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 2021-08-01 to 2025-08-01.)

Article	Citations
OTNet: A CNN Method Based on Hierarchical Attention Maps for Grading Arteriosclerosis of Fundus Images with Small Samples	126
Unraveling Brain Synchronisation Dynamics by Explainable Neural Networks using EEG Signals: Application to Dyslexia Diagnosis	60
Construction of a Pearson- and MIC-Based Co-expression Network to Identify Potential Cancer Genes	58
DP-ID: Interleaving and Denoising to Improve the Quality of DNA Storage Image	52
Deep Clustering-Based Metabolic Stratification of Non-Small Cell Lung Cancer Patients Through Integration of Somatic Mutation Profile and Network Propagation Algorithm	46
ResDeepSurv: A Survival Model for Deep Neural Networks Based on Residual Blocks and Self-attention Mechanism	45
Automated Brain Tumor Classification and Grading Using Multi-scale Graph Neural Network with Spatio-Temporal Transformer Attention Through MRI Scans	45
Computational Study of Methionine Methylation Process Catalyzed by SETD3	39
CA-UNet Segmentation Makes a Good Ischemic Stroke Risk Prediction	39
An Integrated TCN-CrossMHA Model for Predicting circRNA-RBP Binding Sites	36
DCPPS: Prediction of Kinase-Specific Phosphorylation Sites Using Dynamic Embedding and Cross-Representation Interaction	30
PDDGCN: A Parasitic Disease–Drug Association Predictor Based on Multi-view Fusion Graph Convolutional Network	27
Differential Diagnosis of DCIS and Fibroadenoma Based on Ultrasound Images: a Difference-Based Self-Supervised Approach	25
Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	23
Cervical Cancer Classification From Pap Smear Images Using Deep Convolutional Neural Network Models	23
AMFCL: Predicting miRNA-Disease Associations Through Adaptive Multi-source Modality Fusion and Contrastive Learning	22
A Domain Adaptive Interpretable Substructure-Aware Graph Attention Network for Drug–Drug Interaction Prediction	21
Development of Electrochemical Biosensor for miR204-Based Cancer Diagnosis	21
Diagnosis of Pancreatic Cancer Using miRNA30e Biosensor	20
dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events	19
Adaptive Multi-Kernel Graph Neural Network for Drug-Drug Interaction Prediction	19
BiGM-lncLoc: Bi-level Multi-Graph Meta-Learning for Predicting Cell-Specific Long Noncoding RNAs Subcellular Localization	19
ViruSeg: Harnessing the Power of Large Language-Image Model for Enhanced Virus Image Segmentation	17
Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis	17
Developing a Novel Methodology by Integrating Deep Learning and HMM for Segmentation of Retinal Blood Vessels in Fundus Images	16

Cell Fate Dynamics Reconstruction Identifies TPT1 and PTPRZ1 Feedback Loops as Master Regulators of Differentiation in Pediatric Glioblastoma-Immune Cell Networks	16
Development of an Expert-Level Right Ventricular Abnormality Detection Algorithm Based on Deep Learning	16
EfficientNet-resDDSC: A Hybrid Deep Learning Model Integrating Residual Blocks and Dilated Convolutions for Inferring Gene Causality in Single-Cell Data	14
A Multi-view Molecular Pre-training with Generative Contrastive Learning	13
A Hierarchical Error Correction Strategy for Text DNA Storage	13
OptimDase: An Algorithm for Predicting DNA Binding Sites with Combined Feature Encoding	13
Single-Cell Transcriptome Analysis Reveals the Role of Pancreatic Secretome in COVID-19 Associated Multi-organ Dysfunctions	13
Drug Sensitivity Prediction Based on Multi-stage Multi-modal Drug Representation Learning	12
CR-deal: Explainable Neural Network for circRNA-RBP Binding Site Recognition and Interpretation	12
MFFBi-Unet: Merging Dynamic Sparse Attention and Multi-scale Feature Fusion for Medical Image Segmentation	11
Exploring Novel Fentanyl Analogues Using a Graph-Based Transformer Model	11
scVAEBGM: Clustering Analysis of Single-Cell ATAC-seq Data Using a Deep Generative Model	10
Plant lncRNA-miRNA Interaction Prediction Based on Counterfactual Heterogeneous Graph Attention Network	10
