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鍾佳儒

Chung Chia Ru

jjrchris@g.ncu.edu.tw

國科會計畫統計

整合生成與強化學習於多體學驅動抗微生物?之探索
1140201~1150131
[生物資訊 , bioinformatics]
整合生成與強化學習於多體學驅動抗微生物?之探索
1130201~1140131
[生物資訊 , bioinformatics]

期刊著作

DeepOTG: An effective deep learning framework for identifying human protein O-linked threonine glycosylation sites via attention-based information bottleneck
International Journal of Biological Macromolecules, 362, 2026-05-01
[ Deep learning,O-linked glycosylation,Post-translational modification ]
AI-powered rapid detection of multidrug-resistant Klebsiella pneumoniae with informative peaks of MALDI-TOF MS
Bioinformatics Advances, 6, 1, 2026-01-01
ANIA: an inception-attention network for predicting minimum inhibitory concentration of antimicrobial peptides
Briefings in Bioinformatics, 27, 1, 2026-01-01
[ antibiotic resistance,antimicrobial peptides,chaos game representation,deep learning,drug discovery ]
ConsAMPHemo: A computational framework for predicting hemolysis of antimicrobial peptides based on machine learning approaches
Protein Science, 34, 7, 2025-07-01
[ antimicrobial peptides,bioinformatics,contrastive learning,drug discovery,hemolytic activity,machine learning,sequence analysis ]
Caps-ac4C: An effective computational framework for identifying N4-acetylcytidine sites in human mRNA based on deep learning
Journal of Molecular Biology, 437, 6, 2025-03-15
dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era
Nucleic Acids Research, 53, D1, D364-D376, 2025-01-06
DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research
Nucleic Acids Research, 53, D1, D377-D386, 2025-01-06
An ensemble deep learning model for predicting minimum inhibitory concentrations of antimicrobial peptides against pathogenic bacteria
iScience, 27, 9, 2024-09-20
[ Biological sciences,Chemistry,Computer science ]
ACP-CapsPred: An explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network
Briefings in Bioinformatics, 25, 5, 2024-09-01
[ anticancer peptides,bioinformatics,cancers,capsule networks,drug discovery,sequence analysis ]
CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network
Journal of Chemical Information and Modeling, 64, 14, 5725-5736, 2024-07-22
AMPActiPred: A three-stage framework for predicting antibacterial peptides and activity levels with deep forest
Protein Science, 33, 6, 2024-06-01
[ antibacterial peptide,bioinformatics,deep forest,drug discovery,machine learning ]
Qigong Master: A Qigong-Based Attention Training Game Using Action Recognition and Balance Analysis
IEEE Transactions on Games, 16, 2, 376-383, 2024-06-01
[ Action recognition,attention-deficit/hyperactivity disorder (ADHD),Baduanjin,Kinect,virtual reality (VR) ]
KinPred-RNA—kinase activity inference and cancer type classification using machine learning on RNA-seq data
iScience, 27, 4, 2024-04-19
[ Cancer,Machine learning ]
A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy
Briefings in Bioinformatics, 25, 3, 2024-03-27
[ antiviral peptides,contrastive learning,drug discovery,multi-feature fusion strategy,sequence analysis ]
Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species
International Journal of Molecular Sciences, 25, 5, 2024-03-01
[ interpretable prediction,language-based deep learning model,multi-scale biological information analysis,RNA modification ]
Anti-Drugs Chatbot: Chinese BERT-Based Cognitive Intent Analysis
IEEE Transactions on Computational Social Systems, 11, 1, 514-521, 2024-02-01
[ Anti-drug,chatbot,natural language process,pretrained language model ]
Identifying Antitubercular Peptides via Deep Forest Architecture with Effective Feature Representation
Analytical Chemistry, 96, 4, 1538-1546, 2024-01-30
Impaired Brain-Heart Relation in Patients With Methamphetamine Use Disorder During VR Induction of Drug Cue Reactivity
IEEE Journal of Translational Engineering in Health and Medicine, 12, 1-9, 2024-01-01
[ EEG,heart rate variability (HRV),impaired brain-heart relation,methamphetamine use disorder (MUD),Neuronal abnormalities,virtual reality (VR) ]
Virtual-Reality-Based Supermarket for Intellectual Disability Classification, Diagnostics, and Assessment
IEEE Transactions on Learning Technologies, 17, 404-412, 2024-01-01
[ Assessment,intelligent disability (ID),machine learning (ML),virtual reality (VR) ]
Mobile Virtual Assistant for Multi-Modal Depression-Level Stratification
IEEE Transactions on Affective Computing, 2024-01-01
[ Biomedical monitoring,Convolutional neural networks,Depression,depression recognition,Face recognition,Feature extraction,multi-modal fusion,Virtual assistants,virtual human,Visualization ]
Dyslexia Analysis and Diagnosis Based on Eye Movement
IEEE Transactions on Neural Systems and Rehabilitation Engineering, 32, 4109-4119, 2024-01-01
