楊進木

Development and Validation of a Smartphone-Based Hearing Healthcare System for Older Adults: From Clinical Diagnostic Accuracy to mHealth Amplification

生醫科學與工程博士學位學程

行動醫療、聽力篩檢、耳鏡診斷、助聽輔助、遠距醫療、mobile Health、Hearing Screening、Otoendoscopy、Hearing Intervention、Telemedicine

LipPM: An Interpretable Ensemble Model for Liver Disease Progression Prediction

生物資訊及系統生物研究所

代謝功能障礙相關脂肪性肝病／代謝功能障礙相關脂肪性肝炎（MASLD／MASH）、可解釋人工智慧、LipPM、通路－基因－樣本模型、跨物種驗證、代謝–發炎轉換開關、精準醫學、MASLD/MASH、Explainable AI、Pathway-Gene-Sample Model、Cross-Species Validation、Metabolic-to-Inflammatory Switch、Precision Medicine

A Two-Stage Interpretable Machine Learning Framework for Drug Repurposing Revealing Feature Preferences in Off-Target Prediction

生物科技學系

SGLT2抑制劑、舊藥新用、可解釋機器學習、糖尿病、心血管疾病、慢性腎臟病、SGLT2 inhibitors、drug repurposing、interpretable machine learning、diabetes、cardiovascular disease、chronic kidney disease

MAbGPT: Maturation-Aware Modeling for General Antibody Generation and Single Antibody–Driven Antigen-Specific Antibody Design

生物資訊及系統生物研究所

生成式AI、抗體設計、種係偏向、抗體演化、特定抗原抗體、親和力成熟、Generative AI、Antibody Design、Germline Bias、Antibody Evolution、Antigen-Specific Antibody、Affinity maturation

Evo-AttnMPNN: Evolutionary Supervision with Attention-Augmented MPNN for Protein Sequence Design

數據科學與工程研究所

蛋白質序列設計、生成式AI、演化監督、注意力機制、訊息傳遞、可解釋性、Protein Sequence Design、Generative AI、Evolutionary Supervision、Attention、Message Passing、Interpretability

ProTAbGPT: From Protein GPT to Antibody GPT through Attention Reprogramming

數據科學與工程研究所

生成式 AI、抗體設計、抗體演化、注意力機制、可解釋性、Generative AI、Antibody Design、Antibody Evolution、Attention、Interpretability

Encoding Drug-Target-Pathway-Disease profiles for Drug-Cancer Association Prediction using Graph Transformer- Convolution Networks

生物資訊及系統生物研究所

舊藥新用、圖形轉換網路、異質圖學習、注意力機制、藥物作用機制、Drug repurposing、Graph Transformer Networks、Heterogeneous Graph Learning、Attention Mechanism、Mechanism of Action

Integrating Single-Gene Community-Regulated Pathways and Explainable AI to Investigate SDR Mechanisms and Biomarkers in 3HP/1HP

生物資訊及系統生物研究所

生物資訊、可解釋人工智慧、全身性藥物反應、生物標記、bioinformatics、Explainable AI、systemic drug reaction、biomarker

Unveiling potential NAFLD biomarkers and therapeutic reactions via downstream pathways in networks of cross-tissue interaction

生物科技學系

跨組織交互體、不良治療反應、血清生物標誌物、非酒精性脂肪肝病、非酒精性脂肪肝炎、路徑富集、Cross-tissue interactome、Adverse therapeutic reactions、Serum biomarkers、Non-alcoholic fatty liver disease、Non-alcoholic Steatohepatitis、Pathway enrichment

Expanding Chemical Space: Developing a Compound Generative Pre-trained Transformer with Expert Classifier Systems for Enhanced De Novo Drug Design

工程與計算生醫產業碩士專班

分子建模、創新藥物設計、注意力模型、低訓練資料、Molecular Modeling、De novo Drug Design、Attention Models、Low Training Data

GCMDiff :Designing Compounds with Specific Functional Groups Using Diffusion Models

工程與計算生醫產業碩士專班

化合物設計、擴散模型、compound design、diffusion model

Identification of Blood-Based Biomarker Candidates for Liver Cancer Using AI Models and Single Gene-Regulated

