IEEE-ACM Transactions on Computational Biology and Bioinformatics

Papers
(The TQCC of IEEE-ACM Transactions on Computational Biology and Bioinformatics is 13. 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 2021-08-01 to 2025-08-01.)
ArticleCitations
Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology528
Row and Column Structure-Based Biclustering for Gene Expression Data271
Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation146
Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data113
New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction96
POPBic: Pathway-Based Order Preserving Biclustering Algorithm Towards the Analysis of Gene Expression Data96
Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network85
RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow84
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation75
Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE68
Seq-BEL: Sequence-Based Ensemble Learning for Predicting Virus-Human Protein-Protein Interaction67
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies66
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation66
Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations65
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs64
Higher-Order Proximity-Based MiRNA-Disease Associations Prediction63
Protein Fold Recognition by Combining Support Vector Machines and Pairwise Sequence Similarity Scores59
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means58
An Effective Swarm Intelligence Optimization Algorithm for Flexible Ligand Docking56
An Automated Cell Tracking Approach With Multi-Bernoulli Filtering and Ant Colony Labor Division54
Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps54
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites53
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics53
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement51
VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection51
IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling51
The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease50
Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning49
Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction49
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks48
Improving Biomedical Question Answering by Data Augmentation and Model Weighting48
State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications48
Local R-Symmetry Co-Occurrence: Characterising Leaf Image Patterns for Identifying Cultivars46
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network46
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions45
Spatial Stochastic Model of the Pre-B Cell Receptor45
Minimum Functional Length Analysis of K-Mer Based on BPNN45
Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics44
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites42
Blockchain-Based Data Access Security Solutions for Medical Wearables42
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction42
A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics41
Subgroup Identification Using Virtual Twins for Human Microbiome Studies41
Fine-Grained Lesion Classification Framework for Early Auxiliary Diagnosis41
Automated Spot Counting in Microbiology41
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images41
DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction40
Evaluation of Existing Methods for High-Order Epistasis Detection38
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics38
A Neighborhood-Based Global Network Model to Predict Drug-Target Interactions38
Deep Learning in Gene Regulatory Network Inference: A Survey38
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction38
CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data38
Self-Supervised Learning for Label Sparsity in Computational Drug Repositioning37
RNPredATC: A Deep Residual Learning-Based Model With Applications to the Prediction of Drug-ATC Code Association37
Robust and Privacy-Preserving Decentralized Deep Federated Learning Training: Focusing on Digital Healthcare Applications36
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency36
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction36
WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites35
Transfer Learning Based Lightweight Ensemble Model for Imbalanced Breast Cancer Classification34
Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis34
Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions33
MEDA Based Biochips: Detection, Prevention and Rectification Techniques for Cyberphysical Attacks32
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images32
Lossy Compression of Quality Values in Sequencing Data32
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies31
Guest Editorial Guest Editorial for the 20th Asia Pacific Bioinformatics Conference31
The End-to-End Fetal Head Circumference Detection and Estimation in Ultrasound Images31
Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm31
A Deep Learning Approach Considering Image Background for Pneumonia Identification Using Explainable AI (XAI)31
Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications31
CASL: Capturing Activity Semantics Through Location Information for Enhanced Activity Recognition31
Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy30
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 Sets30
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment30
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism30
Morphological Rule-Constrained Object Detection of Key Structures in Infant Fundus Image29
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction29
FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data29
The Intrinsic Similarity of Topological Structure in Biological Neural Networks28
Explainable Knowledge Distillation for On-Device Chest X-Ray Classification28
Alignment-Free Sequence Comparison With Multiple k Values28
Improving Clinical Decision Making With a Two-Stage Recommender System28
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information28
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling28
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction28
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance27
MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data27
iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework27
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association27
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective27
DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations27
PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit27
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants26
An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network26
Generative Biomedical Event Extraction With Constrained Decoding Strategy26
A Hybrid Heuristic-Exact Optimization for Large-Scale Home Health Care Problem26
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks26
Guest Editorial: Deep Learning For Genomics26
A Stochastic Grammar Approach to Mass Classification in Mammograms26
Multi-Label Classification With Dual Tail-Node Augmentation for Drug Repositioning26
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data26
An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks26
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation26
Generic Context-Aware Group Contributions26
Exploring Molecular Descriptors and Fingerprints to Predict mTOR Kinase Inhibitors using Machine Learning Techniques26
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration25
Circular Clustering With Polar Coordinate Reconstruction25
A Multi-Scale Activity Transition Network for Data Translation in EEG Signals Decoding24
A Learning Robust and Discriminative Shape Descriptor for Plant Species Identification24
Estimating Functional Connectivity by Integration of Inherent Brain Function Activity Pattern Priors24
GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network24
MSCET: A Multi-Scenario Offloading Schedule for Biomedical Data Processing and Analysis in Cloud-Edge-Terminal Collaborative Vehicular Networks24
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks24
Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations24
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms24
P2GT: Fine-Grained Genomic Data Access Control With Privacy-Preserving Testing in Cloud Computing24
DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion24
Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization24
Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension24
EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics23
Target Control of Asynchronous Boolean Networks23
APT: An Automated Probe Tracker From Gene Expression Data23
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification23
LipGene: Lipschitz Continuity Guided Adaptive Learning Rates for Fast Convergence on Microarray Expression Data Sets23
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression23
Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks23
Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations22
COMBING: Clustering in Oncology for Mathematical and Biological Identification of Novel Gene Signatures22
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction22
Gene Teams are on the Field: Evaluation of Variants in Gene-Networks Using High Dimensional Modelling22
Towards Optimal Decomposition of Boolean Networks22
StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction22
Optimising Boolean Synthetic Regulatory Networks to Control Cell States22
Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation22
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots22
Lesion Segmentation in Ultrasound Using Semi-Pixel-Wise Cycle Generative Adversarial Nets22
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks22
Design of Constraint Coding Sets for Archive DNA Storage21
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data21
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner21
A Mutual Attention Model for Drug Target Binding Affinity Prediction21
Combining Zhegalkin Polynomials and SAT Solving for Context-Specific Boolean Modeling of Biological Systems21
A Cascaded Mutliresolution Ensemble Deep Learning Framework for Large Scale Alzheimer's Disease Detection Using Brain MRIs20
Integrated CNN and Federated Learning for COVID-19 Detection on Chest X-Ray Images20
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling20
Densely Connected U-Net With Criss-Cross Attention for Automatic Liver Tumor Segmentation in CT Images20
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction20
DMFLDA: A Deep Learning Framework for Predicting lncRNA–Disease Associations20
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction20
Robust KALMAN Filter State Estimation for Gene Regulatory Networks19
iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions19
dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph19
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants19
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming19
An Effective Multi-Label Protein Sub-Chloroplast Localization Prediction by Skipped-Grams of Evolutionary Profiles Using Deep Neural Network19
Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications19
Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks19
Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions19
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns19
The C-SHIFT Algorithm for Normalizing Covariances19
Generative Adversarial Network-Based Augmentation With Noval 2-Step Authentication for Anti-Coronavirus Peptide Prediction18
Circadian Rhythm Regulated by Tumor Suppressor p53 and Time Delay in Unstressed Cells18
CPGL: Prediction of Compound-Protein Interaction by Integrating Graph Attention Network With Long Short-Term Memory Neural Network18
LDA-LNSUBRW: lncRNA-Disease Association Prediction Based on Linear Neighborhood Similarity and Unbalanced bi-Random Walk18
Improved Protein Decoy Selection via Non-Negative Matrix Factorization18
Predicting miRNA-Disease Associations From miRNA-Gene-Disease Heterogeneous Network With Multi-Relational Graph Convolutional Network Model18
I-Health: SDN-Based Fog Architecture for IIoT Applications in Healthcare18
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology18
Feature-Sensitive Deep Convolutional Neural Network for Multi-Instance Breast Cancer Detection18
Efficient Approximate Kernel Based Spike Sequence Classification18
Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments18
MCA-Net: Multi-Feature Coding and Attention Convolutional Neural Network for Predicting lncRNA-Disease Association18
Adaptive Tracking Control for Uncertain Cancer-Tumor-Immune Systems18
NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions18
Supervised Graph Clustering for Cancer Subtyping Based on Survival Analysis and Integration of Multi-Omic Tumor Data17
Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape17
Common Attractors in Multiple Boolean Networks17
scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation17
New Distance-Based approach for Genome-Wide Association Studies17
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance17
BRMCF: Binary Relevance and MLSMOTE Based Computational Framework to Predict Drug Functions From Chemical and Biological Properties of Drugs17
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network17
Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition17
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification17
Prediction of Drug–Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding17
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model17
Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data17
Few-Shot Breast Cancer Metastases Classification via Unsupervised Cell Ranking17
Editorial17
A Review of Fusion Methods for Omics and Imaging Data17
Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network – A Boolean Network Modeling Perspective17
GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network17
In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE217
A Construction Method of Dynamic Protein Interaction Networks by Using Relevant Features of Gene Expression Data17
Prediction of Malignant Breast Cancer Cases Using Ensemble Machine Learning: A Case Study of Pesticides Prone Area17
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations17
exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data16
Age Prediction by DNA Methylation in Neural Networks16
A Novel Method for Identification of Glutarylation Sites Combining Borderline-SMOTE With Tomek Links Technique in Imbalanced Data16
aWCluster: A Novel Integrative Network-Based Clustering of Multiomics for Subtype Analysis of Cancer Data16
Noise Reduction Learning Based on XLNet-CRF for Biomedical Named Entity Recognition16
Integrating Molecular Graph Data of Drugs and Multiple -Omic Data of Cell Lines for Drug Response Prediction16
GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes16
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs16
A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction16
Subject-Independent Emotion Recognition of EEG Signals Based on Dynamic Empirical Convolutional Neural Network16
GeNVoM: Read Mapping Near Non-Volatile Memory16
PiTLiD: Identification of Plant Disease From Leaf Images Based on Convolutional Neural Network16
iLncRNAdis-FB: Identify lncRNA-Disease Associations by Fusing Biological Feature Blocks Through Deep Neural Network15
Constructing Integrative ceRNA Networks and Finding Prognostic Biomarkers in Renal Cell Carcinoma15
An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data15
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks15
TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction15
Using Fully Convolutional Network to Locate Transcription Factor Binding Sites Based on DNA Sequence and Conservation Information15
Significance-Based Essential Protein Discovery15
NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association15
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data15
ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference15
Defining Phylogenetic Network Distances Using Cherry Operations15
Calculation of the Weight of Evidence for Combined Single-Cell and Extracellular Forensic DNA15
ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters15
Cross-Modality LGE-CMR Segmentation Using Image-to-Image Translation Based Data Augmentation15
Patient Graph Deep Learning to Predict Breast Cancer Molecular Subtype15
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread15
A Multiview Clustering Method With Low-Rank and Sparsity Constraints for Cancer Subtyping15
AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles14
MicroRNA Promoter Identification in Human With a Three-level Prediction Method14
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer14
Heterogeneity in Blood Biomarker Trajectories After Mild TBI Revealed by Unsupervised Learning14
Robust Principal Component Analysis Based On Hypergraph Regularization for Sample Clustering and Co-Characteristic Gene Selection14
Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data14
AFExNet: An Adversarial Autoencoder for Differentiating Breast Cancer Sub-Types and Extracting Biologically Relevant Genes14
Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks14
Identifying Gene Signatures for Cancer Drug Repositioning Based on Sample Clustering14
TransSurv: Transformer-Based Survival Analysis Model Integrating Histopathological Images and Genomic Data for Colorectal Cancer14
Tuberculosis Diagnosis Using Deep Transferred EfficientNet14
SAQ: Semi-Algebraic Quartet Reconstruction14
Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction14
An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches14
SCN-MLTPP: A Multi-Label Classifier for Predicting Therapeutic Properties of Peptides Using the Stacked Capsule Network14
PredinID: Predicting Pathogenic Inframe Indels in Human Through Graph Convolution Neural Network With Graph Sampling Technique14
AttentionDTA: Drug–Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism14
Heterogeneous Multi-Task Learning With Expert Diversity14
Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model14
TransRNAm: Identifying Twelve Types of RNA Modifications by an Interpretable Multi-Label Deep Learning Model Based on Transformer13
An Aggregation Method to Identify the RNA Meta-Stable Secondary Structure and its Functionally Interpretable Structure Ensemble13
DeepSG2PPI: A Protein-Protein Interaction Prediction Method Based on Deep Learning13
Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation13
CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data13
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