[ Cognitive assessment,diagnostic tools,dyslexia,eye movement tracking,fusion models,machine learning,physiological data analysis ]
Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning
Journal of Chemical Information and Modeling, 63, 24, 7886-7898, 2023-12-25
Multi-label classification and features investigation of antimicrobial peptides with various functional classes
iScience, 26, 12, 2023-12-15
[ Biochemistry,Microbiology,Pharmacology,Properties of biomolecules ]
A risk assessment framework for multidrug-resistant Staphylococcus aureus using machine learning and mass spectrometry technology
Briefings in Bioinformatics, 24, 6, 2023-11-01
[ machine learning,MALDI-TOF MS,matrix-associated laser desorption and ionization/time-of-flight mass spectrometry,methicillin-resistant Staphylococcus aureus,risk assessment of multidrug-resistant bacteria ]
Trend of HPV Molecular Epidemiology in the Post-Vaccine Era: A 10-Year Study
Viruses, 15, 10, 2023-10-01
[ genotype distribution,high-risk genotypes,HPV,molecular epidemiology,prophylactic HPV vaccination ]
DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning
Protein Science, 32, 10, 2023-10-01
[ antifungal peptides,deep learning,drug discovery,sequence analysis ]
ABPCaps: A Novel Capsule Network-Based Method for the Prediction of Antibacterial Peptides
Applied Sciences (Switzerland), 13, 12, 2023-06-01
[ antibacterial peptide,antibiotic resistance,capsule network,deep learning,feature extraction ]
StackTHPred: Identifying Tumor-Homing Peptides through GBDT-Based Feature Selection with Stacking Ensemble Architecture
International Journal of Molecular Sciences, 24, 12, 2023-06-01
[ feature selection,sequence analysis,stacking architecture,tumor-homing peptide ]
Data-Driven Two-Stage Framework for Identification and Characterization of Different Antibiotic-Resistant Escherichia coli Isolates Based on Mass Spectrometry Data
Microbiology spectrum, 11, 3, 2023-05-01
[ antimicrobial resistance,cephalosporin,cephalosporins,fluoroquinolones,machine learning,MALDI-TOF MS,matrix-assisted laser desorption ionization–time of flight mass spectrometry,penicillin,penicillins ]
Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences
Briefings in Bioinformatics, 24, 2, 2023-03-01
[ adaptive learning,multiple species,N6-methyladinosine sites,random forest,support vector machine ]
Accelerating the Discovery of Anticancer Peptides through Deep Forest Architecture with Deep Graphical Representation
International Journal of Molecular Sciences, 24, 5, 2023-03-01
[ anticancer peptide,deep forest,drug discovery,feature extraction,sequence analysis ]
Towards Accurate Identification of Antibiotic-Resistant Pathogens through the Ensemble of Multiple Preprocessing Methods Based on MALDI-TOF Spectra
International Journal of Molecular Sciences, 24, 2, 2023-01-01
[ antibiotic resistance,machine learning,MALDI-TOF MS ]
Neuronal Correlates of Task Irrelevant Distractions Enhance the Detection of Attention Deficit/Hyperactivity Disorder
IEEE Transactions on Neural Systems and Rehabilitation Engineering, 31, 1302-1310, 2023-01-01
[ Attention deficit/hyperactivity disorder (ADHD),continuous performance test (CPT),distractions,electroencephalography (EEG),go/no-go task,machine learning,virtual reality (VR) ]
Rapid and Accurate Discrimination of Mycobacterium abscessus Subspecies Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Spectrum and Machine Learning Algorithms
Biomedicines, 11, 1, 2023-01-01
[ machine learning,MALDI–TOF,Mycobacterium abscessus subspecies abscessus,Mycobacterium abscessus subspecies massiliense,rapid antibiotic resistance detection ]
Stress Recognition Based on Multiphysiological Data in High-Pressure Driving VR Scene
IEEE Sensors Journal, 22, 20, 19897-19907, 2022-10-15
[ Electrocardiography (ECG),eye tracking,Galvanic skin response (GSR),machine learning (ML),stress recognition,virtual reality (VR) ]
Neuronal Abnormalities Induced by an Intelligent Virtual Reality System for Methamphetamine Use Disorder
IEEE Journal of Biomedical and Health Informatics, 26, 7, 3458-3465, 2022-07-01
[ EEG,methamp-hetamine use disorder (MUD),neuronal abnormalities,resting-state,virtual reality (VR) ]
Efficiently Predicting Vancomycin Resistance of Enterococcus Faecium From MALDI-TOF MS Spectra Using a Deep Learning-Based Approach
Frontiers in Microbiology, 13, 2022-06-06
[ antibacterial drug resistance,convolutional neural network (CNN),MALDI-TOF MS,rapid detection,vancomycin-resistant Enterococcus faecium (VREfm) ]
Rapid Antibiotic Resistance Serial Prediction in Staphylococcus aureus Based on Large-Scale MALDI-TOF Data by Applying XGBoost in Multi-Label Learning
Frontiers in Microbiology, 13, 2022-04-12
