IEEE-ACM Transactions on Computational Biology and Bioinformatics

Papers
(The TQCC of IEEE-ACM Transactions on Computational Biology and Bioinformatics is 12. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2021-07-01 to 2025-07-01.)
ArticleCitations
Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology526
Row and Column Structure-Based Biclustering for Gene Expression Data263
The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease142
Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation110
Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data95
POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data91
New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction84
Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network81
GenSeq+: A Scalable High-Performance Accelerator for Genome Sequencing72
RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow71
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies65
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation65
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites64
Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE63
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks63
Seq-BEL: Sequence-Based Ensemble Learning for Predicting Virus-Human Protein-Protein Interaction63
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs58
Higher-Order Proximity-Based MiRNA-Disease Associations Prediction58
High-Throughput Screening and Quantum Mechanics for Identifying Potent Inhibitors Against Mac1 Domain of SARS-CoV-2 Nsp354
Protein Fold Recognition by Combining Support Vector Machines and Pairwise Sequence Similarity Scores53
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means52
An Effective Swarm Intelligence Optimization Algorithm for Flexible Ligand Docking51
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement50
Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps50
IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling49
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation49
An Automated Cell Tracking Approach With Multi-Bernoulli Filtering and Ant Colony Labor Division49
Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction48
Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning48
Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations47
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics46
VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection46
RNPredATC: A Deep Residual Learning-Based Model With Applications to the Prediction of Drug-ATC Code Association44
Improving Biomedical Question Answering by Data Augmentation and Model Weighting43
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction43
State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications43
Minimum Functional Length Analysis of K-Mer Based on BPNN42
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions42
Spatial Stochastic Model of the Pre-B Cell Receptor42
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network42
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites41
Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics41
Fine-Grained Lesion Classification Framework for Early Auxiliary Diagnosis40
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction40
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images40
A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics40
Blockchain-Based Data Access Security Solutions for Medical Wearables40
Self-Supervised Learning for Label Sparsity in Computational Drug Repositioning38
Subgroup Identification Using Virtual Twins for Human Microbiome Studies38
Automated Spot Counting in Microbiology38
Deep Learning in Gene Regulatory Network Inference: A Survey37
Local R-Symmetry Co-Occurrence: Characterising Leaf Image Patterns for Identifying Cultivars37
Robust and Privacy-Preserving Decentralized Deep Federated Learning Training: Focusing on Digital Healthcare Applications37
Evaluation of Existing Methods for High-Order Epistasis Detection37
CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data36
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction36
DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction36
A Neighborhood-Based Global Network Model to Predict Drug-Target Interactions36
Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions35
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency35
Transfer Learning Based Lightweight Ensemble Model for Imbalanced Breast Cancer Classification35
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics33
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association32
Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis32
WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites32
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance31
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images31
Explainable Knowledge Distillation for On-Device Chest X-Ray Classification31
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective31
Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications31
A Deep Learning Approach Considering Image Background for Pneumonia Identification Using Explainable AI (XAI)31
MEDA Based Biochips: Detection, Prevention and Rectification Techniques for Cyberphysical Attacks31
Lossy Compression of Quality Values in Sequencing Data31
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies30
CASL: Capturing Activity Semantics Through Location Information for Enhanced Activity Recognition30
The End-to-End Fetal Head Circumference Detection and Estimation in Ultrasound Images30
Guest Editorial Guest Editorial for the 20th Asia Pacific Bioinformatics Conference29
How Deepbics Quantifies Intensities of Transcription Factor-DNA Binding and Facilitates Prediction of Single Nucleotide Variant Pathogenicity With a Deep Learning Model Trained On ChIP-Seq Data Sets29
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment29
Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm29
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism29
Finite-Set Model Predictive Control of Melanoma Cancer Treatment Using Signaling Pathway Inhibitor of Cancer Stem Cell28
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction28
FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data28
Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy28
