deep Protein Language Model with Vision Transformers	2
A Unified Probabilistic Framework for Modeling and Inferring Spatial Transcriptomic Data	2
Immune-related Gene-based Prognostic Signature for the Risk Stratification Analysis of Breast Cancer	2
Prediction of DNA-binding Sites in Transcriptions Factor in Fur-like Proteins Using Machine Learning and Molecular Descriptors	2
Predicting Herb-disease Associations Through Graph Convolutional Network	2
Meet the Editorial Board Member	2
Artificial Neural Network Models for Coronary Artery Disease	2
Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis	1
Investigating Full-Length circRNA Transcripts to Reveal circRNAMediated Regulation of Competing Endogenous RNAs in Gastric Cancer	1
Identification of Drug-Disease Associations by Using Multiple Drug and Disease Networks	1
Development of Machine Learning Based Blood-brain Barrier Permeability Prediction Models Using Physicochemical Properties, MACCS and Substructure Fingerprints	1
Effective Classification of Melting Curve in Real-time PCR Based on Dynamic Filter-based Convolutional Neural Network	1
A Review of Biosequences Alignment, Matching, and Mining Based on GPU	1
A graph-based multilevel property extraction network for predicting protein drug target binding affinity	1
Identification of Disease-specific Single Amino Acid Polymorphisms Using a Simple Random Forest at Protein-level	1
PoGB-pred: Prediction of Antifreeze Proteins Sequences Using Amino Acid Composition with Feature Selection Followed by a Sequential-based Ensemble Approach	1
An Automated Model for Target Protein Prediction in PPI	1
Integrated Bioinformatics and Machine Learning Algorithms Analyses Highlight Related Pathways and Genes Associated with Alzheimer's Disease	1
NeuMF: Predicting Anti-cancer Drug Response Through a Neural Matrix Factorization Model	1
Genotype and Phenotype Association Analysis Based on Multi-omics Statistical Data	1
A Machine Learning Perspective on DNA and RNA G-quadruplexes	1
Effect of Various Sequence Descriptors in Predicting Human Proteinprotein Interactions Using ANN-based Prediction Models	1
SVM-Root: Identification of Root-Associated Proteins in Plants by Employing the Support Vector Machine with Sequence-Derived Features	1
Withdrawal Notice: Identifying Genetic Related Neuroimaging Biomarkers of Alzheimer's Disease via Diagnosis-Guided Group Sparse Multitask Learning Method	1
Salient Features, Data and Algorithms for MicroRNA Screening from Plants: A Review on the Gains and Pitfalls of Machine Learning Techniques	1
Transcriptomic Profiling of Ganoderic Acid Me-Mediated Prevention of Sendai Virus Infection	1
PredPVP: A Stacking Model for Predicting Phage Virion Proteins Based on Feature Selection Methods	1
ESREEM: Efficient Short Reads Error Estimation Computational Model for Next-generation Genome Sequencing	1
Prediction of Microbe-drug Associations Based on Chemical Structures and the KATZ Measure	1
MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network	1
Prediction of Drug Bioactivity in Alzheimer’s Disease Using Machine Learning Techniques and Community Networks	1
M-CAMPTM: A Cloud-based Web Platform with a Novel Approach for Species-level Classification of 16S rRNA Microbiome Sequences	1
A Comparison Analysis for Protein-Protein Interaction Network-Based Methods in Prioritizing Arabidopsis Functional Genes	1
Identification of Biomarkers and Functional Modules from Genomic Data in Stage-wise Breast Cancer	1
Identification of Potential Biomarkers in Stomach Adenocarcinoma using Machine Learning Approaches	1
A Novel Multitask Association Analysis Model with Deep Selfreconstruction for Diagnosis of Alzheimer’s Disease	1
MBPathNCP: A Metabolic Pathway Prediction Model for Chemicals and Enzymes Based on Network Consistency Projection	1
An Explainable Multichannel Model for COVID-19 Time Series Prediction	1
Identification of Plasmodium Secreted Proteins Based on MonoDiKGap and Distance-Based Top-n-Gram Methods	1
Promising Novel Biomarkers and Candidate Drugs or Herbs in Osteoarthritis: Evidence from Bioinformatics Analysis of High‐throughput Data	1
Prospects of Identifying Alternative Splicing Events from Single-Cell RNA Sequencing Data	1
Identification of Risk Molecular Subtype of Colon Cancer with Lymphovascular Invasion	1
Rank Matrix Approach for Endometriosis: Integrating Data and Constructing Diagnostic Models	1
Structural Biology Meets Biomolecular Networks: The Post-AlphaFold Era	1
Identification of Key Histone Modifications and Hub Genes for Colorectal Cancer Metastasis	1
GenNBPSeq: Online Web Server to Generate Never Born Protein Sequences Using Toeplitz Matrix Approach with Structure Analysis	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
Modeling Hereditary Disease Behavior Using an Innovative Similarity Criterion and Ensemble Clustering	1
Deep Learning Model for Pathogen Classification Using Feature Fusion and Data Augmentation	1
Graph-Root: Prediction of Root-Associated Proteins in Maize, Sorghum, And Soybean Based on Graph Convolutional Network and Network Embedding Method	1
scADCA: An Anomaly Detection-Based scRNA-seq Dataset Cell Type Annotation Method for Identifying Novel Cells	1
A Roadmap to Sequence Assembly Evaluation Tools	1
Bio-analytical Identification of Key Genes that Could Contribute to the Progression and Metastasis of Osteosarcoma	1
Identifying Key Clinical Indicators Associated with the Risk of Death in Hospitalized COVID-19 Patients	1
A Low Transformed Tubal Rank Tensor Model Using a Spatial-Tubal Constraint for Sample Clustering with Cancer Multi-omics Data	1
New Method for Sequence Similarity Analysis Based on the Position and Frequency of Statistically Significant Repeats	1
COL1A1 as a Potential Prognostic Marker and Therapeutic Target in Non-small Cell Lung Cancer	1
Multi-channel Partial Graph Integration Learning of Partial Multi-omics Data for Cancer Subtyping	1
DSAE-Impute: Learning Discriminative Stacked Autoencoders for Imputing Single-cell RNA-seq Data	1
A Novel Natural Graph for Efficient Clustering of Virus Genome Sequences	1
Using Bioinformatics to Quantify the Variability and Diversity of the Microbial Community Structure in Pond Ecosystems of a Subtropical Catchment	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
m5C-HPromoter: An Ensemble Deep Learning Predictor for Identifying 5-methylcytosine Sites in Human Promoters	1
Insights into Co-Expression Network Analysis of MicroProteins and their Target Transcription Factors in Plant Embryo Development	1
A Path-based Method for Identification of Protein Phenotypic Annotations	1
Enhanced Moth-flame Optimizer with Quasi-Reflection and Refraction Learning with Application to Image Segmentation and Medical Diagnosis	1
A Novel Method for Mining Regulatory sRNAs Related to Rice Resistance Against Blast Fungus from Multi-Omics Data	1