scEM: A New Ensemble Framework for Predicting Cell Type Composition Based on scRNA-Seq Data	10
Review of Progress in Diagnostic Studies of Autism Spectrum Disorder Using Neuroimaging	10
Transformative Deep Neural Network Approaches in Kidney Ultrasound Segmentation: Empirical Validation with an Annotated Dataset	10
easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data	9
Protein Multiple Conformation Prediction Using Multi-Objective Evolution Algorithm	9
Correction to: Machine Learning Accelerates De Novo Design of Antimicrobial Peptides	9
DCDA: CircRNA–Disease Association Prediction with Feed-Forward Neural Network and Deep Autoencoder	9
Exploring the Molecular Basis of Substrate and Product Selectivities of Nocardicin Bifunctional Thioesterase	9
Construction and Application of Traditional Chinese Medicine Knowledge Graph Based on Large Language Model	9
Integrating Protein–Protein Interaction Networks and Somatic Mutation Data to Detect Driver Modules in Pan-Cancer	8
Semantic Consistency Network with Edge Learner and Connectivity Enhancer for Cervical Tumor Segmentation from Histopathology Images	8
DOTAD: A Database of Therapeutic Antibody Developability	8
MVGCNMDA: Multi-view Graph Augmentation Convolutional Network for Uncovering Disease-Related Microbes	8
Improving the Prediction of Potential Kinase Inhibitors with Feature Learning on Multisource Knowledge	8
Biomarker Identification in Membranous Nephropathy Using a Long Non-coding RNA-Mediated Competitive Endogenous RNA Network	8
A Review of Parallel Implementations for the Smith–Waterman Algorithm	7
SMART v1.0: A Database for Small Molecules with Functional Implications in Plants	7
CHL-DTI: A Novel High–Low Order Information Convergence Framework for Effective Drug–Target Interaction Prediction	7
CRBP-HFEF: Prediction of RBP-Binding Sites on circRNAs Based on Hierarchical Feature Expansion and Fusion	7
iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming	7
Correction to: HD5 and LL‑37 Inhibit SARS‑CoV and SARS‑CoV‑2 Binding to Human ACE2 by Molecular Simulation	7
Classification of Glomerular Pathology Images in Children Using Convolutional Neural Networks with Improved SE-ResNet Module	7
PredAPP: Predicting Anti-Parasitic Peptides with Undersampling and Ensemble Approaches	7
IDDLncLoc: Subcellular Localization of LncRNAs Based on a Framework for Imbalanced Data Distributions	7
BMRI-NET: A Deep Stacked Ensemble Model for Multi-class Brain Tumor Classification from MRI Images	7
Identifying Protein Phosphorylation Site-Disease Associations Based on Multi-Similarity Fusion and Negative Sample Selection by Convolutional Neural Network	7
IHDFN-DTI: Interpretable Hybrid Deep Feature Fusion Network for Drug–Target Interaction Prediction	7
Multi-kernel Learning Fusion Algorithm Based on RNN and GRU for ASD Diagnosis and Pathogenic Brain Region Extraction	7
PmliHFM: Predicting Plant miRNA-lncRNA Interactions with Hybrid Feature Mining Network	7
A Novel Deep Learning Model for Medical Image Segmentation with Convolutional Neural Network and Transformer	6
In silico Methods for Identification of Potential Therapeutic Targets	6
Combining Global-Constrained Concept Factorization and a Regularized Gaussian Graphical Model for Clustering Single-Cell RNA-seq Data	6
Discovery of a Natural Product with Potent Efficacy Against SARS-CoV-2 by Drug Screening	6
Dual Attention Mechanisms and Feature Fusion Networks Based Method for Predicting LncRNA-Disease Associations	6
Predicting Drug Synergy and Discovering New Drug Combinations Based on a Graph Autoencoder and Convolutional Neural Network	6
CD47Binder: Identify CD47 Binding Peptides by Combining Next-Generation Phage Display Data and Multiple Peptide Descriptors	6
RicENN: Prediction of Rice Enhancers with Neural Network Based on DNA Sequences	6

MTGGF: A Metabolism Type-Aware Graph Generative Model for Molecular Metabolite Prediction	6
stGNN: Spatially Informed Cell-Type Deconvolution Based on Deep Graph Learning and Statistical Modeling	6