生物資訊及系統生物研究所

生物標記、肝細胞癌、慢性肝病、循環上皮細胞、循環腫瘤細胞、隨機森林、單基因調控途徑、biomarker、Hepatocellular Carcinoma、Chronic Liver Disease、Circulating Epithelial Cells、Circulating Tumor Cells、Random Forest、Single-Gene Regulated Pathway

A Two-Layer Ensemble Learning Model for Predicting Kinase Inhibitor and Type with Grid-based Protein-Ligand Interactions and Multidimensional Compound Descriptors

生物資訊及系統生物研究所

激酶抑制劑、激酶抑制劑類型、選擇性機制、交互作用能量、結合環境、kinase inhibitors、inhibitor types、binding environment、interaction、selectivity

Integrating Drug-like Moieties and Binding Site Evolution for Kinase Inhibitor Prediction Using Ensemble Learning Models

生物資訊及系統生物研究所

蛋白質激酶、激酶抑制劑預測、機器學習、特徵整合方法、選擇性機制、Protein kinase、Kinase inhibitor prediction、Machine learning、Feature integration method、Selectivity mechanism

A single-gene-based AI model to identify core and context-specific essential genes by biological interpretation from pooled genome-wide CRISPR/Cas9 and omics data

生物資訊及系統生物研究所

全基因組CRISPR基因敲除資料、泛癌核心必需基因、特定環境必需基因、系統性篩選生存必需基因方法、特定環境生存特有度富集分析方法、以單基因為基礎之調控途徑、Genome-wide CRISPR knockout data、pan-cancer core essential genes、context-specific essential genes、systematic identification for essential genes approach、context-specific enrichment approach、single gene-regulated pathways

Intelligent Hierarchical Systems Biology Models: Unveiling Disease Mechanisms and Identifying Biomarkers

生物資訊及系統生物研究所

生物標誌、系統生物、智能階層式系統生物學模型、基因調控生化途徑、乳癌、潛伏性肺結核、biomarkers、systems biology、intelligent hierarchical systems biology model、single gene-regulated pathway、breast cancer、latent tuberculosis infection

Computational genomic approaches and intelligence models for pan-cancer analysis

生物資訊及系統生物研究所

計算基因組學、智慧模型、短期記憶之隨機森林遞迴特徵消除、頭頸癌、泛癌研究、神經元乙酰膽鹼受體亞基β-4、computational genomic approaches、artificial intelligence、pan-cancer、head and neck cancer、neuronal acetylcholine receptor subunit beta-4

Transcriptomic Analysis of Pulmonary Inflammation Induced by World Trade Center Dust and Its Drug Treatment

理學院應用科技學程

世貿粉塵、肺部發炎、次世代定序、階層式生物學模型、Rosoxacin、Dexamethasone、World trade center dust、Pulmonary inflammation、Next generation sequencing、Hierarchical system biology model

Bioinformatics Approach to Explore the Evolutional Origins and the Triplex Binding Sites of Human LncRNAs

生物資訊及系統生物研究所・共同指導：蔡懷寬

長鏈非編碼核糖核酸、長基因間非編碼 RNA、假基因化、假基因、三鏈體預測、lncRNA、lincRNA、pseudogenization、pseudogene、triplex prediction

Off-target prediction of SGLT2 inhibitors: an integrative bioinformatics approach to uncover structural mechanisms

生物資訊及系統生物研究所

SGLT2 抑制劑、脫靶蛋白預測、吡喃糖、propensity、蛋白質口袋大小、SGLT2 inhibitor、off-target prediction、pyranose、pocket size

A novel bioinformatics pipeline for discovering SUPT4H selective inhibitors from large zinc finger families

生物資訊及系統生物研究所

亨丁頓舞蹈症、SUPT4H、鋅指蛋白質結構域、虛擬篩選、選擇性抑制劑、藥效基團模型、Huntington's disease、zinc finger domain、virtual screening、selective inhibitors、pharmacophore model

Discover moiety preference in protein kinase family using random forest models

生醫工程研究所

蛋白質激酶、蛋白質激酶家族、機器學習、隨機森林、protein kinase、protein kinase family、machine learning、random forest