Morphological Rule-Constrained Object Detection of Key Structures in Infant Fundus Image28
Alignment-Free Sequence Comparison With Multiple k Values27
MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data27
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information27
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling27
PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit27
The Intrinsic Similarity of Topological Structure in Biological Neural Networks27
Improving Clinical Decision Making With a Two-Stage Recommender System27
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation26
An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks26
iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework26
Guest Editorial: Deep Learning For Genomics26
DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations26
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants26
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction26
An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network25
Generic Context-Aware Group Contributions25
Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets25
A Stochastic Grammar Approach to Mass Classification in Mammograms25
Discriminant Projection Shared Dictionary Learning for Classification of Tumors Using Gene Expression Data25
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks25
Exploring Molecular Descriptors and Fingerprints to Predict mTOR Kinase Inhibitors using Machine Learning Techniques24
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data24
Multi-Label Classification With Dual Tail-Node Augmentation for Drug Repositioning24
A Hybrid Heuristic-Exact Optimization for Large-Scale Home Health Care Problem24
Generative Biomedical Event Extraction With Constrained Decoding Strategy24
Circular Clustering With Polar Coordinate Reconstruction24
DORMAN: Database of Reconstructed MetAbolic Networks23
DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion23
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks23
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression23
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification23
EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics23
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms23
A Multi-Scale Activity Transition Network for Data Translation in EEG Signals Decoding23
Target Control of Asynchronous Boolean Networks23
P2GT: Fine-Grained Genomic Data Access Control With Privacy-Preserving Testing in Cloud Computing23
Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension23
Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization23
Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations22
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration22
Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks22
Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations22
Towards Optimal Decomposition of Boolean Networks22
Estimating Functional Connectivity by Integration of Inherent Brain Function Activity Pattern Priors22
MSCET: A Multi-Scenario Offloading Schedule for Biomedical Data Processing and Analysis in Cloud-Edge-Terminal Collaborative Vehicular Networks22
GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network22
Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation22
APT: An Automated Probe Tracker From Gene Expression Data22
A Learning Robust and Discriminative Shape Descriptor for Plant Species Identification22
LipGene: Lipschitz Continuity Guided Adaptive Learning Rates for Fast Convergence on Microarray Expression Data Sets22
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling22
COMBING: Clustering in Oncology for Mathematical and Biological Identification of Novel Gene Signatures22
Optimising Boolean Synthetic Regulatory Networks to Control Cell States21
Gene Teams are on the Field: Evaluation of Variants in Gene-Networks Using High Dimensional Modelling21
A Mutual Attention Model for Drug Target Binding Affinity Prediction21
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks21
StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction21
Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression21
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots21
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction20
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner20
Design of Constraint Coding Sets for Archive DNA Storage20
A Cascaded Mutliresolution Ensemble Deep Learning Framework for Large Scale Alzheimer's Disease Detection Using Brain MRIs20
Lesion Segmentation in Ultrasound Using Semi-Pixel-Wise Cycle Generative Adversarial Nets20
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction20
iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions20
A Fast and Furious Bayesian Network and Its Application of Identifying Colon Cancer to Liver Metastasis Gene Regulatory Networks20
Densely Connected U-Net With Criss-Cross Attention for Automatic Liver Tumor Segmentation in CT Images20
Combining Zhegalkin Polynomials and SAT Solving for Context-Specific Boolean Modeling of Biological Systems20
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data20
Integrated CNN and Federated Learning for COVID-19 Detection on Chest X-Ray Images19
Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions19
Feature-Sensitive Deep Convolutional Neural Network for Multi-Instance Breast Cancer Detection19
Improved Protein Decoy Selection via Non-Negative Matrix Factorization19
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns19
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming19
DMFLDA: A Deep Learning Framework for Predicting lncRNA–Disease Associations19
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction19
An Effective Multi-Label Protein Sub-Chloroplast Localization Prediction by Skipped-Grams of Evolutionary Profiles Using Deep Neural Network19
NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions18
Generative Adversarial Network-Based Augmentation With Noval 2-Step Authentication for Anti-Coronavirus Peptide Prediction18
dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph18
Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments18
Adaptive Tracking Control for Uncertain Cancer-Tumor-Immune Systems18
The C-SHIFT Algorithm for Normalizing Covariances18
Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications18
Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks18
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants18
Robust KALMAN Filter State Estimation for Gene Regulatory Networks18
LDA-LNSUBRW: lncRNA-Disease Association Prediction Based on Linear Neighborhood Similarity and Unbalanced bi-Random Walk17
MCA-Net: Multi-Feature Coding and Attention Convolutional Neural Network for Predicting lncRNA-Disease Association17
Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape17
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification17
2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV17
CPGL: Prediction of Compound-Protein Interaction by Integrating Graph Attention Network With Long Short-Term Memory Neural Network17
Circadian Rhythm Regulated by Tumor Suppressor p53 and Time Delay in Unstressed Cells17
Predicting miRNA-Disease Associations From miRNA-Gene-Disease Heterogeneous Network With Multi-Relational Graph Convolutional Network Model17
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model17
Prediction of Drug–Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding17
I-Health: SDN-Based Fog Architecture for IIoT Applications in Healthcare17
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology17
Efficient Approximate Kernel Based Spike Sequence Classification17
GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network17
scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation17
Common Attractors in Multiple Boolean Networks17
In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE217
Supervised Graph Clustering for Cancer Subtyping Based on Survival Analysis and Integration of Multi-Omic Tumor Data16
A Novel Method for Identification of Glutarylation Sites Combining Borderline-SMOTE With Tomek Links Technique in Imbalanced Data16
A Construction Method of Dynamic Protein Interaction Networks by Using Relevant Features of Gene Expression Data16
GeNVoM: Read Mapping Near Non-Volatile Memory16
An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data16
Patient Graph Deep Learning to Predict Breast Cancer Molecular Subtype16
A Review of Fusion Methods for Omics and Imaging Data16
Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network – A Boolean Network Modeling Perspective16
Editorial16
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network16
Integrating Molecular Graph Data of Drugs and Multiple -Omic Data of Cell Lines for Drug Response Prediction16
New Distance-Based approach for Genome-Wide Association Studies16
Prediction of Malignant Breast Cancer Cases Using Ensemble Machine Learning: A Case Study of Pesticides Prone Area16
Age Prediction by DNA Methylation in Neural Networks15
Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition15
GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes15
NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association15
A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction15
Significance-Based Essential Protein Discovery15
Identify Consistent Cross-Modality Imaging Genetic Patterns via Discriminant Sparse Canonical Correlation Analysis15
Subject-Independent Emotion Recognition of EEG Signals Based on Dynamic Empirical Convolutional Neural Network15
exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data15
Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data15
BRMCF: Binary Relevance and MLSMOTE Based Computational Framework to Predict Drug Functions From Chemical and Biological Properties of Drugs15
Noise Reduction Learning Based on XLNet-CRF for Biomedical Named Entity Recognition15
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs15
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer15
ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference15
Constructing Integrative ceRNA Networks and Finding Prognostic Biomarkers in Renal Cell Carcinoma15
aWCluster: A Novel Integrative Network-Based Clustering of Multiomics for Subtype Analysis of Cancer Data15
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance15
Few-Shot Breast Cancer Metastases Classification via Unsupervised Cell Ranking15
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data15
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations15
PiTLiD: Identification of Plant Disease From Leaf Images Based on Convolutional Neural Network15
TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction15
ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters15
Cross-Modality LGE-CMR Segmentation Using Image-to-Image Translation Based Data Augmentation15
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks15
A Multiview Clustering Method With Low-Rank and Sparsity Constraints for Cancer Subtyping14
Using Fully Convolutional Network to Locate Transcription Factor Binding Sites Based on DNA Sequence and Conservation Information14
AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles14
SCN-MLTPP: A Multi-Label Classifier for Predicting Therapeutic Properties of Peptides Using the Stacked Capsule Network14
iLncRNAdis-FB: Identify lncRNA-Disease Associations by Fusing Biological Feature Blocks Through Deep Neural Network14
EPGA-SC : A Framework forde novoAssembly of Single-Cell Sequencing Reads14
Calculation of the Weight of Evidence for Combined Single-Cell and Extracellular Forensic DNA14
AFExNet: An Adversarial Autoencoder for Differentiating Breast Cancer Sub-Types and Extracting Biologically Relevant Genes14
MicroRNA Promoter Identification in Human With a Three-level Prediction Method14
Defining Phylogenetic Network Distances Using Cherry Operations14
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread14
Tuberculosis Diagnosis Using Deep Transferred EfficientNet14
Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks14
Heterogeneity in Blood Biomarker Trajectories After Mild TBI Revealed by Unsupervised Learning14
TransRNAm: Identifying Twelve Types of RNA Modifications by an Interpretable Multi-Label Deep Learning Model Based on Transformer13
MISSH: Fast Hashing of Multiple Spaced Seeds13
Identifying Differentially Expressed Genes in RNA Sequencing Data With Small Labelled Samples13
SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features13
AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants13
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