IEEE-ACM Transactions on Computational Biology and Bioinformatics

Article	Citations
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation	155
Row and Column Structure-Based Biclustering for Gene Expression Data	132
Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation	117
Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data	88
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement	85
New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction	82
Higher-Order Proximity-Based MiRNA-Disease Associations Prediction	79
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation	78
Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology	75
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies	72
The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease	71
Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE	70
Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps	69
Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network	68
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means	67
An Effective Swarm Intelligence Optimization Algorithm for Flexible Ligand Docking	67
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs	66
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks	61
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics	59
Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning	59
VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection	59
Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations	56
Seq-BEL: Sequence-Based Ensemble Learning for Predicting Virus-Human Protein-Protein Interaction	54
Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction	51
IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling	51

ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites	50
Fine-Grained Lesion Classification Framework for Early Auxiliary Diagnosis	49
Spatial Stochastic Model of the Pre-B Cell Receptor	48
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites	47
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images	46
Deep Learning in Gene Regulatory Network Inference: A Survey	46
Local R-Symmetry Co-Occurrence: Characterising Leaf Image Patterns for Identifying Cultivars	46
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction	45
Subgroup Identification Using Virtual Twins for Human Microbiome Studies	45
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction	45
DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction	44
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions	43
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction	43
Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions	42
Improving Biomedical Question Answering by Data Augmentation and Model Weighting	42
Evaluation of Existing Methods for High-Order Epistasis Detection	42
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network	42
RNPredATC: A Deep Residual Learning-Based Model With Applications to the Prediction of Drug-ATC Code Association	41
Automated Spot Counting in Microbiology	41
WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites	40
Self-Supervised Learning for Label Sparsity in Computational Drug Repositioning	39
Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics	37
Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis	37
State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications	36
A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics	36
Minimum Functional Length Analysis of K-Mer Based on BPNN	36
Blockchain-Based Data Access Security Solutions for Medical Wearables	36
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency	35
CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data	35
Transfer Learning Based Lightweight Ensemble Model for Imbalanced Breast Cancer Classification	35
Robust and Privacy-Preserving Decentralized Deep Federated Learning Training: Focusing on Digital Healthcare Applications	34
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction	34
A Neighborhood-Based Global Network Model to Predict Drug-Target Interactions	34
MEDA Based Biochips: Detection, Prevention and Rectification Techniques for Cyberphysical Attacks	34
Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications	33
Morphological Rule-Constrained Object Detection of Key Structures in Infant Fundus Image	33
The End-to-End Fetal Head Circumference Detection and Estimation in Ultrasound Images	33
Improving Clinical Decision Making With a Two-Stage Recommender System	32
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	32
CASL: Capturing Activity Semantics Through Location Information for Enhanced Activity Recognition	32
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information	32
Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm	32
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction	32
FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data	32
Guest Editorial Guest Editorial for the 20th Asia Pacific Bioinformatics Conference	32
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling	31
The Intrinsic Similarity of Topological Structure in Biological Neural Networks	31
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies	31
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment	31
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association	31

PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit	31
iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework	30
Explainable Knowledge Distillation for On-Device Chest X-Ray Classification	30
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images	29
Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy	29
A Deep Learning Approach Considering Image Background for Pneumonia Identification Using Explainable AI (XAI)	29
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance	29
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective	29
Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension	28
Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations	28
DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations	28
P2GT: Fine-Grained Genomic Data Access Control With Privacy-Preserving Testing in Cloud Computing	28
A Stochastic Grammar Approach to Mass Classification in Mammograms	28
MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data	28
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms	28
A Hybrid Heuristic-Exact Optimization for Large-Scale Home Health Care Problem	28
DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion	28
Circular Clustering With Polar Coordinate Reconstruction	27
Guest Editorial: Deep Learning For Genomics	27
Generative Biomedical Event Extraction With Constrained Decoding Strategy	27
An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network	27
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants	27
A Learning Robust and Discriminative Shape Descriptor for Plant Species Identification	27
An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks	27
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks	27
GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network	26
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation	26
Generic Context-Aware Group Contributions	26
Target Control of Asynchronous Boolean Networks	26
EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics	26
Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization	26
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression	25
Multi-Label Classification With Dual Tail-Node Augmentation for Drug Repositioning	25
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data	25
MSCET: A Multi-Scenario Offloading Schedule for Biomedical Data Processing and Analysis in Cloud-Edge-Terminal Collaborative Vehicular Networks	25
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification	25
StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction	25
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration	25
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks	25
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots	24
COMBING: Clustering in Oncology for Mathematical and Biological Identification of Novel Gene Signatures	24
LipGene: Lipschitz Continuity Guided Adaptive Learning Rates for Fast Convergence on Microarray Expression Data Sets	24
Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks	24
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction	24
Design of Constraint Coding Sets for Archive DNA Storage	23
Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations	23
Integrated CNN and Federated Learning for COVID-19 Detection on Chest X-Ray Images	23
Combining Zhegalkin Polynomials and SAT Solving for Context-Specific Boolean Modeling of Biological Systems	23
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling	22
Densely Connected U-Net With Criss-Cross Attention for Automatic Liver Tumor Segmentation in CT Images	22
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner	22
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction	22
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data	22
iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions	22
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks	21
A Mutual Attention Model for Drug Target Binding Affinity Prediction	21
A Cascaded Mutliresolution Ensemble Deep Learning Framework for Large Scale Alzheimer's Disease Detection Using Brain MRIs	21
Improved Protein Decoy Selection via Non-Negative Matrix Factorization	21
Generative Adversarial Network-Based Augmentation With Noval 2-Step Authentication for Anti-Coronavirus Peptide Prediction	21
Gene Teams are on the Field: Evaluation of Variants in Gene-Networks Using High Dimensional Modelling	21
dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph	21
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming	21
Circadian Rhythm Regulated by Tumor Suppressor p53 and Time Delay in Unstressed Cells	21
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction	21
The C-SHIFT Algorithm for Normalizing Covariances	21
Efficient Approximate Kernel Based Spike Sequence Classification	21
Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments	21
Predicting miRNA-Disease Associations From miRNA-Gene-Disease Heterogeneous Network With Multi-Relational Graph Convolutional Network Model	20
Feature-Sensitive Deep Convolutional Neural Network for Multi-Instance Breast Cancer Detection	20
An Effective Multi-Label Protein Sub-Chloroplast Localization Prediction by Skipped-Grams of Evolutionary Profiles Using Deep Neural Network	20
Robust KALMAN Filter State Estimation for Gene Regulatory Networks	20
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants	20
I-Health: SDN-Based Fog Architecture for IIoT Applications in Healthcare	20
Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions	20
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns	20
NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions	19
CPGL: Prediction of Compound-Protein Interaction by Integrating Graph Attention Network With Long Short-Term Memory Neural Network	19
Editorial	19
A Construction Method of Dynamic Protein Interaction Networks by Using Relevant Features of Gene Expression Data	19
LDA-LNSUBRW: lncRNA-Disease Association Prediction Based on Linear Neighborhood Similarity and Unbalanced bi-Random Walk	19

Assessment of Prediction Uncertainty Quantification Methods in Systems Biology	19
scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation	19
New Distance-Based approach for Genome-Wide Association Studies	19
Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications	19
MCA-Net: Multi-Feature Coding and Attention Convolutional Neural Network for Predicting lncRNA-Disease Association	19
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model	19
Common Attractors in Multiple Boolean Networks	19
GeNVoM: Read Mapping Near Non-Volatile Memory	18
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network	18
Prediction of Malignant Breast Cancer Cases Using Ensemble Machine Learning: A Case Study of Pesticides Prone Area	18
Age Prediction by DNA Methylation in Neural Networks	18
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations	18
GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes	18
GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network	18
aWCluster: A Novel Integrative Network-Based Clustering of Multiomics for Subtype Analysis of Cancer Data	18
Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition	18
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification	18
Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data	18
exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data	18
Prediction of Drug–Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding	17
A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction	17
In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE2	17
Noise Reduction Learning Based on XLNet-CRF for Biomedical Named Entity Recognition	17
Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape	17
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs	17
Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network – A Boolean Network Modeling Perspective	17
BRMCF: Binary Relevance and MLSMOTE Based Computational Framework to Predict Drug Functions From Chemical and Biological Properties of Drugs	17
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance	17
Supervised Graph Clustering for Cancer Subtyping Based on Survival Analysis and Integration of Multi-Omic Tumor Data	17
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data	17
PiTLiD: Identification of Plant Disease From Leaf Images Based on Convolutional Neural Network	17
Integrating Molecular Graph Data of Drugs and Multiple -Omic Data of Cell Lines for Drug Response Prediction	17
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks	16
Constructing Integrative ceRNA Networks and Finding Prognostic Biomarkers in Renal Cell Carcinoma	16
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread	16
Identifying Gene Signatures for Cancer Drug Repositioning Based on Sample Clustering	16
An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data	16
Patient Graph Deep Learning to Predict Breast Cancer Molecular Subtype	16
TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction	16
Significance-Based Essential Protein Discovery	16
PredinID: Predicting Pathogenic Inframe Indels in Human Through Graph Convolution Neural Network With Graph Sampling Technique	16
Cross-Modality LGE-CMR Segmentation Using Image-to-Image Translation Based Data Augmentation	16
NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association	16
A Novel Method for Identification of Glutarylation Sites Combining Borderline-SMOTE With Tomek Links Technique in Imbalanced Data	16
Using Fully Convolutional Network to Locate Transcription Factor Binding Sites Based on DNA Sequence and Conservation Information	16
Heterogeneity in Blood Biomarker Trajectories After Mild TBI Revealed by Unsupervised Learning	16
ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters	16
A Review of Fusion Methods for Omics and Imaging Data	16
MicroRNA Promoter Identification in Human With a Three-level Prediction Method	15
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer	15
An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches	15
SCN-MLTPP: A Multi-Label Classifier for Predicting Therapeutic Properties of Peptides Using the Stacked Capsule Network	15
Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction	15
Heterogeneous Multi-Task Learning With Expert Diversity	15
AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles	15
Calculation of the Weight of Evidence for Combined Single-Cell and Extracellular Forensic DNA	15
AFExNet: An Adversarial Autoencoder for Differentiating Breast Cancer Sub-Types and Extracting Biologically Relevant Genes	15
AttentionDTA: Drug–Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism	15
Robust Principal Component Analysis Based On Hypergraph Regularization for Sample Clustering and Co-Characteristic Gene Selection	15
Tuberculosis Diagnosis Using Deep Transferred EfficientNet	15
Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks	15
Defining Phylogenetic Network Distances Using Cherry Operations	15
TransSurv: Transformer-Based Survival Analysis Model Integrating Histopathological Images and Genomic Data for Colorectal Cancer	15
A Multiview Clustering Method With Low-Rank and Sparsity Constraints for Cancer Subtyping	15
Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data	15
TransRNAm: Identifying Twelve Types of RNA Modifications by an Interpretable Multi-Label Deep Learning Model Based on Transformer	14
PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel	14
Prediction of Enhancers in DNA Sequence Data using a Hybrid CNN-DLSTM Model	14
Multi-Modal Classification for Human Breast Cancer Prognosis Prediction: Proposal of Deep-Learning Based Stacked Ensemble Model	14
Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model	14
Functional Neural Networks for High-Dimensional Genetic Data Analysis	14
MISSH: Fast Hashing of Multiple Spaced Seeds	14
Identifying Differentially Expressed Genes in RNA Sequencing Data With Small Labelled Samples	14
DeepSG2PPI: A Protein-Protein Interaction Prediction Method Based on Deep Learning	14
A Method for Predicting DNA Motif Length Based On Deep Learning	14
MSF-LRR: Multi-Similarity Information Fusion Through Low-Rank Representation to Predict Disease-Associated Microbes	14
Multi-Modality Fusion & Inductive Knowledge Transfer Underlying Non-Sparse Multi-Kernel Learning and Distribution Adaption	14
Time-Aware Multi-Type Data Fusion Representation Learning Framework for Risk Prediction of Cardiovascular Diseases	14
SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features	14
De Novo Drug Design by Multi-Objective Path Consistency Learning With Beam A* Search	14
Identifying Gene Network Rewiring Based on Partial Correlation	14
scCDG: A Method Based on DAE and GCN for scRNA-Seq Data Analysis	14
AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants	14
Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation	14
An Aggregation Method to Identify the RNA Meta-Stable Secondary Structure and its Functionally Interpretable Structure Ensemble	14
Computational Prediction of Drug-Disease Association Based on Graph-Regularized One Bit Matrix Completion	14
RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms	14
SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism	14
CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data	14
Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem	14