Construct deep neural networks to predict kinase family inhibitors and uncover family-moiety prefer-ence

分子醫學與生物工程研究所

激酶、激酶家族、深度神經網路、夏普利值、二分類、Kinase、Kinase family、Deep neural networks、Shapley value、Binary classification

Identify pan-kinase-family inhibitors with graph convolutional networks to reveal family-sensitive pre-moieties

生物資訊及系統生物研究所

圖域卷積網路、泛蛋白激酶家族抑制劑、梯度權重類別激發映射、激酶家族感知前導官能基、graph convolutional network、pan-kinase family inhibitor、gradient-weighted class activation mapping、family-sensitive pre-moiety

Configurational differences and binding mechanisms of Interleukin-1 receptor-associated kinase 1

生物科技學系

白血球介素1受體蛋白激酶1、蛋白質激酶抑制劑、選擇性抑制劑、Interleukin-1 receptor-associated kinase、IRAK1、IRAK4、kinase inhibitors

FooDisNET: a database of food-compound-protein-disease associations

生物科技學系

天然產物、植化素、植物化學成份、飲食與健康、疾病預防、藥物發展、食物-疾病交互作用網路、natural products、phytochemicals、diet and health、disease prevention、drug development、food-disease interaction network

Computational models of kinase inhibitor selectivity and their applications

生物科技學系

激酶、抑制劑、選擇性、kinase、inhibitor、selective

Boolean Function Networks and applications

生物資訊及系統生物研究所・共同指導：盧鴻興、楊振翔

生物資訊、計算生物學、基因調控網路推論、布爾函數網路、生理時鐘、Bioinformatics、Computational biology、Gene regulatory network inference、Boolean function networks、Circadian rhythms

Integrated bioinformatics approaches to study the mechanisms of HCV-induced type 2 diabetes mellitus and discover potential agents

生物資訊及系統生物研究所

C型肝炎、第二型糖尿病、發病機制、開發藥物、DNA微陣列、L1000資料庫、hepatitis C、type 2 diabetes、mechanisms、potential agents、DNA microarray、L1000 database

iCDrug: A graphical interface drug design system by integrating automatic molecular docking and post-screening analysis

生醫工程研究所

圖形介面軟體、藥物篩選後分析、藥物發展軟體、graphical interface software、iGemdock

A Hierarchical System Biology Model (HiSBiM) for studying mechanisms and identifying biomarkers of diabetes mellitus, Virus induced hepatitis, NASH and Hepatocellular carcinoma

生物資訊及系統生物研究所

階層式系統生物模型、糖尿病、C型肝炎、B型肝炎、非酒精性脂肪肝炎、肝癌、Hierarchical System Biology Model、diabetes mellitus、Hepatitis C、Hepatitis B、non alcoholic steatohepatitis、hepatocellular carcinoma

Computational models of protein-phosphorylation protein interfaces and their applications

生物科技學系

磷酸化蛋白結合域、相互資訊、分子演化、磷酸酪胺酸結合域、磷酸絲氨酸/蘇胺酸結合域、phosphoprotein binding domains、Mutual Information、Molecular evolution、Phosphotyrosine-binding domains、Phosphoserine/threonine-binding domains

Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data

生物科技學系

癌症、體學資料、蛋白質交互作用網路、卷積神經網路、譜分群、cancer、omics data、protein-protein interaction networks、convolutional neural network、spectral clustering

A new combination therapies on hepatocellular carcinoma by computational omics and structure-based drug design on membrane proteins and alternative splicing proteins

光電系統研究所・共同指導：許根玉

肝癌、膜蛋白、選擇性剪切、複方、combination therapy、hepatocellular carcinoma、structure-based drug design、membrane proteins、alternative splicing proteins

A Hierarchical-Systems Biology Model (HiSBiM) for studying Cigarette and Hookah constituents-gene/protein-pathway-disease relationships

生物資訊及系統生物研究所

系統生物模型、水煙、香菸、成分、尼古丁、顯著差異基因、生物路徑、Systems Biology Model、Hookah smoking、Cigarettes smoking、Constituents、Nicotine、Differentially expressed genes、Pathway