Large-Scale Samples Based Rapid Detection of Ciprofloxacin Resistance in Klebsiella pneumoniae Using Machine Learning Methods
Frontiers in Microbiology, 13, 2022-03-08
Investigating Unfavorable Factors That Impede MALDI-TOF-Based AI in Predicting Antibiotic Resistance
Diagnostics, 12, 2, 2022-02-01
Energy Efficiency of Inference Algorithms for Clinical Laboratory Data Sets: Green Artificial Intelligence Study
Journal of Medical Internet Research, 24, 1, 2022-01-01
An Intelligent Motor Assessment Method Utilizing a Bi-Lateral Virtual-Reality Task for Stroke Rehabilitation on Upper Extremity
IEEE Journal of Translational Engineering in Health and Medicine, 10, 2022-01-01
[ machine learning,motor training,Stroke rehabilitation,virtual reality ]
dbAMP 2.0: Updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data
Nucleic Acids Research, 50, 1, D460-D470, 2022-01-01
MDRSA: A Web Based-Tool for Rapid Identification of Multidrug Resistant Staphylococcus aureus Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Frontiers in Microbiology, 12, 2021-12-03
[ antibiotics susceptibility test,AST (antibiotic susceptibility testing),machine learning,MALDI-TOF MS,multidrug resistance ]
Clinically Applicable System for Rapidly Predicting Enterococcus faecium Susceptibility to Vancomycin
Microbiology spectrum, 9, 3, 2021-12-01
[ Antibacterial drug resistance,Clinical methods,Enterococcus faecium,Machine learning,Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry,Microbiology,Rapid detection,Vancomycin resistance,Vancomycin-resistant Enterococcus faecium ]
Large-scale mass spectrometry data combined with demographics analysis rapidly predicts methicillin resistance in Staphylococcus aureus
Briefings in Bioinformatics, 22, 4, 2021-07-20
[ logistic regression,mass spectrometry,methicillin resistance,MRSA ]
An intelligent virtual-reality system with multi-model sensing for cue-elicited craving in patients with methamphetamine use disorder
IEEE Transactions on Biomedical Engineering, 68, 7, 2270-2280, 2021-07-01
[ electrocardiogram (ECG),eye tracking,Galvanic Skin Response (GSR),Heart Rate Variability (HRV),machine learning,Methamphetamine,virtual reality (VR) ]
A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra
Briefings in Bioinformatics, 22, 3, 2021-05-20
[ binning method,feature selection,machine learning,MALDI-TOF,mass spectrometry,Methicillin-resistant Staphylococcus aureus,MRSA ]
Motor indicators for the assessment of frozen shoulder rehabilitation via a virtual reality training system
Electronics (Switzerland), 10, 6, 1-14, 2021-03-02
[ Frozen shoulder,Motor assessment,Rehabilitation,Virtual reality (VR) ]
A Machine-Learning-Based Assessment Method for Early-Stage Neurocognitive Impairment by an Immersive Virtual Supermarket
IEEE Transactions on Neural Systems and Rehabilitation Engineering, 29, 2124-2132, 2021-01-01
[ Alzheimer’s disease,assessment,Cognitive impairment,machine learning,virtual reality ]
Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins
Scientific Reports, 10, 1, 2020-12-01
A Virtual-Reality System Integrated with Neuro-Behavior Sensing for Attention-Deficit/Hyperactivity Disorder Intelligent Assessment
IEEE Transactions on Neural Systems and Rehabilitation Engineering, 28, 9, 1899-1907, 2020-09-01
[ assessment,Attention deficit and hyperactivity disorder,machine learning,neuro-behavior,virtual reality ]
Improving multi-tumor biomarker health check-up tests with machine learning algorithms
Cancers, 12, 6, 2020-06-01
[ Cancer screening,Health check-up,Machine learning,Tumor marker ]
Characterization and identification of antimicrobial peptides with different functional activities
Briefings in Bioinformatics, 21, 3, 1098-1114, 2020-05-21
[ antimicrobial peptide , functional activity , machine learning , prediction tools ]
Characterization and identification of natural antimicrobial peptides on different organisms
International Journal of Molecular Sciences, 21, 3, 2020-02-01
[ Antimicrobial peptides , Feature selection , Machine learning , Organisms , Sequence analysis ]
Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques
BMC Bioinformatics, 20, 2019-12-24
[ GBS , Group B streptococcus , Machine learning , MALDI-TOF-MS , Serotypes ]
Using a large margin context-aware convolutional neural network to automatically extract disease-disease association from literature: Comparative analytic study
JMIR Medical Informatics, 7, 4, 2019-10-01
Incorporating Statistical Test and Machine Intelligence Into Strain Typing of Staphylococcus haemolyticus Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Frontiers in Microbiology, 10, 2019-09-13
[ Fisher's exact test , machine learning , MALDI-TOF MS , Staphylococcus haemolyticus , strain typing ]

