IEEE-ACM Transactions on Computational Biology and Bioinformatics

Article	Citations
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation	141
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics	108
New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction	106
Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology	99
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites	94
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks	83
Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations	82
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means	82
Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network	81
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation	81
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies	78
An Effective Swarm Intelligence Optimization Algorithm for Flexible Ligand Docking	77
Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE	66
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement	66
IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling	60
VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection	58
Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction	57
Fine-Grained Lesion Classification Framework for Early Auxiliary Diagnosis	56
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites	55
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction	55
Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions	54
Improving Biomedical Question Answering by Data Augmentation and Model Weighting	52
A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics	52
RNPredATC: A Deep Residual Learning-Based Model With Applications to the Prediction of Drug-ATC Code Association	51
A Neighborhood-Based Global Network Model to Predict Drug-Target Interactions	51

Self-Supervised Learning for Label Sparsity in Computational Drug Repositioning	47
State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications	47
Robust and Privacy-Preserving Decentralized Deep Federated Learning Training: Focusing on Digital Healthcare Applications	46
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images	46
Minimum Functional Length Analysis of K-Mer Based on BPNN	44
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network	44
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction	43
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction	43
Automated Spot Counting in Microbiology	43
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions	42
Subgroup Identification Using Virtual Twins for Human Microbiome Studies	42
Deep Learning in Gene Regulatory Network Inference: A Survey	42
WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites	41
Spatial Stochastic Model of the Pre-B Cell Receptor	41
Transfer Learning Based Lightweight Ensemble Model for Imbalanced Breast Cancer Classification	40
Blockchain-Based Data Access Security Solutions for Medical Wearables	40
Morphological Rule-Constrained Object Detection of Key Structures in Infant Fundus Image	40
DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction	40
MEDA Based Biochips: Detection, Prevention and Rectification Techniques for Cyberphysical Attacks	40
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency	40
CASL: Capturing Activity Semantics Through Location Information for Enhanced Activity Recognition	40
Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm	39
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 Sets	39
Guest Editorial Guest Editorial for the 20th Asia Pacific Bioinformatics Conference	39
FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data	38
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association	38
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction	37
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective	37
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images	36
The Intrinsic Similarity of Topological Structure in Biological Neural Networks	36
MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data	36
Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy	35
DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations	35
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment	35
PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit	35
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies	35
A Deep Learning Approach Considering Image Background for Pneumonia Identification Using Explainable AI (XAI)	35
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction	34
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance	34
The End-to-End Fetal Head Circumference Detection and Estimation in Ultrasound Images	34
Improving Clinical Decision Making With a Two-Stage Recommender System	33
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information	33
iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework	33
Explainable Knowledge Distillation for On-Device Chest X-Ray Classification	33
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling	32
DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion	32
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data	32
Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension	32
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks	32
P2GT: Fine-Grained Genomic Data Access Control With Privacy-Preserving Testing in Cloud Computing	32

A Hybrid Heuristic-Exact Optimization for Large-Scale Home Health Care Problem	31
A Stochastic Grammar Approach to Mass Classification in Mammograms	31
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks	31
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression	30
Generative Biomedical Event Extraction With Constrained Decoding Strategy	30
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation	30
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants	30
Multi-Label Classification With Dual Tail-Node Augmentation for Drug Repositioning	30
Target Control of Asynchronous Boolean Networks	29
Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization	29
Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations	28
A Learning Robust and Discriminative Shape Descriptor for Plant Species Identification	28
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification	27
MSCET: A Multi-Scenario Offloading Schedule for Biomedical Data Processing and Analysis in Cloud-Edge-Terminal Collaborative Vehicular Networks	27
Circular Clustering With Polar Coordinate Reconstruction	27
EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics	27
GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network	27
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots	26
A Cascaded Mutliresolution Ensemble Deep Learning Framework for Large Scale Alzheimer's Disease Detection Using Brain MRIs	26
Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks	26
COMBING: Clustering in Oncology for Mathematical and Biological Identification of Novel Gene Signatures	26
LipGene: Lipschitz Continuity Guided Adaptive Learning Rates for Fast Convergence on Microarray Expression Data Sets	26
StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction	26
Integrated CNN and Federated Learning for COVID-19 Detection on Chest X-Ray Images	25
Gene Teams are on the Field: Evaluation of Variants in Gene-Networks Using High Dimensional Modelling	25
A Mutual Attention Model for Drug Target Binding Affinity Prediction	25
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks	25
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner	25
Combining Zhegalkin Polynomials and SAT Solving for Context-Specific Boolean Modeling of Biological Systems	25
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling	24
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction	24
Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations	24
Densely Connected U-Net With Criss-Cross Attention for Automatic Liver Tumor Segmentation in CT Images	24
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data	24
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction	24
Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions	23
Design of Constraint Coding Sets for Archive DNA Storage	23
Feature-Sensitive Deep Convolutional Neural Network for Multi-Instance Breast Cancer Detection	23
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming	23
Robust KALMAN Filter State Estimation for Gene Regulatory Networks	23
dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph	23
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants	22
Efficient Approximate Kernel Based Spike Sequence Classification	22
Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications	22
MCA-Net: Multi-Feature Coding and Attention Convolutional Neural Network for Predicting lncRNA-Disease Association	22
The C-SHIFT Algorithm for Normalizing Covariances	22
NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions	22
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns	22
CPGL: Prediction of Compound-Protein Interaction by Integrating Graph Attention Network With Long Short-Term Memory Neural Network	22
Generative Adversarial Network-Based Augmentation With Noval 2-Step Authentication for Anti-Coronavirus Peptide Prediction	21
scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation	21
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network	21
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology	21
Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments	21
New Distance-Based approach for Genome-Wide Association Studies	21
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations	21
I-Health: SDN-Based Fog Architecture for IIoT Applications in Healthcare	21
Predicting miRNA-Disease Associations From miRNA-Gene-Disease Heterogeneous Network With Multi-Relational Graph Convolutional Network Model	21
An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data	21
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data	20
GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network	20
GeNVoM: Read Mapping Near Non-Volatile Memory	20
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model	20
Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition	20
Noise Reduction Learning Based on XLNet-CRF for Biomedical Named Entity Recognition	20
exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data	20
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance	20
A Review of Fusion Methods for Omics and Imaging Data	20
Common Attractors in Multiple Boolean Networks	20
Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data	20
A Construction Method of Dynamic Protein Interaction Networks by Using Relevant Features of Gene Expression Data	19
A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction	19
GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes	19
PiTLiD: Identification of Plant Disease From Leaf Images Based on Convolutional Neural Network	19
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs	19
Cross-Modality LGE-CMR Segmentation Using Image-to-Image Translation Based Data Augmentation	19
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks	19
NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association	19
A Novel Method for Identification of Glutarylation Sites Combining Borderline-SMOTE With Tomek Links Technique in Imbalanced Data	19
Patient Graph Deep Learning to Predict Breast Cancer Molecular Subtype	18

ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters	18
Calculation of the Weight of Evidence for Combined Single-Cell and Extracellular Forensic DNA	18
PredinID: Predicting Pathogenic Inframe Indels in Human Through Graph Convolution Neural Network With Graph Sampling Technique	18
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer	18
Prediction of Drug–Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding	18
BRMCF: Binary Relevance and MLSMOTE Based Computational Framework to Predict Drug Functions From Chemical and Biological Properties of Drugs	18
AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles	18
Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks	18
Heterogeneous Multi-Task Learning With Expert Diversity	18
Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape	18
Constructing Integrative ceRNA Networks and Finding Prognostic Biomarkers in Renal Cell Carcinoma	18
TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction	18
MicroRNA Promoter Identification in Human With a Three-level Prediction Method	18
Tuberculosis Diagnosis Using Deep Transferred EfficientNet	18
SCN-MLTPP: A Multi-Label Classifier for Predicting Therapeutic Properties of Peptides Using the Stacked Capsule Network	18
Defining Phylogenetic Network Distances Using Cherry Operations	17
TransSurv: Transformer-Based Survival Analysis Model Integrating Histopathological Images and Genomic Data for Colorectal Cancer	17
Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem	17
A Multiview Clustering Method With Low-Rank and Sparsity Constraints for Cancer Subtyping	17
Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data	17
AttentionDTA: Drug–Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism	17
AFExNet: An Adversarial Autoencoder for Differentiating Breast Cancer Sub-Types and Extracting Biologically Relevant Genes	17
Using Fully Convolutional Network to Locate Transcription Factor Binding Sites Based on DNA Sequence and Conservation Information	17
Identifying Differentially Expressed Genes in RNA Sequencing Data With Small Labelled Samples	17
Robust Principal Component Analysis Based On Hypergraph Regularization for Sample Clustering and Co-Characteristic Gene Selection	16
De Novo Drug Design by Multi-Objective Path Consistency Learning With Beam A* Search	16
MISSH: Fast Hashing of Multiple Spaced Seeds	16
AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants	16
Computational Prediction of Drug-Disease Association Based on Graph-Regularized One Bit Matrix Completion	16
Prediction of Enhancers in DNA Sequence Data using a Hybrid CNN-DLSTM Model	16
MSF-LRR: Multi-Similarity Information Fusion Through Low-Rank Representation to Predict Disease-Associated Microbes	16
DeepSG2PPI: A Protein-Protein Interaction Prediction Method Based on Deep Learning	16
CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data	16
Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation	16
SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features	16
RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms	15
PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel	15
Semi-Supervised Deep Learning for Cell Type Identification From Single-Cell Transcriptomic Data	15
A Method for Predicting DNA Motif Length Based On Deep Learning	15
scCDG: A Method Based on DAE and GCN for scRNA-Seq Data Analysis	15
TransRNAm: Identifying Twelve Types of RNA Modifications by an Interpretable Multi-Label Deep Learning Model Based on Transformer	15
Parallel Protein Community Detection in Large-scale PPI Networks Based on Multi-source Learning	15
BERT2OME: Prediction of 2′-O-Methylation Modifications From RNA Sequence by Transformer Architecture Based on BERT	15
Time-Aware Multi-Type Data Fusion Representation Learning Framework for Risk Prediction of Cardiovascular Diseases	15
Multi-Modality Fusion & Inductive Knowledge Transfer Underlying Non-Sparse Multi-Kernel Learning and Distribution Adaption	15
Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance	15
Functional Neural Networks for High-Dimensional Genetic Data Analysis	15