From Bed to Bench - Investigate the Relationship Between Chronic Rhinitis and Tumors

生物科技學系

頭頸癌、慢性鼻炎、炎症反應、同源藥理、藥理體、head and neck cancers、chronic rhinitis、inflammation、homopharma、pharmacomics

Integrating genome-wide expression profiles and structural protein-protein interactions for comprehensive network analysis and applications

生物資訊及系統生物研究所

結構蛋白質交互作用、基因表現圖譜、生物標記、功能性模組、蛋白質交互作用網路、Structural protein-protein interaction、Gene expression profile、Biomarker、Functional module、Protein-protein interaction network

DAGS-a novel multi-dimensional omics approach to study the mechanisms of comorbidity between diabetes mellitus and dengue fever

生物科技學系

糖尿病、登革熱、共病症、系統型資料、diabetes mellitus、dengue fever、comorbidity、omics data

Genome-wide analysis of multigenerational spontaneous breast-to-lung metastasis model for metastasis, drug resistance and cancer stem cells

生物資訊及系統生物研究所

自發性轉移模型、乳癌、轉移、抗藥性、幹細胞、Spontaneous metastasis model、Breast cancer、Metastasis、Drug resistance、Cancer stem cell

PCa24 : Gene expression profiling predicts clinical outcome of prostate cancer

理學院應用科技學程

前列腺癌、臨床預後、基因表達譜、基因、攝護腺癌、prostate cancer、prostate adenocarcinoma、gene、gene expression profiling、clinical outcome

Constructing computational models of DENV NS2B/NS3 protease for drug repurposing

生物科技學系

登革熱、登革NS2B/NS3蛋白酶、空間藥理模板、凝血酶、蛋白結合位點-化合物官能基輿圖、Dengue virus、Dengue NS2B / NS3 protease、Space-related pharma-motifs(SRP)、Thrombin、SiMMap

Identification of kinase inhibitors using Homopharma and KIDFamMap

生物科技學系

蛋白激酶、同源藥理、激酶抑制劑、protein kinase、homopharma、kinase inhibitors、KIDFamMap

Multiple Clinical Strategies for Head and Neck Cancer Treatment

生物科技學系

頭頸癌、下頷皮瓣、二極體雷射、微創手術、下頷腺切除、腮腺影像、Head and Neck Cancer、Submental Flap、Diode Laser、Minimally Invasive Surgery、Submandibular Gland Excision、Parotid Gland Image

Revealing the mechanisms of breast cancer metastasis using protein-protein interaction networks with gene expressions of high-metastatic tumor model

生物資訊及系統生物研究所

乳腺癌、轉移、目標識別、breast cancer、metastasis、TARGET IDENTIFICATION

Site-site interaction maps for exploring protein-protein interfaces

生物資訊及系統生物研究所

區域-區域交互作用地圖、蛋白質交互作用、核心錨點、專一性錨點、site-site interaction maps、protein-protein interaction、PPI family、core anchor、specific anchor

Structure-based Analysis and Drug Discover of Protein Lysine Methyltransferase

分子醫學與生物工程研究所

甲基轉移酶、結構化藥物設計、分子結合、Lysine Methyltransferase、structure-based drug design、molecular binding

Drug repurposing: the first FDA drug inhibits IRAK4 and pathways for anti-inflammation

生物資訊及系統生物研究所

舊藥新用、蛋白質激酶抑制劑、抗發炎反應、同源藥理、Drug repurposing、Protein kinase inhibitor、Anti-inflammation、Homopharma

CoMI: Consensus Mutual Information for discovering biomarkers and analyzing genome-wide expression profiling

生物資訊及系統生物研究所

互信息、亂度、全基因組表達譜、生物標誌、Mutual Information、Entropy、Genome-wide expression profiling、Biomarker

HNC88 : Gene expression profiling predicts clinical outcome and subtypes of head and neck cancer

生物科技學系

頭頸癌、分類、臨床預後、生物標記、head and neck cancer、classification、clinical outcome、biomarker

Using ATC classification system and homopharma for cancer treatments by non-cancer drugs

