IEEE-ACM Transactions on Computational Biology and Bioinformatics

Article	Citations
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation	119
New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction	114
Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology	95
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites	93
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks	93
Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network	86
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means	86
An Effective Swarm Intelligence Optimization Algorithm for Flexible Ligand Docking	82
Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction	81
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement	69
VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection	67
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics	67
Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE	65
IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling	64
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation	61
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies	61
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites	60
Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions	58
State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications	56
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images	56
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network	53
Minimum Functional Length Analysis of K-Mer Based on BPNN	52
Automated Spot Counting in Microbiology	49
Subgroup Identification Using Virtual Twins for Human Microbiome Studies	48
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions	48

A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics	47
Spatial Stochastic Model of the Pre-B Cell Receptor	47
WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites	46
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency	45
Blockchain-Based Data Access Security Solutions for Medical Wearables	45
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction	45
Self-Supervised Learning for Label Sparsity in Computational Drug Repositioning	44
Fine-Grained Lesion Classification Framework for Early Auxiliary Diagnosis	44
Improving Biomedical Question Answering by Data Augmentation and Model Weighting	44
Transfer Learning Based Lightweight Ensemble Model for Imbalanced Breast Cancer Classification	43
DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction	43
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction	43
Morphological Rule-Constrained Object Detection of Key Structures in Infant Fundus Image	41
Deep Learning in Gene Regulatory Network Inference: A Survey	41
RNPredATC: A Deep Residual Learning-Based Model With Applications to the Prediction of Drug-ATC Code Association	41
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction	41
Robust and Privacy-Preserving Decentralized Deep Federated Learning Training: Focusing on Digital Healthcare Applications	41
Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm	40
Guest Editorial Guest Editorial for the 20th Asia Pacific Bioinformatics Conference	40
CASL: Capturing Activity Semantics Through Location Information for Enhanced Activity Recognition	40
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	40
The Intrinsic Similarity of Topological Structure in Biological Neural Networks	39
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information	39
A Deep Learning Approach Considering Image Background for Pneumonia Identification Using Explainable AI (XAI)	39
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association	39
iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework	38
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction	38
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling	38
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies	37
MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data	37
Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy	37
PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit	37
FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data	36
The End-to-End Fetal Head Circumference Detection and Estimation in Ultrasound Images	35
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance	35
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective	35
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction	35
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment	35
DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations	35
Improving Clinical Decision Making With a Two-Stage Recommender System	34
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks	33
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data	33
Explainable Knowledge Distillation for On-Device Chest X-Ray Classification	33
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks	32
A Hybrid Heuristic-Exact Optimization for Large-Scale Home Health Care Problem	32
Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension	32
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants	31
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression	30
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification	30
Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations	30

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

Using Fully Convolutional Network to Locate Transcription Factor Binding Sites Based on DNA Sequence and Conservation Information	18
Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks	18
AttentionDTA: Drug–Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism	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
Heterogeneous Multi-Task Learning With Expert Diversity	17
Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem	17
Tuberculosis Diagnosis Using Deep Transferred EfficientNet	17
Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data	17
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer	17
TransSurv: Transformer-Based Survival Analysis Model Integrating Histopathological Images and Genomic Data for Colorectal Cancer	17
PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel	16
Multi-Modality Fusion & Inductive Knowledge Transfer Underlying Non-Sparse Multi-Kernel Learning and Distribution Adaption	16
AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants	16
DeepSG2PPI: A Protein-Protein Interaction Prediction Method Based on Deep Learning	16
TransRNAm: Identifying Twelve Types of RNA Modifications by an Interpretable Multi-Label Deep Learning Model Based on Transformer	16
Functional Neural Networks for High-Dimensional Genetic Data Analysis	16
Parallel Protein Community Detection in Large-scale PPI Networks Based on Multi-source Learning	16
Identifying Differentially Expressed Genes in RNA Sequencing Data With Small Labelled Samples	16
MISSH: Fast Hashing of Multiple Spaced Seeds	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	16
scCDG: A Method Based on DAE and GCN for scRNA-Seq Data Analysis	16
Prediction of Enhancers in DNA Sequence Data using a Hybrid CNN-DLSTM Model	16
CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data	16
Computational Prediction of Drug-Disease Association Based on Graph-Regularized One Bit Matrix Completion	16
De Novo Drug Design by Multi-Objective Path Consistency Learning With Beam A* Search	16
MSF-LRR: Multi-Similarity Information Fusion Through Low-Rank Representation to Predict Disease-Associated Microbes	16
Time-Aware Multi-Type Data Fusion Representation Learning Framework for Risk Prediction of Cardiovascular Diseases	16
Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation	16