研討會著作

Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics
2025-08-20
[ Phosphoproteomics data,Kinase activity profiles,deep learning ]
Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq
2025-08-20
[ single-cell RNA-seq,Dirichlet distribution,pseudo-bulk simulation,peripheral blood mononuclear cells,peripheral blood mononuclear cells, cell type annotation ]
AI-Enhanced MALDI-TOF MS Analysis for Important Peaks on Predicting Ciprofloxacin Resistance across Different Gram-Negative Bacteria
2025-08-20
[ c2luZ2xlLWNlbGwgUk5BLXNlcQ== ]
AI-Enhanced MALDI-TOF MS Analysis for Important Peaks on Predicting Ciprofloxacin Resistance across Different Gram-Negative Bacteria
2025-01-01
[ antimicrobial resistance detection,ciprofloxacin resistance,convolutional neural network,feature selection,Gram-negative bacteria,MALDI-TOF MS,random forest ]
Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq
2025-01-01
[ cell type annotation,Dirichlet distribution,peripheral blood mononuclear cells,pseudo-bulk simulation,single-cell RNA-seq ]
Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics
2025-01-01
[ deep learning,Kinase activity profiles,Phosphoproteomics data ]
Integrative Framework for Functional analysis of multiple Traditional Chinese Medicines based on transcriptome-driven systems biology and supervised learning strategy
2025-01-01
[ gene rank-based (pathway-based) functional analysis,RNA-sequencing,supervised learning,Traditional Chinese Medicine ]

校內獲獎

114 新聘國鼎青年獎勵
113 傑出論文貢獻獎
113 新聘卓越人才獎勵
112 新聘國鼎青年獎勵

演講

利用人工智慧應對抗生素抗藥性挑戰 (1131109 ~ 1131110)
多體學與精準醫學研究，是橫跨多項領域的科學，不論從體學技術的發展至資料分析與轉化，從基礎研究、轉譯醫學、進而臨床應用，皆需多方領域的通力合作與交流。2019年，由台灣生物資訊暨系統生物學會、台灣蛋白體學會與台灣基因醫學暨生物標記學會，以促進科學社群之交流與合作，激發多體學與精準醫學研究的研發量能為宗旨，起草舉辦「多體學與精準醫學聯合會議(MOPM)」，為國內第一個多體學領域之聯合學術會議。2020年，台灣演化與計算生物學會、台灣精準醫學學會與台灣胞外體學加入，讓這個會議內容更完整與全面。「多體學與精準醫學聯合會議(MOPM)」今年已步入第六屆，本年度會議主題為「Precision Medicine Revolution: Exploring Frontiers and Implementing Applications」，將焦點聚於精準醫療，並同步邀請國內外講者進行專題演講、安排最新研究壁報發表和競賽、規劃產業新興技術和儀器介紹等，以期能促進跨領域之多面向合作。

鍾佳儒

Chung Chia Ru

現職

專長

專長簡述

最高學歷

相關連結

科技部學門領域

政府GRB研究專長領域

教育部學門領域

國科會計畫統計

整合生成與強化學習於多體學驅動抗微生物?之探索 1140201~1150131 [生物資訊 , bioinformatics]

整合生成與強化學習於多體學驅動抗微生物?之探索 1130201~1140131 [生物資訊 , bioinformatics]

期刊著作

DeepOTG: An effective deep learning framework for identifying human protein O-linked threonine glycosylation sites via attention-based information bottleneck International Journal of Biological Macromolecules, 362, 2026-05-01 [ Deep learning,O-linked glycosylation,Post-translational modification ]

AI-powered rapid detection of multidrug-resistant Klebsiella pneumoniae with informative peaks of MALDI-TOF MS Bioinformatics Advances, 6, 1, 2026-01-01

ANIA: an inception-attention network for predicting minimum inhibitory concentration of antimicrobial peptides Briefings in Bioinformatics, 27, 1, 2026-01-01 [ antibiotic resistance,antimicrobial peptides,chaos game representation,deep learning,drug discovery ]

ConsAMPHemo: A computational framework for predicting hemolysis of antimicrobial peptides based on machine learning approaches Protein Science, 34, 7, 2025-07-01 [ antimicrobial peptides,bioinformatics,contrastive learning,drug discovery,hemolytic activity,machine learning,sequence analysis ]

Caps-ac4C: An effective computational framework for identifying N4-acetylcytidine sites in human mRNA based on deep learning Journal of Molecular Biology, 437, 6, 2025-03-15

dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era Nucleic Acids Research, 53, D1, D364-D376, 2025-01-06

DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research Nucleic Acids Research, 53, D1, D377-D386, 2025-01-06

An ensemble deep learning model for predicting minimum inhibitory concentrations of antimicrobial peptides against pathogenic bacteria iScience, 27, 9, 2024-09-20 [ Biological sciences,Chemistry,Computer science ]

ACP-CapsPred: An explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network Briefings in Bioinformatics, 25, 5, 2024-09-01 [ anticancer peptides,bioinformatics,cancers,capsule networks,drug discovery,sequence analysis ]