生物資訊及系統生物研究所

舊要新用、藥物開發、蛋白質化合物交互作用、Drug repurposing、Drug discovery、protein-compound interaction

Module-based differential expression for exploring tumor heterogeneity in 22 tumor types

生物科技學系

癌症、腫瘤、模組、基因表現圖譜、蛋白資交互作用、腫瘤異質性、Cancer、Tumor、Module、Gene expression、Protein-protein interaction、Tumor heterogeneity

Exploring kinase inhibitor selectivity and binding mechanisms for anticancer drug development

生物資訊及系統生物研究所

激酶抑制劑、選擇性、結合機制、抗癌、kinase inhibitor、selectivity、binding mechanisms、anticancer

Homopharma reveals drug repurposing and protein-compound interaction network

生物資訊及系統生物研究所

舊藥新用、蛋白質化合物交互作用網路、藥物副作用、蛋白質激脢、drug repurposing、protein-compound interaction network、side effect、protein kinase

Dynamic homologous mapping networks reveal cell behaviors and disease mechanisms

生物資訊及系統生物研究所

蛋白質交互作用網路、同源映射、蛋白質模組、模組交互作用網路、細胞行為、疾病機制、動態模組、動態網路、腫瘤異質性、protein-protein interaction networks、homologous mapping、module、module-module interaction network、cell behaviors、disease mechanisms、dynamic modules、dynamic networks、tumor heterogeneity

iGemdock 2.0 and SiMMap: Post-screening analysis for structure-based drug design

生物資訊及系統生物研究所

虛擬篩選、分子嵌合、藥物開發、區域官能基地圖、Virtual-Screening、Drug discovery、site-moiety map、SiMMap、GEMDOCK、IGEMDOCK

Drug repositioning using homologous protein-compound complexes

生物資訊及系統生物研究所

蛋白質-化合物交互作用、舊藥新用、同源蛋白質-化合物複合物、protein-compound interaction、drug reposition、homologous protein-compound complexes

Genome-wide Structural TCR-pMHC Modeling Reveals Peptide Antigen Families in Multiple Pathogens

生物資訊及系統生物研究所

胜肽抗原家族、TCR-pMHC複合體、以模板為基礎的計分函式、抗原識別、iMatrix、Peptide antigen family、TCR-pMHC complex、Template-based scoring function、Antigen recognition

Inferring comprehensive modules from evolutionary core components and protein-protein interaction networks

生物資訊及系統生物研究所

network、module、PPI family、module family、module dynamic、comprehensive module、evolutionary core component、connectivity cohesiveness、網路、模組、蛋白質交互作用家族、模組家族、模組的動態、全面性模組、演化核心模組、連通-演化內聚性

Environment-moiety relationships for discovering tyrosine kinase inhibitors

生物資訊及系統生物研究所

蛋白激酶、區域官能基地圖、環境─官能基關係、Protein kinase、SiMMap、KIDFamMap、Environment-moiety relationship

Homologous protein-protein interactions and protein complexes reveal interactome behavior

生物資訊及系統生物研究所

蛋白質交互作用家族、蛋白質複合體家族、蛋白質交互作用網路、protein-protein interaction family、protein complex family、3d-domain interologs、protein interaction network

Design and Implementation of MoNetFamily Web Service : using homologous modules and module-module interaction network in vertebrates

生物資訊及系統生物研究所

模組、網路、跨物種、家族、module、network、cross species、family

Moiety-based Site-moiety Map

生物資訊及系統生物研究所

區域官能基地圖、蛋白質、結合區域、官能基、site-moiety map、protein、binding site、moiety

Core site-moiety maps of histone demethylase family for multi-target inhibitors and binding mechanisms

生物資訊及系統生物研究所

多標靶抑制劑、核心區域官能基地圖、組蛋白去甲基化酶、Core site-moiety maps、histone demethylase、multi-target inhibitors、JMJD family

Site-moiety maps reveal the selectivity and mechanisms of human protein kinases

分子醫學與生物工程研究所

蛋白激酶、藥物設計、kinases、drug design