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 2021-09-01 to 2025-09-01.)
ArticleCitations
Gene Co-Expression Networks Offer New Perspectives on Sepsis Pathophysiology531
Row and Column Structure-Based Biclustering for Gene Expression Data278
Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation150
Data-Driven and Knowledge-Based Algorithms for Gene Network Reconstruction on High-Dimensional Data120
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 Network87
RNASeqR: An R Package for Automated Two-Group RNA-Seq Analysis Workflow85
Contrasting Multi-Source Temporal Knowledge Graphs for Biomedical Hypothesis Generation78
An Automated Cell Tracking Approach With Multi-Bernoulli Filtering and Ant Colony Labor Division71
Protein Fold Recognition by Combining Support Vector Machines and Pairwise Sequence Similarity Scores67
An Effective Swarm Intelligence Optimization Algorithm for Flexible Ligand Docking67
Higher-Order Proximity-Based MiRNA-Disease Associations Prediction67
scBKAP: A Clustering Model for Single-Cell RNA-Seq Data Based on Bisecting K-Means67
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs67
Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps65
An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation61
IPP: An Intelligent Privacy-Preserving Scheme for Detecting Interactions in Genome Association Studies61
Graph Convolutional Auto-Encoders for Predicting Novel lncRNA-Disease Associations58
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics55
Hybrid Projective Synchronization via PI Controller Based on DNA Strand Displacement55
The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease55
Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning54
Prediction of circRNA-MiRNA Association Using Singular Value Decomposition and Graph Neural Networks53
ELMo4m6A: A Contextual Language Embedding-Based Predictor for Detecting RNA N6-Methyladenosine Sites53
IGNSCDA: Predicting CircRNA-Disease Associations Based on Improved Graph Convolutional Network and Negative Sampling53
VMF-SSD: A Novel V-Space Based Multi-Scale Feature Fusion SSD for Apple Leaf Disease Detection51
Seq-BEL: Sequence-Based Ensemble Learning for Predicting Virus-Human Protein-Protein Interaction50
Modality-DTA: Multimodality Fusion Strategy for Drug–Target Affinity Prediction49
Improving Biomedical Question Answering by Data Augmentation and Model Weighting49
Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE49
State Observer Design of Coupled Genetic Regulatory Networks With Reaction-Diffusion Terms via Time-Space Sampled-Data Communications49
CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data48
Local R-Symmetry Co-Occurrence: Characterising Leaf Image Patterns for Identifying Cultivars48
Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics47
Evaluation of Existing Methods for High-Order Epistasis Detection47
Deep Learning in Gene Regulatory Network Inference: A Survey47
Self-Supervised Learning for Label Sparsity in Computational Drug Repositioning46
Robust and Privacy-Preserving Decentralized Deep Federated Learning Training: Focusing on Digital Healthcare Applications46
Minimum Functional Length Analysis of K-Mer Based on BPNN43
Transfer Learning Based Lightweight Ensemble Model for Imbalanced Breast Cancer Classification42
A Neighborhood-Based Global Network Model to Predict Drug-Target Interactions42
Identifying Molecular Biomarkers for Diseases With Machine Learning Based on Integrative Omics42
Analyzing Effect of Multi-Modality in Predicting Protein-Protein Interactions41
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites41
An Approach of Epistasis Detection Using Integer Linear Programming Optimizing Bayesian Network41
Spatial Stochastic Model of the Pre-B Cell Receptor41
SGNet: Sequence-Based Convolution and Ligand Graph Network for Protein Binding Affinity Prediction40
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images40
Fine-Grained Lesion Classification Framework for Early Auxiliary Diagnosis39
Automated Spot Counting in Microbiology39
PSPGO: Cross-Species Heterogeneous Network Propagation for Protein Function Prediction38
Blockchain-Based Data Access Security Solutions for Medical Wearables38
Subgroup Identification Using Virtual Twins for Human Microbiome Studies38
Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions38
DGANDDI: Double Generative Adversarial Networks for Drug-Drug Interaction Prediction37
NMTF-DTI: A Nonnegative Matrix Tri-factorization Approach With Multiple Kernel Fusion for Drug-Target Interaction Prediction37
TransCrispr: Transformer Based Hybrid Model for Predicting CRISPR/Cas9 Single Guide RNA Cleavage Efficiency36
RNPredATC: A Deep Residual Learning-Based Model With Applications to the Prediction of Drug-ATC Code Association36
A Multi-Task Deep Feature Selection Method for Brain Imaging Genetics34
WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites34
Lossy Compression of Quality Values in Sequencing Data34
Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis34
MEDA Based Biochips: Detection, Prevention and Rectification Techniques for Cyberphysical Attacks33
Pathogenicity Prediction of Single Amino Acid Variants With Machine Learning Model Based on Protein Structural Energies33
SAU-Net: A Unified Network for Cell Counting in 2D and 3D Microscopy Images33
Guest Editors’ Introduction to the Special Section on Bioinformatics Research and Applications33
A Deep Learning Approach Considering Image Background for Pneumonia Identification Using Explainable AI (XAI)33
Guest Editorial Guest Editorial for the 20th Asia Pacific Bioinformatics Conference32
CASL: Capturing Activity Semantics Through Location Information for Enhanced Activity Recognition32
Identification of Enriched Regions in ChIP-Seq Data via a Linear-Time Multi-Level Thresholding Algorithm32
The End-to-End Fetal Head Circumference Detection and Estimation in Ultrasound Images32
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction31
Discovering Essential Multiple Gene Effects Through Large Scale Optimization: An Application to Human Cancer Metabolism31
Helical Three Dimensional Reconstruction Using Bayesian Optimization for Cryogenic Electron Microscopy31
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 Sets31
DiagAF: A More Accurate and Efficient Pre-Alignment Filter for Sequence Alignment31
Morphological Rule-Constrained Object Detection of Key Structures in Infant Fundus Image30
Alignment-Free Sequence Comparison With Multiple k Values30
SIG: Graph-Based Cancer Subtype Stratification With Gene Mutation Structural Information30
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling30
The Intrinsic Similarity of Topological Structure in Biological Neural Networks30
Improving Clinical Decision Making With a Two-Stage Recommender System29
Bi-SeqCNN: A Novel Light-Weight Bi-Directional CNN Architecture for Protein Function Prediction29
FGFICA: Independent Component Analysis of Fusion Genomic Features for Mining Epi-Transcriptome Profiling Data29
Convolution Neural Networks Using Deep Matrix Factorization for Predicting Circrna-Disease Association29
MTGDC: A Multi-Scale Tensor Graph Diffusion Clustering for Single-Cell RNA Sequencing Data29
PreVFs-RG: A Deep Hybrid Model for Identifying Virulence Factors Based on Residual Block and Gated Recurrent Unit29
iSnoDi-MDRF: Identifying snoRNA-Disease Associations Based on Multiple Biological Data by Ranking Framework29
DGCddG: Deep Graph Convolution for Predicting Protein-Protein Binding Affinity Changes Upon Mutations28
Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective28
Explainable Knowledge Distillation for On-Device Chest X-Ray Classification28
MLDEG: A Machine Learning Approach to Identify Differentially Expressed Genes Using Network Property and Network Propagation27
LDSSNV: A Linkage Disequilibrium-Based Method for the Detection of Somatic Single-Nucleotide Variants27
Generative Biomedical Event Extraction With Constrained Decoding Strategy27
Exploring Molecular Descriptors and Fingerprints to Predict mTOR Kinase Inhibitors using Machine Learning Techniques27
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance27
Guest Editorial: Deep Learning For Genomics27
Generic Context-Aware Group Contributions27
A Stochastic Grammar Approach to Mass Classification in Mammograms27
An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks27
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks27
Multi-Label Classification With Dual Tail-Node Augmentation for Drug Repositioning27
DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion26
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks26
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration26
A Hybrid Heuristic-Exact Optimization for Large-Scale Home Health Care Problem26
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms26
Clustering Single-Cell RNA Sequence Data Using Information Maximized and Noise-Invariant Representations26
Circular Clustering With Polar Coordinate Reconstruction26
Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data26
Predicting Drug Synergism by Means of Non-Negative Matrix Tri-Factorization26
Estimating Functional Connectivity by Integration of Inherent Brain Function Activity Pattern Priors26
Knowledge Adaptive Multi-Way Matching Network for Biomedical Named Entity Recognition via Machine Reading Comprehension26
GRA-GCN: Dense Granule Protein Prediction in Apicomplexa Protozoa Through Graph Convolutional Network25
Multiview Robust Graph-Based Clustering for Cancer Subtype Identification25
A Multi-Scale Activity Transition Network for Data Translation in EEG Signals Decoding25
MSCET: A Multi-Scenario Offloading Schedule for Biomedical Data Processing and Analysis in Cloud-Edge-Terminal Collaborative Vehicular Networks25
P2GT: Fine-Grained Genomic Data Access Control With Privacy-Preserving Testing in Cloud Computing25
EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics25
Target Control of Asynchronous Boolean Networks24
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression24
LipGene: Lipschitz Continuity Guided Adaptive Learning Rates for Fast Convergence on Microarray Expression Data Sets24
An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network24
A Learning Robust and Discriminative Shape Descriptor for Plant Species Identification24
Algorithms and Hardness for Scaffold Filling to Maximize Increased Duo-Preservations23
Protein Crystallization Identification via Fuzzy Model on Linear Neighborhood Representation23
APT: An Automated Probe Tracker From Gene Expression Data23
Inferring Gene Co-Expression Networks by Incorporating Prior Protein-Protein Interaction Networks23
COMBING: Clustering in Oncology for Mathematical and Biological Identification of Novel Gene Signatures23
Towards Optimal Decomposition of Boolean Networks22
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks22
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner22
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data22
Gene Teams are on the Field: Evaluation of Variants in Gene-Networks Using High Dimensional Modelling22
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction22
Densely Connected U-Net With Criss-Cross Attention for Automatic Liver Tumor Segmentation in CT Images22
Optimising Boolean Synthetic Regulatory Networks to Control Cell States22
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots22
StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction22
Adaptive Stochastic Optimization to Improve Protein Conformation Sampling22
Combining Zhegalkin Polynomials and SAT Solving for Context-Specific Boolean Modeling of Biological Systems21
A Mutual Attention Model for Drug Target Binding Affinity Prediction21
DMFLDA: A Deep Learning Framework for Predicting lncRNA–Disease Associations21
Design of Constraint Coding Sets for Archive DNA Storage21
Lesion Segmentation in Ultrasound Using Semi-Pixel-Wise Cycle Generative Adversarial Nets21
iPhosS(Deep)-PseAAC: Identification of Phosphoserine Sites in Proteins Using Deep Learning on General Pseudo Amino Acid Compositions20
The C-SHIFT Algorithm for Normalizing Covariances20
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns20
DeepSide: A Deep Learning Approach for Drug Side Effect Prediction20
Construction of Gene Expression Patterns to Identify Critical Genes Under SARS-CoV-2 Infection Conditions20
dwMLCS: An Efficient MLCS Algorithm Based on Dynamic and Weighted Directed Acyclic Graph20
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants20
Integrated CNN and Federated Learning for COVID-19 Detection on Chest X-Ray Images20
An Effective Multi-Label Protein Sub-Chloroplast Localization Prediction by Skipped-Grams of Evolutionary Profiles Using Deep Neural Network20
