林峻宇

Inferring Small Extracellular Vesicle-Mediated Cell-Cell Communication from Spatial Transcriptomics with Graph Transformers

生物資訊及系統生物研究所

小型細胞外囊泡、細胞間通訊、空間轉錄體、圖轉換器、對比學習、單細胞網路、小型細胞外囊泡分子內容物、功能富集分析、small extracellular vesicles、cell–cell communication、spatial transcriptomics、graph transformer、contrastive learning、single-cell network、sEV cargo、functional enrichment analysis

Patient-Specific Network-Based Interpretable Machine Learning Predicts Response to Immune Checkpoint Inhibitors in Melanoma Patients

生物資訊及系統生物研究所

免疫檢查點抑制劑、黑色素瘤、患者特定網路、可解釋性機器學習、生物途徑特徵、免疫治療反應預測、精準醫學、immune checkpoint inhibitors、melanoma、patient-specific network、interpretable machine learning、pathway signatures、immunotherapy response prediction、precision medicine

Comparative analysis and application of single-cell network inference methods for scRNA-seq data

生物資訊及系統生物研究所

單細胞定序、比較分析、單細胞網路推論、空間定位、基因調控網路、生物途徑富集分析、細胞聚類、軌跡推斷、個人化醫療、single-cell RNA sequencing、comparative analysis、single-cell network inference、spatial localization、gene regulatory network、pathway enrichment analysis、cell clustering、trajectory inference、personalized medicine

Inference of extracellular vesicle-mediated cell-cell communication using single-cell networks

生物資訊及系統生物研究所

胞外體、細胞間通訊、單細胞RNA測序、單細胞網路、網路傳播、腫瘤微環境、基因集富集、extracellular vesicle、cell-cell communication、scRNA-seq、single-cell network、network propagation、tumor microenvironment、gene set enrichment

Single-sample subnetwork extractor for individual characterization using transcriptomic data

生物資訊及系統生物研究所

單樣本網路、子網路推測、RNA 定序、單細胞 RNA 定序、個人化醫療、軌跡推測、single-sample network、subnetwork inference、RNA sequencing、single-cell RNA sequencing、personalized medicine、trajectory inference

A single-sample network-based framework for investigating epithelial-mesenchymal transition at different parts of tumors in head and neck cancer patients

生物科技學系

單樣本網路、重啟隨機漫步演算法、頭頸癌、RNA定序、上皮細胞間質轉化、網路連接富集分析、多區域腫瘤、single-sample network、random walk with restart、head and neck cancer、RNA sequencing、epithelial-mesenchymal transition、network edge-based enrichment analysis、multi-region tumors

Estimating single-sample network-based drug-disease proximity for prediction of drug efficacy

生物科技學系

單樣本網路、藥物療效預測、患者間異質性、超幾何分布、藥物-疾病鄰近度分析、精準醫療、single-sample network、drug efficacy prediction、inter-patient heterogeneity、hypergeometric distribution、drug-disease proximity analysis、precision medicine

Comparison and assessment of pathway analysis methods for gene expression data interpretation

生物資訊及系統生物研究所

基因表達資料、生化途徑分析、富集分析、基因集分析、共表達網路、功能註解、gene expression、enrichment analysis、pathway analysis、gene set analysis、coexpression network、functional annotation

Chi-square estimate of single-cell network with transcriptomic correlation for scRNA-seq data analysis

生物資訊及系統生物研究所

單細胞RNA測序、單細胞網路、卡方檢定、轉錄組相關性、細胞異質性、無尺度網路、細胞亞群辨識、scRNA-seq、single-cell network、chi-square test、transcriptomic weight、cellular heterogeneity、scale-free network、cell type clustering

Construction and analysis of cancer-focused protein-module interaction networks

生物資訊及系統生物研究所

蛋白質—模組交互作用、模組—模組交互作用、無尺度網路、癌症生物標記、第二癌症、潛在藥物標靶基因、protein-module interactions、module-module interactions、network inference、scale-free network、cancer biomarkers、second cancer、therapeutic targets

Comparison and evaluation of single-sample network inference methods for gene expression data analysis

生物資訊及系統生物研究所

單一樣本網路、樣本特定加權相關網路、樣本權重、網路推測、體細胞突變基因、突變驅動基因、必要基因、舊藥新用、精準醫療、single-sample network、sample-specific weighted correlation network、sample weight、network inference、somatic mutation gene、mutation driver gene、essential gene、drug repurposing、precision medicine

Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles

生物資訊及系統生物研究所

功能富集分析、過表徵分析、網路富集分析、共表現網路分析、基因集關聯富集分析、隱性關聯、顯性關聯、functional enrichment analysis、over-representation analysis、network enrichment analysis、co-expression network analysis、gene set correlation enrichment analysis、implicit association、explicit association

Design and implementation of web service and software package: annotating gene expression profiles by using gene set correlation enrichment analysis

生物資訊及系統生物研究所

過表徵分析、網路富集分析、共表現網路分析、基因集關聯富集分析、超幾何分布、Over-Representation Analysis、Network Enrichment Analysis、co-expression network analysis、Gene set correlation enrichment、Hypergeometric distribution

Inference of single-cell network using mutual information with cell transcriptomic correlation

生物資訊及系統生物研究所

單一樣本特定網路、樣本特定加權相關網路、樣本權重、無尺度網路、轉錄體分析、亞型辨識、single sample network、sample-specific weighted correlation network、sample weight、scale-free network、transcriptome analysis、subtype identification

Sample-specific weighted correlation network for individual characterization of diseases

生物資訊及系統生物研究所

單一樣本特定網路、樣本特定加權相關網路、樣本權重、無尺度網路、精準醫療、疾病分類、亞型辨識、藥物標靶檢測、舊藥新用、生物標記、single sample network、sample-specific weighted correlation network、sample weight、scale-free network、precision medicine、disease classification、subtype identification、drug target detection、drug repurposing、biomarker