OOIR: Observatory of International Research

Papers

(The median citation count of Interdisciplinary Sciences-Computational Life Sciences is 2. 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 2021-03-01 to 2025-03-01.)

Article	Citations
Mixed Distribution Models Based on Single-Cell RNA Sequencing Data	151
FEAMR: A Database for Surveillance of Food and Environment-Associated Antimicrobial Resistance	106
BoT-Net: a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction	52
iDHS-FFLG: Identifying DNase I Hypersensitive Sites by Feature Fusion and Local–Global Feature Extraction Network	48
A Novel Multitasking Ant Colony Optimization Method for Detecting Multiorder SNP Interactions	44
ASI-DBNet: An Adaptive Sparse Interactive ResNet-Vision Transformer Dual-Branch Network for the Grading of Brain Cancer Histopathological Images	43
MSResG: Using GAE and Residual GCN to Predict Drug–Drug Interactions Based on Multi-source Drug Features	41
Spatial–Temporal EEG Fusion Based on Neural Network for Major Depressive Disorder Detection	41
Integration of IDPC Clustering Analysis and Interpretable Machine Learning for Survival Risk Prediction of Patients with ESCC	36
scFED: Clustering Identifying Cell Types of scRNA-Seq Data Based on Feature Engineering Denoising	34
A Deep Neural Network for Predicting Synergistic Drug Combinations on Cancer	30
DeepPI: Alignment-Free Analysis of Flexible Length Proteins Based on Deep Learning and Image Generator	28
Deep Canonical Correlation Fusion Algorithm Based on Denoising Autoencoder for ASD Diagnosis and Pathogenic Brain Region Identification	27
Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure	26
PPSNO: A Feature-Rich SNO Sites Predictor by Stacking Ensemble Strategy from Protein Sequence-Derived Information	23
Identifying Diffuse Glioma Subtypes Based on Pathway Enrichment Evaluation	20
Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification	20
Function-Genes and Disease-Genes Prediction Based on Network Embedding and One-Class Classification	19
DOTAD: A Database of Therapeutic Antibody Developability	19
Luteinizing Hormone Receptor Mutation (LHRN316S) Causes Abnormal Follicular Development Revealed by Follicle Single-Cell Analysis and CRISPR/Cas9	19
Viral Rebound After Antiviral Treatment: A Mathematical Modeling Study of the Role of Antiviral Mechanism of Action	17
Identification of Multi-functional Therapeutic Peptides Based on Prototypical Supervised Contrastive Learning	16
EnDM-CPP: A Multi-view Explainable Framework Based on Deep Learning and Machine Learning for Identifying Cell-Penetrating Peptides with Transformers and Analyzing Sequence Information	15
Bilinear Perceptual Fusion Algorithm Based on Brain Functional and Structural Data for ASD Diagnosis and Regions of Interest Identification	15
HTRPCA: Hypergraph Regularized Tensor Robust Principal Component Analysis for Sample Clustering in Tumor Omics Data	15

Unraveling Brain Synchronisation Dynamics by Explainable Neural Networks using EEG Signals: Application to Dyslexia Diagnosis	15
Correction to: Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	15
CEGSO: Boosting Essential Proteins Prediction by Integrating Protein Complex, Gene Expression, Gene Ontology, Subcellular Localization and Orthology Information	15
DP-ID: Interleaving and Denoising to Improve the Quality of DNA Storage Image	15
TUPDB: Target-Unrelated Peptide Data Bank	14
Using Network Distance Analysis to Predict lncRNA–miRNA Interactions	14
Using an Ensemble to Identify and Classify Macroalgae Antimicrobial Peptides	13
Are the Allergic Reactions of COVID-19 Vaccines Caused by mRNA Constructs or Nanocarriers? Immunological Insights	12
SBTD: A Novel Method for Detecting Topological Associated Domains from Hi-C Data	12