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network Journal of Chemical Information and Modeling, 64, 14, 5725-5736, 2024-07-22

AMPActiPred: A three-stage framework for predicting antibacterial peptides and activity levels with deep forest Protein Science, 33, 6, 2024-06-01 [ antibacterial peptide,bioinformatics,deep forest,drug discovery,machine learning ]

Qigong Master: A Qigong-Based Attention Training Game Using Action Recognition and Balance Analysis IEEE Transactions on Games, 16, 2, 376-383, 2024-06-01 [ Action recognition,attention-deficit/hyperactivity disorder (ADHD),Baduanjin,Kinect,virtual reality (VR) ]

KinPred-RNA—kinase activity inference and cancer type classification using machine learning on RNA-seq data iScience, 27, 4, 2024-04-19 [ Cancer,Machine learning ]

Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species International Journal of Molecular Sciences, 25, 5, 2024-03-01 [ interpretable prediction,language-based deep learning model,multi-scale biological information analysis,RNA modification ]

Anti-Drugs Chatbot: Chinese BERT-Based Cognitive Intent Analysis IEEE Transactions on Computational Social Systems, 11, 1, 514-521, 2024-02-01 [ Anti-drug,chatbot,natural language process,pretrained language model ]

Identifying Antitubercular Peptides via Deep Forest Architecture with Effective Feature Representation Analytical Chemistry, 96, 4, 1538-1546, 2024-01-30

Virtual-Reality-Based Supermarket for Intellectual Disability Classification, Diagnostics, and Assessment IEEE Transactions on Learning Technologies, 17, 404-412, 2024-01-01 [ Assessment,intelligent disability (ID),machine learning (ML),virtual reality (VR) ]

Dyslexia Analysis and Diagnosis Based on Eye Movement IEEE Transactions on Neural Systems and Rehabilitation Engineering, 32, 4109-4119, 2024-01-01 [ Cognitive assessment,diagnostic tools,dyslexia,eye movement tracking,fusion models,machine learning,physiological data analysis ]

Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning Journal of Chemical Information and Modeling, 63, 24, 7886-7898, 2023-12-25

Multi-label classification and features investigation of antimicrobial peptides with various functional classes iScience, 26, 12, 2023-12-15 [ Biochemistry,Microbiology,Pharmacology,Properties of biomolecules ]

Trend of HPV Molecular Epidemiology in the Post-Vaccine Era: A 10-Year Study Viruses, 15, 10, 2023-10-01 [ genotype distribution,high-risk genotypes,HPV,molecular epidemiology,prophylactic HPV vaccination ]

DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning Protein Science, 32, 10, 2023-10-01 [ antifungal peptides,deep learning,drug discovery,sequence analysis ]

ABPCaps: A Novel Capsule Network-Based Method for the Prediction of Antibacterial Peptides Applied Sciences (Switzerland), 13, 12, 2023-06-01 [ antibacterial peptide,antibiotic resistance,capsule network,deep learning,feature extraction ]

StackTHPred: Identifying Tumor-Homing Peptides through GBDT-Based Feature Selection with Stacking Ensemble Architecture International Journal of Molecular Sciences, 24, 12, 2023-06-01 [ feature selection,sequence analysis,stacking architecture,tumor-homing peptide ]

Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences Briefings in Bioinformatics, 24, 2, 2023-03-01 [ adaptive learning,multiple species,N6-methyladinosine sites,random forest,support vector machine ]

Accelerating the Discovery of Anticancer Peptides through Deep Forest Architecture with Deep Graphical Representation International Journal of Molecular Sciences, 24, 5, 2023-03-01 [ anticancer peptide,deep forest,drug discovery,feature extraction,sequence analysis ]

Towards Accurate Identification of Antibiotic-Resistant Pathogens through the Ensemble of Multiple Preprocessing Methods Based on MALDI-TOF Spectra International Journal of Molecular Sciences, 24, 2, 2023-01-01 [ antibiotic resistance,machine learning,MALDI-TOF MS ]

Stress Recognition Based on Multiphysiological Data in High-Pressure Driving VR Scene IEEE Sensors Journal, 22, 20, 19897-19907, 2022-10-15 [ Electrocardiography (ECG),eye tracking,Galvanic skin response (GSR),machine learning (ML),stress recognition,virtual reality (VR) ]

Neuronal Abnormalities Induced by an Intelligent Virtual Reality System for Methamphetamine Use Disorder IEEE Journal of Biomedical and Health Informatics, 26, 7, 3458-3465, 2022-07-01 [ EEG,methamp-hetamine use disorder (MUD),neuronal abnormalities,resting-state,virtual reality (VR) ]

Rapid Antibiotic Resistance Serial Prediction in Staphylococcus aureus Based on Large-Scale MALDI-TOF Data by Applying XGBoost in Multi-Label Learning Frontiers in Microbiology, 13, 2022-04-12