NPI-HGNN: A Heterogeneous Graph Neural Network-Based Approach for Predicting ncRNA-Protein Interactions	6
Complex Prediction in Large PPI Networks Using Expansion and Stripe of Core Cliques	5
Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers	5
Efficient Storage and Analysis of Genomic Data: A k-mer Frequency Mapping and Image Representation Method	5
Design and Simulation of an Autonomous Molecular Mechanism Using Spatially Localized DNA Computation	5
A Semi-supervised Reinforcement Learning Framework Incorporating the Multi-scale IncepMambaNet Network for Glaucoma Progression Prediction	5
scRDiT: Generating Single-cell RNA-seq Data by Diffusion Transformers and Accelerating Sampling	5
DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representation	5
AMPFLDAP: Adaptive Message Passing and Feature Fusion on Heterogeneous Network for LncRNA-Disease Associations Prediction	5
Reinforced Collaborative-Competitive Representation for Biomedical Image Recognition	5
EPI-Mind: Identifying Enhancer–Promoter Interactions Based on Transformer Mechanism	5
RNA Folding Based on 5 Beads Model and Multiscale Simulation	5
A Self-attention Graph Convolutional Network for Precision Multi-tumor Early Diagnostics with DNA Methylation Data	4
Bilinear Perceptual Fusion Algorithm Based on Brain Functional and Structural Data for ASD Diagnosis and Regions of Interest Identification	4
Viral Rebound After Antiviral Treatment: A Mathematical Modeling Study of the Role of Antiviral Mechanism of Action	4
CSEL-BGC: A Bioinformatics Framework Integrating Machine Learning for Defining the Biosynthetic Evolutionary Landscape of Uncharacterized Antibacterial Natural Products	4
Visualizing a Field of Research for the Coronavirus Replication in Humans with Knowledge Mapping: Evidence from Web of Science	4
Classification of Brain Tumors in MRI Images with Brain-CNXSAMNet: Integrating Hybrid ConvNeXt and Spatial Attention Module Networks	4
PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest	4
DASNet: A Convolutional Neural Network with SE Attention Mechanism for ccRCC Tumor Grading	4
BoT-Net: a lightweight bag of tricks-based neural network for efficient LncRNA–miRNA interaction prediction	4
A Multi-perspective Model for Protein–Ligand-Binding Affinity Prediction	4
Predicting Protein–Ligand Binding Affinity Using Fusion Model of Spatial-Temporal Graph Neural Network and 3D Structure-Based Complex Graph	4
DeepPI: Alignment-Free Analysis of Flexible Length Proteins Based on Deep Learning and Image Generator	4
Multi-feature Fusion Method Based on Linear Neighborhood Propagation Predict Plant LncRNA–Protein Interactions	4
Improving language model of human genome for DNA–protein binding prediction based on task-specific pre-training	3
Identification of Type II Toxin-Antitoxin Loci in Levilactobacillus brevis	3
WDGBANDTI: A Deep Graph Convolutional Network-Based Bilinear Attention Network for Drug-Target Interaction Prediction with Domain Adaptation	3
BMPMDA: Prediction of MiRNA-Disease Associations Using a Space Projection Model Based on Block Matrix	3
A Multi-modal Drug Target Affinity Prediction Based on Graph Features and Pre-trained Sequence Embeddings	3
A Novel Drug–Disease Association Prediction Method Based on Deep Non-Negative Matrix Factorization with Local Graph Feature	3
MF-MNER: Multi-models Fusion for MNER in Chinese Clinical Electronic Medical Records	3
FTWSVM-SR: DNA-Binding Proteins Identification via Fuzzy Twin Support Vector Machines on Self-Representation	3
Machine Learning Applications in Drug Repurposing	3
Correction to: Brain Tumor Detection and Classification Using Cycle Generative Adversarial Networks	3
TP-DDI: A Two-Pathway Deep Neural Network for Drug–Drug Interaction Prediction	3
tensorGSEA: Detecting Differential Pathways in Type 2 Diabetes via Tensor-Based Data Reconstruction	3
Drug Repositioning Based on Deep Sparse Autoencoder and Drug–Disease Similarity	3