Integrating Protein–Protein Interaction Networks and Somatic Mutation Data to Detect Driver Modules in Pan-Cancer	11
A Review of Parallel Implementations for the Smith–Waterman Algorithm	11
Multi-feature Fusion Method Based on Linear Neighborhood Propagation Predict Plant LncRNA–Protein Interactions	11
Prediction of Protein Solubility Based on Sequence Feature Fusion and DDcCNN	11
Clinical and Laboratory Approach to Diagnose COVID-19 Using Machine Learning	10
Exploring the Molecular Basis of Substrate and Product Selectivities of Nocardicin Bifunctional Thioesterase	10
OTNet: A CNN Method Based on Hierarchical Attention Maps for Grading Arteriosclerosis of Fundus Images with Small Samples	10
Improving the Prediction of Potential Kinase Inhibitors with Feature Learning on Multisource Knowledge	9
Construction of a Pearson- and MIC-Based Co-expression Network to Identify Potential Cancer Genes	9
easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data	9
MVGCNMDA: Multi-view Graph Augmentation Convolutional Network for Uncovering Disease-Related Microbes	9
EnANNDeep: An Ensemble-based lncRNA–protein Interaction Prediction Framework with Adaptive k-Nearest Neighbor Classifier and Deep Models	8
Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference	8
Identifiable Temporal Feature Selection via Horizontal Visibility Graph Towards Smart Medical Applications	8
Pharmacogenomic Cluster Analysis of Lung Cancer Cell Lines Provides Insights into Preclinical Model Selection in NSCLC	8
Adaptive Weighted Neighbors Method for Sensitivity Analysis	8
Metapath-Based Deep Convolutional Neural Network for Predicting miRNA-Target Association on Heterogeneous Network	7
NTMFF-DTA: Prediction of Drug-Target Affinity Based on Network Topology and Multi-feature Fusion	7
Nonclinical Features in Predictive Modeling of Cardiovascular Diseases: A Machine Learning Approach	7
PredAPP: Predicting Anti-Parasitic Peptides with Undersampling and Ensemble Approaches	7
Classification of Breast Cancer and Breast Neoplasm Scenarios Based on Machine Learning and Sequence Features from lncRNAs–miRNAs-Diseases Associations	7
Exploring the Binding Mechanism of NRG1–ERBB3 Complex and Discovery of Potent Natural Products to Reduce Diabetes-Assisted Breast Cancer Progression	7
Molecular Dynamics Simulations Reveal the Modulated Mechanism of STING Conformation	7
In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations	7
FTWSVM-SR: DNA-Binding Proteins Identification via Fuzzy Twin Support Vector Machines on Self-Representation	7
Biomarker Identification in Membranous Nephropathy Using a Long Non-coding RNA-Mediated Competitive Endogenous RNA Network	7
BMRI-NET: A Deep Stacked Ensemble Model for Multi-class Brain Tumor Classification from MRI Images	7
StoneNet: An Efficient Lightweight Model Based on Depthwise Separable Convolutions for Kidney Stone Detection from CT Images	7
Rhythmic Component Analysis Tool (RCAT): A Precise, Efficient and User-Friendly Tool for Circadian Clock Genes Analysis	7
Machine Learning Applications in Drug Repurposing	6
SMART v1.0: A Database for Small Molecules with Functional Implications in Plants	6
Identifying Visual Attention Features Accurately Discerning Between Autism and Typically Developing: a Deep Learning Framework	6
sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs	6
Anti-cancer Peptide Recognition Based on Grouped Sequence and Spatial Dimension Integrated Networks	6
Identification of Chemical–Disease Associations Through Integration of Molecular Fingerprint, Gene Ontology and Pathway Information	6
Cervical Cancer Classification From Pap Smear Images Using Deep Convolutional Neural Network Models	6
Sex Differences of Cerebellum and Cerebrum: Evidence from Graph Convolutional Network	6
