IEEE-ACM Transactions on Computational Biology and Bioinformatics

Papers
(The median citation count of IEEE-ACM Transactions on Computational Biology and Bioinformatics is 5. 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 2021-06-01 to 2025-06-01.)
ArticleCitations
Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology523
Row and Column Structure-Based Biclustering for Gene Expression Data255
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics137
The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease106
Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation95
Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data88
POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data82
New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction78
Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network70
GenSeq+: A Scalable High-Performance Accelerator for Genome Sequencing69
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation64
RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow64
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement62
Seq-BEL: Sequence-Based Ensemble Learning for Predicting Virus-Human Protein-Protein Interaction61
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies61
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs61
Higher-Order Proximity-Based MiRNA-Disease Associations Prediction56
High-Throughput Screening and Quantum Mechanics for Identifying Potent Inhibitors Against Mac1 Domain of SARS-CoV-2 Nsp355
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-Means50
Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations49
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation48
Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps48
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks48
An Effective Swarm Intelligence Optimization Algorithm for Flexible Ligand Docking48
An Automated Cell Tracking Approach With Multi-Bernoulli Filtering and Ant Colony Labor Division47
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites47
Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning47
IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling46
VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection46
Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction45
Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE44
RNPredATC: A Deep Residual Learning-Based Model With Applications to the Prediction of Drug-ATC Code Association43
A Neighborhood-Based Global Network Model to Predict Drug-Target Interactions43
Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions42
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction42
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions41
Spatial Stochastic Model of the Pre-B Cell Receptor41
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network41
Minimum Functional Length Analysis of K-Mer Based on BPNN41
WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites41
Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics40
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction39
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites39
Blockchain-Based Data Access Security Solutions for Medical Wearables38
Fine-Grained Lesion Classification Framework for Early Auxiliary Diagnosis38
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images38
A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics37
Automated Spot Counting in Microbiology37
Self-Supervised Learning for Label Sparsity in Computational Drug Repositioning37
State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications36
Local R-Symmetry Co-Occurrence: Characterising Leaf Image Patterns for Identifying Cultivars36
Subgroup Identification Using Virtual Twins for Human Microbiome Studies36
Deep Learning in Gene Regulatory Network Inference: A Survey35
Improving Biomedical Question Answering by Data Augmentation and Model Weighting35
Robust and Privacy-Preserving Decentralized Deep Federated Learning Training: Focusing on Digital Healthcare Applications35
Evaluation of Existing Methods for High-Order Epistasis Detection34
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency34
CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data33
DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction33
Transfer Learning Based Lightweight Ensemble Model for Imbalanced Breast Cancer Classification32
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics31
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction31
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images31
Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis31
MEDA Based Biochips: Detection, Prevention and Rectification Techniques for Cyberphysical Attacks31
Lossy Compression of Quality Values in Sequencing Data31
DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations31
CASL: Capturing Activity Semantics Through Location Information for Enhanced Activity Recognition30
Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications30
The End-to-End Fetal Head Circumference Detection and Estimation in Ultrasound Images30
Explainable Knowledge Distillation for On-Device Chest X-Ray Classification30
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies30
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
Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm29
Finite-Set Model Predictive Control of Melanoma Cancer Treatment Using Signaling Pathway Inhibitor of Cancer Stem Cell28
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism28
FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data28
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment28
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction28
Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy28
MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data28
Alignment-Free Sequence Comparison With Multiple k Values27
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information27
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction27
Morphological Rule-Constrained Object Detection of Key Structures in Infant Fundus Image27
The Intrinsic Similarity of Topological Structure in Biological Neural Networks27
iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework26