SeFilter-DIA: Squeeze-and-Excitation Network for Filtering High-Confidence Peptides of Data-Independent Acquisition Proteomics	3
DNA Methylation Recognition Using Hybrid Deep Learning with Dual Nucleotide Visualization Fusion Feature Encoding	3
Adap-BDCM: Adaptive Bilinear Dynamic Cascade Model for Classification Tasks on CNV Datasets	3
sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs	3
Self-Supervised Graph Representation Learning for Single-Cell Classification	3
LRT-CLUSTER: A New Clustering Algorithm Based on Likelihood Ratio Test to Identify Driving Genes	3
ABTrans: A Transformer-based Model for Predicting Interaction between Anti-Aβ Antibodies and Peptides	2
A Combined Manual Annotation and Deep-Learning Natural Language Processing Study on Accurate Entity Extraction in Hereditary Disease Related Biomedical Literature	2
Predicting CircRNA-Disease Associations Based on Heterogeneous Graph Neural Network and Knowledge Graph Attribute Mining Attention	2
Enhancing the Feature Representation of Protein Sequence Descriptors in Protein-Protein Interaction Prediction	2
ScAGCN: Graph Convolutional Network with Adaptive Aggregation Mechanism for scRNA-seq Data Dimensionality Reduction	2
BES-Designer: A Web Tool to Design Guide RNAs for Base Editing to Simplify Library	2
Inferring Gene Regulatory Networks Using the Improved Markov Blanket Discovery Algorithm	2
Lung Cancer Detection and Improving Accuracy Using Linear Subspace Image Classification Algorithm	2
Application of Semi-supervised Fuzzy Clustering Based on Knowledge Weighting and Cluster Center Learning to Mammary Molybdenum Target Image Segmentation	2
MLWNNR: LncRNA-Disease Association Prediction with Multi-Kernel Learning-Driven Weighted Nuclear Norm Regularization	2
Towards Reliable Healthcare Imaging: A Multifaceted Approach in Class Imbalance Handling for Medical Image Segmentation	2
Rhythmic Component Analysis Tool (RCAT): A Precise, Efficient and User-Friendly Tool for Circadian Clock Genes Analysis	2
HAFMMDA: HIN2vec-Based Attentional Factorization Machines for Predicting Microbe-Drug Associations	2
U-shaped Retinal Vessel Segmentation Based on Adaptive Aggregation of Feature Information	2
Sensing Compound Substructures Combined with Molecular Fingerprinting to Predict Drug-Target Interactions	2
A Deep Neural Network for Predicting Synergistic Drug Combinations on Cancer	2
Deep Learning-Based Modeling of Drug–Target Interaction Prediction Incorporating Binding Site Information of Proteins	2
CMedRAGBot: A Chinese Medical Chatbot Based on Graph RAG and Large Language Models	2
Multiple Protein Subcellular Locations Prediction Based on Deep Convolutional Neural Networks with Self-Attention Mechanism	2
Empowering Graph Neural Network-Based Computational Drug Repositioning with Large Language Model-Inferred Knowledge Representation	2
FSCAM: CAM-Based Feature Selection for Clustering scRNA-seq	2
Reconstructing Waddington Landscape from Cell Migration and Proliferation	2
Identification of Benign and Malignant Lung Nodules in CT Images Based on Ensemble Learning Method	2
Ensemble Machine Learning and Predicted Properties Promote Antimicrobial Peptide Identification	2
Clinical and Laboratory Approach to Diagnose COVID-19 Using Machine Learning	2
MetaV: A Pioneer in feature Augmented Meta-Learning Based Vision Transformer for Medical Image Classification	2
Identify Modules Associated with Immunotherapy Response from Mouse Tumor Profiles for Stratifying Cancer Patients	2
A Novel Detection Method for High-Order SNP Epistatic Interactions Based on Explicit-Encoding-Based Multitasking Harmony Search	2
LPI-SKMSC: Predicting LncRNA–Protein Interactions with Segmented k-mer Frequencies and Multi-space Clustering	2
PDBms—An online tool for PDB file splitting and interactive molecular visualization	2
Enabling Artificial Intelligence for Genome Sequence Analysis of COVID-19 and Alike Viruses	2
GEnDDn: An lncRNA–Disease Association Identification Framework Based on Dual-Net Neural Architecture and Deep Neural Network	2