Large-Scale Samples Based Rapid Detection of Ciprofloxacin Resistance in Klebsiella pneumoniae Using Machine Learning Methods Frontiers in Microbiology, 13, 2022-03-08

Investigating Unfavorable Factors That Impede MALDI-TOF-Based AI in Predicting Antibiotic Resistance Diagnostics, 12, 2, 2022-02-01

Energy Efficiency of Inference Algorithms for Clinical Laboratory Data Sets: Green Artificial Intelligence Study Journal of Medical Internet Research, 24, 1, 2022-01-01

An Intelligent Motor Assessment Method Utilizing a Bi-Lateral Virtual-Reality Task for Stroke Rehabilitation on Upper Extremity IEEE Journal of Translational Engineering in Health and Medicine, 10, 2022-01-01 [ machine learning,motor training,Stroke rehabilitation,virtual reality ]

dbAMP 2.0: Updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data Nucleic Acids Research, 50, 1, D460-D470, 2022-01-01

Large-scale mass spectrometry data combined with demographics analysis rapidly predicts methicillin resistance in Staphylococcus aureus Briefings in Bioinformatics, 22, 4, 2021-07-20 [ logistic regression,mass spectrometry,methicillin resistance,MRSA ]

Motor indicators for the assessment of frozen shoulder rehabilitation via a virtual reality training system Electronics (Switzerland), 10, 6, 1-14, 2021-03-02 [ Frozen shoulder,Motor assessment,Rehabilitation,Virtual reality (VR) ]

Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins Scientific Reports, 10, 1, 2020-12-01

Improving multi-tumor biomarker health check-up tests with machine learning algorithms Cancers, 12, 6, 2020-06-01 [ Cancer screening,Health check-up,Machine learning,Tumor marker ]

Characterization and identification of antimicrobial peptides with different functional activities Briefings in Bioinformatics, 21, 3, 1098-1114, 2020-05-21 [ antimicrobial peptide , functional activity , machine learning , prediction tools ]

Characterization and identification of natural antimicrobial peptides on different organisms International Journal of Molecular Sciences, 21, 3, 2020-02-01 [ Antimicrobial peptides , Feature selection , Machine learning , Organisms , Sequence analysis ]

Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques BMC Bioinformatics, 20, 2019-12-24 [ GBS , Group B streptococcus , Machine learning , MALDI-TOF-MS , Serotypes ]

Using a large margin context-aware convolutional neural network to automatically extract disease-disease association from literature: Comparative analytic study JMIR Medical Informatics, 7, 4, 2019-10-01

研討會著作

Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics 2025-08-20 [ Phosphoproteomics data,Kinase activity profiles,deep learning ]

Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq 2025-08-20 [ single-cell RNA-seq,Dirichlet distribution,pseudo-bulk simulation,peripheral blood mononuclear cells,peripheral blood mononuclear cells, cell type annotation ]

AI-Enhanced MALDI-TOF MS Analysis for Important Peaks on Predicting Ciprofloxacin Resistance across Different Gram-Negative Bacteria 2025-08-20 [ c2luZ2xlLWNlbGwgUk5BLXNlcQ== ]

Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq 2025-01-01 [ cell type annotation,Dirichlet distribution,peripheral blood mononuclear cells,pseudo-bulk simulation,single-cell RNA-seq ]

Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics 2025-01-01 [ deep learning,Kinase activity profiles,Phosphoproteomics data ]

Integrative Framework for Functional analysis of multiple Traditional Chinese Medicines based on transcriptome-driven systems biology and supervised learning strategy 2025-01-01 [ gene rank-based (pathway-based) functional analysis,RNA-sequencing,supervised learning,Traditional Chinese Medicine ]

校內獲獎

演講

整合生成與強化學習於多體學驅動抗微生物?之探索
1140201~1150131
[生物資訊 , bioinformatics]

整合生成與強化學習於多體學驅動抗微生物?之探索
1130201~1140131
[生物資訊 , bioinformatics]

DeepOTG: An effective deep learning framework for identifying human protein O-linked threonine glycosylation sites via attention-based information bottleneck
International Journal of Biological Macromolecules, 362, 2026-05-01
[ Deep learning,O-linked glycosylation,Post-translational modification ]

AI-powered rapid detection of multidrug-resistant Klebsiella pneumoniae with informative peaks of MALDI-TOF MS
Bioinformatics Advances, 6, 1, 2026-01-01

ANIA: an inception-attention network for predicting minimum inhibitory concentration of antimicrobial peptides
Briefings in Bioinformatics, 27, 1, 2026-01-01
[ antibiotic resistance,antimicrobial peptides,chaos game representation,deep learning,drug discovery ]

ConsAMPHemo: A computational framework for predicting hemolysis of antimicrobial peptides based on machine learning approaches
Protein Science, 34, 7, 2025-07-01
[ antimicrobial peptides,bioinformatics,contrastive learning,drug discovery,hemolytic activity,machine learning,sequence analysis ]