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance26
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective26
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling26
A Deep Learning Approach Considering Image Background for Pneumonia Identification Using Explainable AI (XAI)26
PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit25
Improving Clinical Decision Making With a Two-Stage Recommender System25
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association25
Guest Editorial: Deep Learning For Genomics25
An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks25
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants25
A Stochastic Grammar Approach to Mass Classification in Mammograms24
An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network24
Generative Biomedical Event Extraction With Constrained Decoding Strategy24
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks24
Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets24
Generic Context-Aware Group Contributions24
Discriminant Projection Shared Dictionary Learning for Classification of Tumors Using Gene Expression Data24
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation24
Exploring Molecular Descriptors and Fingerprints to Predict mTOR Kinase Inhibitors using Machine Learning Techniques23
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration23
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification23
A Hybrid Heuristic-Exact Optimization for Large-Scale Home Health Care Problem23
MSCET: A Multi-Scenario Offloading Schedule for Biomedical Data Processing and Analysis in Cloud-Edge-Terminal Collaborative Vehicular Networks23
A Multi-Scale Activity Transition Network for Data Translation in EEG Signals Decoding23
Multi-Label Classification With Dual Tail-Node Augmentation for Drug Repositioning23
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data23
DORMAN: Database of Reconstructed MetAbolic Networks23
Circular Clustering With Polar Coordinate Reconstruction23
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression22
P2GT: Fine-Grained Genomic Data Access Control With Privacy-Preserving Testing in Cloud Computing22
A Learning Robust and Discriminative Shape Descriptor for Plant Species Identification22
Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks22
GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network22
Combining Zhegalkin Polynomials and SAT Solving for Context-Specific Boolean Modeling of Biological Systems22
DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion22
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms22
Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension22
EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics22
LipGene: Lipschitz Continuity Guided Adaptive Learning Rates for Fast Convergence on Microarray Expression Data Sets22
Estimating Functional Connectivity by Integration of Inherent Brain Function Activity Pattern Priors22
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks22
Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization22
Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations22
Target Control of Asynchronous Boolean Networks22
APT: An Automated Probe Tracker From Gene Expression Data22
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction21
Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations21
StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction21
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks21
COMBING: Clustering in Oncology for Mathematical and Biological Identification of Novel Gene Signatures21
Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation21
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots21
Gene Teams are on the Field: Evaluation of Variants in Gene-Networks Using High Dimensional Modelling21
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling21
Towards Optimal Decomposition of Boolean Networks21
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data20
Time-Varying Differential Network Analysis for Revealing Network Rewiring over Cancer Progression20
Integrated CNN and Federated Learning for COVID-19 Detection on Chest X-Ray Images20
A Mutual Attention Model for Drug Target Binding Affinity Prediction20
iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions20
Optimising Boolean Synthetic Regulatory Networks to Control Cell States20
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner19
DMFLDA: A Deep Learning Framework for Predicting lncRNA–Disease Associations19
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction19
Design of Constraint Coding Sets for Archive DNA Storage19
Lesion Segmentation in Ultrasound Using Semi-Pixel-Wise Cycle Generative Adversarial Nets19
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction19
A Fast and Furious Bayesian Network and Its Application of Identifying Colon Cancer to Liver Metastasis Gene Regulatory Networks18
Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments18
Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions18
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns18
An Effective Multi-Label Protein Sub-Chloroplast Localization Prediction by Skipped-Grams of Evolutionary Profiles Using Deep Neural Network18
A Cascaded Mutliresolution Ensemble Deep Learning Framework for Large Scale Alzheimer's Disease Detection Using Brain MRIs18
Adaptive Tracking Control for Uncertain Cancer-Tumor-Immune Systems18
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants18
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming18
Densely Connected U-Net With Criss-Cross Attention for Automatic Liver Tumor Segmentation in CT Images18
Improved Protein Decoy Selection via Non-Negative Matrix Factorization18
Feature-Sensitive Deep Convolutional Neural Network for Multi-Instance Breast Cancer Detection18
dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph18
The C-SHIFT Algorithm for Normalizing Covariances17
Generative Adversarial Network-Based Augmentation With Noval 2-Step Authentication for Anti-Coronavirus Peptide Prediction17
Circadian Rhythm Regulated by Tumor Suppressor p53 and Time Delay in Unstressed Cells17
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology17
Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications17
I-Health: SDN-Based Fog Architecture for IIoT Applications in Healthcare17
CPGL: Prediction of Compound-Protein Interaction by Integrating Graph Attention Network With Long Short-Term Memory Neural Network17
2019nCoVAS: Developing the Web Service for Epidemic Transmission Prediction, Genome Analysis, and Psychological Stress Assessment for 2019-nCoV17
Robust KALMAN Filter State Estimation for Gene Regulatory Networks17
Efficient Approximate Kernel Based Spike Sequence Classification17
Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks17
Predicting miRNA-Disease Associations From miRNA-Gene-Disease Heterogeneous Network With Multi-Relational Graph Convolutional Network Model17
aWCluster: A Novel Integrative Network-Based Clustering of Multiomics for Subtype Analysis of Cancer Data16
GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network16
In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE216
A Construction Method of Dynamic Protein Interaction Networks by Using Relevant Features of Gene Expression Data16
MCA-Net: Multi-Feature Coding and Attention Convolutional Neural Network for Predicting lncRNA-Disease Association16
Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape16
NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions16
scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation16
Common Attractors in Multiple Boolean Networks16
LDA-LNSUBRW: lncRNA-Disease Association Prediction Based on Linear Neighborhood Similarity and Unbalanced bi-Random Walk16
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification16
Prediction of Drug–Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding16
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model16
New Distance-Based approach for Genome-Wide Association Studies15
Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition15
BRMCF: Binary Relevance and MLSMOTE Based Computational Framework to Predict Drug Functions From Chemical and Biological Properties of Drugs15
Few-Shot Breast Cancer Metastases Classification via Unsupervised Cell Ranking15
Patient Graph Deep Learning to Predict Breast Cancer Molecular Subtype15
Supervised Graph Clustering for Cancer Subtyping Based on Survival Analysis and Integration of Multi-Omic Tumor Data15
GeNVoM: Read Mapping Near Non-Volatile Memory15
GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes15
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations15
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs15
Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network – A Boolean Network Modeling Perspective15
Editorial15
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network15
Identify Consistent Cross-Modality Imaging Genetic Patterns via Discriminant Sparse Canonical Correlation Analysis15
Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data15
Age Prediction by DNA Methylation in Neural Networks14
A Novel Method for Identification of Glutarylation Sites Combining Borderline-SMOTE With Tomek Links Technique in Imbalanced Data14
Cross-Modality LGE-CMR Segmentation Using Image-to-Image Translation Based Data Augmentation14
An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data14
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks14
ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters14
Prediction of Malignant Breast Cancer Cases Using Ensemble Machine Learning: A Case Study of Pesticides Prone Area14
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance14
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data14
PiTLiD: Identification of Plant Disease From Leaf Images Based on Convolutional Neural Network14
exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data14
MicroRNA Promoter Identification in Human With a Three-level Prediction Method14
ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference14
A Review of Fusion Methods for Omics and Imaging Data14
Noise Reduction Learning Based on XLNet-CRF for Biomedical Named Entity Recognition14
Integrating Molecular Graph Data of Drugs and Multiple -Omic Data of Cell Lines for Drug Response Prediction14
NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association14
A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction14
Constructing Integrative ceRNA Networks and Finding Prognostic Biomarkers in Renal Cell Carcinoma14
Subject-Independent Emotion Recognition of EEG Signals Based on Dynamic Empirical Convolutional Neural Network14
Heterogeneity in Blood Biomarker Trajectories After Mild TBI Revealed by Unsupervised Learning13
Identifying Gene Signatures for Cancer Drug Repositioning Based on Sample Clustering13
Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks13
SCN-MLTPP: A Multi-Label Classifier for Predicting Therapeutic Properties of Peptides Using the Stacked Capsule Network13
EPGA-SC : A Framework forde novoAssembly of Single-Cell Sequencing Reads13
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer13
iLncRNAdis-FB: Identify lncRNA-Disease Associations by Fusing Biological Feature Blocks Through Deep Neural Network13
PredinID: Predicting Pathogenic Inframe Indels in Human Through Graph Convolution Neural Network With Graph Sampling Technique13
Tuberculosis Diagnosis Using Deep Transferred EfficientNet13
An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches13
AFExNet: An Adversarial Autoencoder for Differentiating Breast Cancer Sub-Types and Extracting Biologically Relevant Genes13
A Multiview Clustering Method With Low-Rank and Sparsity Constraints for Cancer Subtyping13
TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction13
Defining Phylogenetic Network Distances Using Cherry Operations13
TransSurv: Transformer-Based Survival Analysis Model Integrating Histopathological Images and Genomic Data for Colorectal Cancer13
AttentionDTA: Drug–Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism13
SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism13
AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles13
Heterogeneous Multi-Task Learning With Expert Diversity13
Significance-Based Essential Protein Discovery13
Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction13
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