Robust KALMAN Filter State Estimation for Gene Regulatory Networks20
Feature-Sensitive Deep Convolutional Neural Network for Multi-Instance Breast Cancer Detection20
A Cascaded Mutliresolution Ensemble Deep Learning Framework for Large Scale Alzheimer's Disease Detection Using Brain MRIs20
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction20
MCA-Net: Multi-Feature Coding and Attention Convolutional Neural Network for Predicting lncRNA-Disease Association19
Protein Fold Recognition From Sequences Using Convolutional and Recurrent Neural Networks19
Improved Protein Decoy Selection via Non-Negative Matrix Factorization19
A Novel Method for Inferring Chemical Compounds With Prescribed Topological Substructures Based on Integer Programming19
Predicting miRNA-Disease Associations From miRNA-Gene-Disease Heterogeneous Network With Multi-Relational Graph Convolutional Network Model19
Gene Differential Co-Expression Networks Based on RNA-Seq: Construction and Its Applications19
Generative Adversarial Network-Based Augmentation With Noval 2-Step Authentication for Anti-Coronavirus Peptide Prediction19
Incremental RPN: Hierarchical Region Proposal Network for Apple Leaf Disease Detection in Natural Environments19
I-Health: SDN-Based Fog Architecture for IIoT Applications in Healthcare19
Assessment of Prediction Uncertainty Quantification Methods in Systems Biology19
Circadian Rhythm Regulated by Tumor Suppressor p53 and Time Delay in Unstressed Cells19
NGCICM: A Novel Deep Learning-Based Method for Predicting circRNA-miRNA Interactions19
LDA-LNSUBRW: lncRNA-Disease Association Prediction Based on Linear Neighborhood Similarity and Unbalanced bi-Random Walk19
Adaptive Tracking Control for Uncertain Cancer-Tumor-Immune Systems19
A Construction Method of Dynamic Protein Interaction Networks by Using Relevant Features of Gene Expression Data18
CPGL: Prediction of Compound-Protein Interaction by Integrating Graph Attention Network With Long Short-Term Memory Neural Network18
Common Attractors in Multiple Boolean Networks18
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model18
Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network – A Boolean Network Modeling Perspective18
Efficient Approximate Kernel Based Spike Sequence Classification18
Prediction of Drug–Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding18
In Silico Prediction of New Mutations That Can Improve the Binding Abilities Between 2019-nCoV Coronavirus and Human ACE218
Predicting In-Vitro DNA-Protein Binding With a Spatially Aligned Fusion of Sequence and Shape18
scTSSR2: Imputing Dropout Events for Single-Cell RNA Sequencing Using Fast Two-Side Self-Representation18
exp2GO: Improving Prediction of Functions in the Gene Ontology With Expression Data17
GOGCN: Graph Convolutional Network on Gene Ontology for Functional Similarity Analysis of Genes17
Supervised Graph Clustering for Cancer Subtyping Based on Survival Analysis and Integration of Multi-Omic Tumor Data17
An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data17
A Multimodal Framework for Improving in Silico Drug Repositioning With the Prior Knowledge From Knowledge Graphs17
Prediction of Malignant Breast Cancer Cases Using Ensemble Machine Learning: A Case Study of Pesticides Prone Area17
BRMCF: Binary Relevance and MLSMOTE Based Computational Framework to Predict Drug Functions From Chemical and Biological Properties of Drugs17
Constrained Pseudo-Time Ordering for Clinical Transcriptomics Data17
Cross-Modality LGE-CMR Segmentation Using Image-to-Image Translation Based Data Augmentation17
aWCluster: A Novel Integrative Network-Based Clustering of Multiomics for Subtype Analysis of Cancer Data17
Noise Reduction Learning Based on XLNet-CRF for Biomedical Named Entity Recognition17
A Review of Fusion Methods for Omics and Imaging Data17
Editorial17
New Distance-Based approach for Genome-Wide Association Studies17
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations17
DomBpred: Protein Domain Boundary Prediction Based on Domain-Residue Clustering Using Inter-Residue Distance17
A Comprehensive Survey of Deep Learning Techniques in Protein Function Prediction17
Game-Theoretic Flux Balance Analysis Model for Predicting Stable Community Composition17