Correction to: HD5 and LL‑37 Inhibit SARS‑CoV and SARS‑CoV‑2 Binding to Human ACE2 by Molecular Simulation	6
Identification of Type II Toxin-Antitoxin Loci in Levilactobacillus brevis	6
Differential Diagnosis of DCIS and Fibroadenoma Based on Ultrasound Images: a Difference-Based Self-Supervised Approach	6
ResDeepSurv: A Survival Model for Deep Neural Networks Based on Residual Blocks and Self-attention Mechanism	5

A Combined Manual Annotation and Deep-Learning Natural Language Processing Study on Accurate Entity Extraction in Hereditary Disease Related Biomedical Literature	5
An Integrated TCN-CrossMHA Model for Predicting circRNA-RBP Binding Sites	5
The Dynamical Biomarkers in Functional Connectivity of Autism Spectrum Disorder Based on Dynamic Graph Embedding	5
GraphsformerCPI: Graph Transformer for Compound–Protein Interaction Prediction	5
PDDGCN: A Parasitic Disease–Drug Association Predictor Based on Multi-view Fusion Graph Convolutional Network	5
ABTrans: A Transformer-based Model for Predicting Interaction between Anti-Aβ Antibodies and Peptides	5
CA-UNet Segmentation Makes a Good Ischemic Stroke Risk Prediction	5
Identifying Protein Phosphorylation Site-Disease Associations Based on Multi-Similarity Fusion and Negative Sample Selection by Convolutional Neural Network	5
CHL-DTI: A Novel High–Low Order Information Convergence Framework for Effective Drug–Target Interaction Prediction	5
AI Prediction of Structural Stability of Nanoproteins Based on Structures and Residue Properties by Mean Pooled Dual Graph Convolutional Network	5
Deep Residual Network for Diagnosis of Retinal Diseases Using Optical Coherence Tomography Images	4
Classification of Glomerular Pathology Images in Children Using Convolutional Neural Networks with Improved SE-ResNet Module	4
U-shaped Retinal Vessel Segmentation Based on Adaptive Aggregation of Feature Information	4
CEL: A Continual Learning Model for Disease Outbreak Prediction by Leveraging Domain Adaptation via Elastic Weight Consolidation	4
HD5 and LL-37 Inhibit SARS-CoV and SARS-CoV-2 Binding to Human ACE2 by Molecular Simulation	4
Gene Selection in a Single Cell Gene Space Based on D–S Evidence Theory	4
A New Framework for Discovering Protein Complex and Disease Association via Mining Multiple Databases	4
Adaptive Multi-Kernel Graph Neural Network for Drug-Drug Interaction Prediction	4
DeepPD: A Deep Learning Method for Predicting Peptide Detectability Based on Multi-feature Representation and Information Bottleneck	4
Prediction of Multimorbidity Network Evolution in Middle-Aged and Elderly Population Based on CE-GCN	4
Computational Study of Methionine Methylation Process Catalyzed by SETD3	4
Identification of Benign and Malignant Lung Nodules in CT Images Based on Ensemble Learning Method	4
CSEL-BGC: A Bioinformatics Framework Integrating Machine Learning for Defining the Biosynthetic Evolutionary Landscape of Uncharacterized Antibacterial Natural Products	4
RicENN: Prediction of Rice Enhancers with Neural Network Based on DNA Sequences	3
Correction to: Brain Tumor Detection and Classification Using Cycle Generative Adversarial Networks	3
Discovery of Genetic Biomarkers for Alzheimer’s Disease Using Adaptive Convolutional Neural Networks Ensemble and Genome-Wide Association Studies	3
Development of Electrochemical Biosensor for miR204-Based Cancer Diagnosis	3
BMPMDA: Prediction of MiRNA-Disease Associations Using a Space Projection Model Based on Block Matrix	3
Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis	3
Improving language model of human genome for DNA–protein binding prediction based on task-specific pre-training	3
A Review of the Application of Spatial Transcriptomics in Neuroscience	3