Caps-ac4C: An effective computational framework for identifying N4-acetylcytidine sites in human mRNA based on deep learning
Journal of Molecular Biology, 437, 6, 2025-03-15

dbAMP 3.0: updated resource of antimicrobial activity and structural annotation of peptides in the post-pandemic era
Nucleic Acids Research, 53, D1, D364-D376, 2025-01-06

DbPTM 2025 update: Comprehensive integration of PTMs and proteomic data for advanced insights into cancer research
Nucleic Acids Research, 53, D1, D377-D386, 2025-01-06

An ensemble deep learning model for predicting minimum inhibitory concentrations of antimicrobial peptides against pathogenic bacteria
iScience, 27, 9, 2024-09-20
[ Biological sciences,Chemistry,Computer science ]

ACP-CapsPred: An explainable computational framework for identification and functional prediction of anticancer peptides based on capsule network
Briefings in Bioinformatics, 25, 5, 2024-09-01
[ anticancer peptides,bioinformatics,cancers,capsule networks,drug discovery,sequence analysis ]

CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network
Journal of Chemical Information and Modeling, 64, 14, 5725-5736, 2024-07-22

AMPActiPred: A three-stage framework for predicting antibacterial peptides and activity levels with deep forest
Protein Science, 33, 6, 2024-06-01
[ antibacterial peptide,bioinformatics,deep forest,drug discovery,machine learning ]

Qigong Master: A Qigong-Based Attention Training Game Using Action Recognition and Balance Analysis
IEEE Transactions on Games, 16, 2, 376-383, 2024-06-01
[ Action recognition,attention-deficit/hyperactivity disorder (ADHD),Baduanjin,Kinect,virtual reality (VR) ]

KinPred-RNA—kinase activity inference and cancer type classification using machine learning on RNA-seq data
iScience, 27, 4, 2024-04-19
[ Cancer,Machine learning ]

Interpretable Multi-Scale Deep Learning for RNA Methylation Analysis across Multiple Species
International Journal of Molecular Sciences, 25, 5, 2024-03-01
[ interpretable prediction,language-based deep learning model,multi-scale biological information analysis,RNA modification ]

Anti-Drugs Chatbot: Chinese BERT-Based Cognitive Intent Analysis
IEEE Transactions on Computational Social Systems, 11, 1, 514-521, 2024-02-01
[ Anti-drug,chatbot,natural language process,pretrained language model ]

Identifying Antitubercular Peptides via Deep Forest Architecture with Effective Feature Representation
Analytical Chemistry, 96, 4, 1538-1546, 2024-01-30

Virtual-Reality-Based Supermarket for Intellectual Disability Classification, Diagnostics, and Assessment
IEEE Transactions on Learning Technologies, 17, 404-412, 2024-01-01
[ Assessment,intelligent disability (ID),machine learning (ML),virtual reality (VR) ]

Dyslexia Analysis and Diagnosis Based on Eye Movement
IEEE Transactions on Neural Systems and Rehabilitation Engineering, 32, 4109-4119, 2024-01-01
[ Cognitive assessment,diagnostic tools,dyslexia,eye movement tracking,fusion models,machine learning,physiological data analysis ]

Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning
Journal of Chemical Information and Modeling, 63, 24, 7886-7898, 2023-12-25

Multi-label classification and features investigation of antimicrobial peptides with various functional classes
iScience, 26, 12, 2023-12-15
[ Biochemistry,Microbiology,Pharmacology,Properties of biomolecules ]

Trend of HPV Molecular Epidemiology in the Post-Vaccine Era: A 10-Year Study
Viruses, 15, 10, 2023-10-01
[ genotype distribution,high-risk genotypes,HPV,molecular epidemiology,prophylactic HPV vaccination ]

DeepAFP: An effective computational framework for identifying antifungal peptides based on deep learning
Protein Science, 32, 10, 2023-10-01
[ antifungal peptides,deep learning,drug discovery,sequence analysis ]

ABPCaps: A Novel Capsule Network-Based Method for the Prediction of Antibacterial Peptides
Applied Sciences (Switzerland), 13, 12, 2023-06-01
[ antibacterial peptide,antibiotic resistance,capsule network,deep learning,feature extraction ]

StackTHPred: Identifying Tumor-Homing Peptides through GBDT-Based Feature Selection with Stacking Ensemble Architecture
International Journal of Molecular Sciences, 24, 12, 2023-06-01
[ feature selection,sequence analysis,stacking architecture,tumor-homing peptide ]

Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences
Briefings in Bioinformatics, 24, 2, 2023-03-01
[ adaptive learning,multiple species,N6-methyladinosine sites,random forest,support vector machine ]

Accelerating the Discovery of Anticancer Peptides through Deep Forest Architecture with Deep Graphical Representation
International Journal of Molecular Sciences, 24, 5, 2023-03-01
[ anticancer peptide,deep forest,drug discovery,feature extraction,sequence analysis ]

Towards Accurate Identification of Antibiotic-Resistant Pathogens through the Ensemble of Multiple Preprocessing Methods Based on MALDI-TOF Spectra
International Journal of Molecular Sciences, 24, 2, 2023-01-01
[ antibiotic resistance,machine learning,MALDI-TOF MS ]