Integrating Molecular Graph Data of Drugs and Multiple -Omic Data of Cell Lines for Drug Response Prediction17
PointDE: Protein Docking Evaluation Using 3D Point Cloud Neural Network17
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data17
Subject-Independent Emotion Recognition of EEG Signals Based on Dynamic Empirical Convolutional Neural Network17
Few-Shot Breast Cancer Metastases Classification via Unsupervised Cell Ranking17
GeNVoM: Read Mapping Near Non-Volatile Memory16
Age Prediction by DNA Methylation in Neural Networks16
PiTLiD: Identification of Plant Disease From Leaf Images Based on Convolutional Neural Network16
GraphPLBR: Protein-Ligand Binding Residue Prediction With Deep Graph Convolution Network16
Enhancing Drug-Drug Interaction Prediction Using Deep Attention Neural Networks16
Constructing Integrative ceRNA Networks and Finding Prognostic Biomarkers in Renal Cell Carcinoma16
A Novel Method for Identification of Glutarylation Sites Combining Borderline-SMOTE With Tomek Links Technique in Imbalanced Data16
Patient Graph Deep Learning to Predict Breast Cancer Molecular Subtype16
NCMD: Node2vec-Based Neural Collaborative Filtering for Predicting MiRNA-Disease Association16
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification16
Calculation of the Weight of Evidence for Combined Single-Cell and Extracellular Forensic DNA15
Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction15
PredinID: Predicting Pathogenic Inframe Indels in Human Through Graph Convolution Neural Network With Graph Sampling Technique15
iLncRNAdis-FB: Identify lncRNA-Disease Associations by Fusing Biological Feature Blocks Through Deep Neural Network15
ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference15
A Multiview Clustering Method With Low-Rank and Sparsity Constraints for Cancer Subtyping15
Efficient Inference of Spatially-Varying Gaussian Markov Random Fields With Applications in Gene Regulatory Networks15
Heterogeneity in Blood Biomarker Trajectories After Mild TBI Revealed by Unsupervised Learning15
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer15
Identifying Gene Signatures for Cancer Drug Repositioning Based on Sample Clustering15
AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles15
Significance-Based Essential Protein Discovery15
Using Fully Convolutional Network to Locate Transcription Factor Binding Sites Based on DNA Sequence and Conservation Information15
SCN-MLTPP: A Multi-Label Classifier for Predicting Therapeutic Properties of Peptides Using the Stacked Capsule Network15
MicroRNA Promoter Identification in Human With a Three-level Prediction Method15
Heterogeneous Multi-Task Learning With Expert Diversity15
ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters15
TemPred: A Novel Protein Template Search Engine to Improve Protein Structure Prediction15
AFExNet: An Adversarial Autoencoder for Differentiating Breast Cancer Sub-Types and Extracting Biologically Relevant Genes14
AttentionDTA: Drug–Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism14
De Novo Drug Design by Multi-Objective Path Consistency Learning With Beam A* Search14
An Effective Biclustering-Based Framework for Identifying Cell Subpopulations From scRNA-seq Data14
RabbitFX: Efficient Framework for FASTA/Q File Parsing on Modern Multi-Core Platforms14
Identifying Differentially Expressed Genes in RNA Sequencing Data With Small Labelled Samples14
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread14
Robust Principal Component Analysis Based On Hypergraph Regularization for Sample Clustering and Co-Characteristic Gene Selection14
Large-Scale Multiple Sequence Alignment and the Maximum Weight Trace Alignment Merging Problem14
Identifying Gene Network Rewiring Based on Partial Correlation14
Functional Neural Networks for High-Dimensional Genetic Data Analysis14
Defining Phylogenetic Network Distances Using Cherry Operations14
Reconciliation Reconsidered: In Search of a Most Representative Reconciliation in the Duplication-Transfer-Loss Model14
Differential Gene Expression Prediction by Ensemble Deep Networks on Histone Modification Data14
scCDG: A Method Based on DAE and GCN for scRNA-Seq Data Analysis14
MISSH: Fast Hashing of Multiple Spaced Seeds14
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