IDDLncLoc: Subcellular Localization of LncRNAs Based on a Framework for Imbalanced Data Distributions	3
Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	3
PmliHFM: Predicting Plant miRNA-lncRNA Interactions with Hybrid Feature Mining Network	3
A Novel Deep Learning Model for Medical Image Segmentation with Convolutional Neural Network and Transformer	3
A Novel Deep-Learning-Based CADx Architecture for Classification of Thyroid Nodules Using Ultrasound Images	3
CRBP-HFEF: Prediction of RBP-Binding Sites on circRNAs Based on Hierarchical Feature Expansion and Fusion	3
SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics	3
Multi-kernel Learning Fusion Algorithm Based on RNN and GRU for ASD Diagnosis and Pathogenic Brain Region Extraction	3
Diagnosis of Pancreatic Cancer Using miRNA30e Biosensor	3
TP-DDI: A Two-Pathway Deep Neural Network for Drug–Drug Interaction Prediction	3
In silico Methods for Identification of Potential Therapeutic Targets	3
A Multi-View Feature-Based Interpretable Deep Learning Framework for Drug-Drug Interaction Prediction	3
Adaptive Total-Variation Regularized Low-Rank Representation for Analyzing Single-Cell RNA-seq Data	3
dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events	3
Synchronous Mutual Learning Network and Asynchronous Multi-Scale Embedding Network for miRNA-Disease Association Prediction	3
Computer-Aided Diagnosis of Complications After Liver Transplantation Based on Transfer Learning	3
Utilization of Deep Convolutional Neural Networks for Accurate Chest X-Ray Diagnosis and Disease Detection	2
Hessian Regularized $$L_{2,1}$$-Nonnegative Matrix Factorization and Deep Learning for miRNA–Disease Associations Prediction	2
iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming	2
Adap-BDCM: Adaptive Bilinear Dynamic Cascade Model for Classification Tasks on CNV Datasets	2
Developing a Novel Methodology by Integrating Deep Learning and HMM for Segmentation of Retinal Blood Vessels in Fundus Images	2
Combining Global-Constrained Concept Factorization and a Regularized Gaussian Graphical Model for Clustering Single-Cell RNA-seq Data	2
Predicting Drug Synergy and Discovering New Drug Combinations Based on a Graph Autoencoder and Convolutional Neural Network	2
LRT-CLUSTER: A New Clustering Algorithm Based on Likelihood Ratio Test to Identify Driving Genes	2
Drug Repositioning Based on Deep Sparse Autoencoder and Drug–Disease Similarity	2
Cell Fate Dynamics Reconstruction Identifies TPT1 and PTPRZ1 Feedback Loops as Master Regulators of Differentiation in Pediatric Glioblastoma-Immune Cell Networks	2
A Molecular Fragment Representation Learning Framework for Drug–Drug Interaction Prediction	2
SCINet: A Segmentation and Classification Interaction CNN Method for Arteriosclerotic Retinopathy Grading	2
CVGAE: A Self-Supervised Generative Method for Gene Regulatory Network Inference Using Single-Cell RNA Sequencing Data	2
Development of an Expert-Level Right Ventricular Abnormality Detection Algorithm Based on Deep Learning	2
Analysis of CRISPR-Cas Loci and their Targets in Levilactobacillus brevis	2
Cell Features Reconstruction from Gene Association Network of Single Cell	2
BiGM-lncLoc: Bi-level Multi-Graph Meta-Learning for Predicting Cell-Specific Long Noncoding RNAs Subcellular Localization	2
PLMC: Language Model of Protein Sequences Enhances Protein Crystallization Prediction	2
misORFPred: A Novel Method to Mine Translatable sORFs in Plant Pri-miRNAs Using Enhanced Scalable k-mer and Dynamic Ensemble Voting Strategy	2
NRGCNMDA: Microbe-Drug Association Prediction Based on Residual Graph Convolutional Networks and Conditional Random Fields	2
A Domain Adaptive Interpretable Substructure-Aware Graph Attention Network for Drug–Drug Interaction Prediction	2