Stress Recognition Based on Multiphysiological Data in High-Pressure Driving VR Scene
IEEE Sensors Journal, 22, 20, 19897-19907, 2022-10-15
[ Electrocardiography (ECG),eye tracking,Galvanic skin response (GSR),machine learning (ML),stress recognition,virtual reality (VR) ]

Neuronal Abnormalities Induced by an Intelligent Virtual Reality System for Methamphetamine Use Disorder
IEEE Journal of Biomedical and Health Informatics, 26, 7, 3458-3465, 2022-07-01
[ EEG,methamp-hetamine use disorder (MUD),neuronal abnormalities,resting-state,virtual reality (VR) ]

Rapid Antibiotic Resistance Serial Prediction in Staphylococcus aureus Based on Large-Scale MALDI-TOF Data by Applying XGBoost in Multi-Label Learning
Frontiers in Microbiology, 13, 2022-04-12

Large-Scale Samples Based Rapid Detection of Ciprofloxacin Resistance in Klebsiella pneumoniae Using Machine Learning Methods
Frontiers in Microbiology, 13, 2022-03-08

Investigating Unfavorable Factors That Impede MALDI-TOF-Based AI in Predicting Antibiotic Resistance
Diagnostics, 12, 2, 2022-02-01

Energy Efficiency of Inference Algorithms for Clinical Laboratory Data Sets: Green Artificial Intelligence Study
Journal of Medical Internet Research, 24, 1, 2022-01-01

An Intelligent Motor Assessment Method Utilizing a Bi-Lateral Virtual-Reality Task for Stroke Rehabilitation on Upper Extremity
IEEE Journal of Translational Engineering in Health and Medicine, 10, 2022-01-01
[ machine learning,motor training,Stroke rehabilitation,virtual reality ]

dbAMP 2.0: Updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data
Nucleic Acids Research, 50, 1, D460-D470, 2022-01-01

Large-scale mass spectrometry data combined with demographics analysis rapidly predicts methicillin resistance in Staphylococcus aureus
Briefings in Bioinformatics, 22, 4, 2021-07-20
[ logistic regression,mass spectrometry,methicillin resistance,MRSA ]

Motor indicators for the assessment of frozen shoulder rehabilitation via a virtual reality training system
Electronics (Switzerland), 10, 6, 1-14, 2021-03-02
[ Frozen shoulder,Motor assessment,Rehabilitation,Virtual reality (VR) ]

Incorporating hybrid models into lysine malonylation sites prediction on mammalian and plant proteins
Scientific Reports, 10, 1, 2020-12-01

Improving multi-tumor biomarker health check-up tests with machine learning algorithms
Cancers, 12, 6, 2020-06-01
[ Cancer screening,Health check-up,Machine learning,Tumor marker ]

Characterization and identification of antimicrobial peptides with different functional activities
Briefings in Bioinformatics, 21, 3, 1098-1114, 2020-05-21
[ antimicrobial peptide , functional activity , machine learning , prediction tools ]

Characterization and identification of natural antimicrobial peptides on different organisms
International Journal of Molecular Sciences, 21, 3, 2020-02-01
[ Antimicrobial peptides , Feature selection , Machine learning , Organisms , Sequence analysis ]

Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques
BMC Bioinformatics, 20, 2019-12-24
[ GBS , Group B streptococcus , Machine learning , MALDI-TOF-MS , Serotypes ]

Using a large margin context-aware convolutional neural network to automatically extract disease-disease association from literature: Comparative analytic study
JMIR Medical Informatics, 7, 4, 2019-10-01

Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics
2025-08-20
[ Phosphoproteomics data,Kinase activity profiles,deep learning ]

Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq
2025-08-20
[ single-cell RNA-seq,Dirichlet distribution,pseudo-bulk simulation,peripheral blood mononuclear cells,peripheral blood mononuclear cells, cell type annotation ]

AI-Enhanced MALDI-TOF MS Analysis for Important Peaks on Predicting Ciprofloxacin Resistance across Different Gram-Negative Bacteria
2025-08-20
[ c2luZ2xlLWNlbGwgUk5BLXNlcQ== ]

Self-Attention Enhanced Deep Learning Models for Immune Cell Deconvolution from Bulk RNA-Seq
2025-01-01
[ cell type annotation,Dirichlet distribution,peripheral blood mononuclear cells,pseudo-bulk simulation,single-cell RNA-seq ]

Explainable AI-Enhanced Kinase Activity Profiling Through Phosphoproteomics
2025-01-01
[ deep learning,Kinase activity profiles,Phosphoproteomics data ]

Integrative Framework for Functional analysis of multiple Traditional Chinese Medicines based on transcriptome-driven systems biology and supervised learning strategy
2025-01-01
[ gene rank-based (pathway-based) functional analysis,RNA-sequencing,supervised learning,Traditional Chinese Medicine ]