Cho-Yi (Joey) Chen = Olympic Swimmer + Bioinformatician + Data Scientist in Biomedicine & Healthcare
ORCiD: 0000-0002-7915-7814
Education & Training
- 2015-2017:
美國哈佛大學 達納法伯癌症研究中心 博士後研究員
Postdoctoral Research Fellow, Dana-Farber Cancer Institute (DFCI), Harvard University - 2014:
美國匹茲堡大學 生物統計學系訪問學者
Predoctoral Visiting Scholar, Department of Biostatistics, University of Pittsburgh (UPitt) - 2010-2015:
國立臺灣大學 暨 中央研究院 基因體與系統生物學 博士
Ph.D., Joint Degree Program in Genome and Systems Biology, National Taiwan University (NTU) & Academia Sinica - 2007-2009:
國立臺灣大學 電機資訊學院 生醫電子與資訊學 碩士 (GPA: 4.0/4.0; Rank: 1st/26)
M.S., Institute of Biomedical Electronics and Bioinformatics (BEBI), National Taiwan University (NTU) - 2003-2007:
國立臺灣大學 電機資訊學院 資訊工程學 學士 (GPA: 3.94/4.0; Rank: 7th/108)
B.S., Department of Computer Science and Information Engineering (CSIE), National Taiwan University (NTU)
Research Interests
- 生物資訊與計算生物學 Bioinformatics & Computational Biology
- 基因體與系統生物學 Genomics & Systems Biology
- 數位醫學與資料科學 Data Science in Biomedicine & Healthcare
- 機器學習與智慧計算 Machine Learning & Intelligent Computing
- 競技游泳 Competitive Swimming
Experiences
Work
- 2017-present:
國立陽明交通大學 生物醫學資訊研究所 助理教授
Assistant Professor, Institute of Biomedical Informatics, National Yang Ming Chiao Tung University
Teaching
- 生物醫學資訊學基礎(國立陽明交通大學)
Foundations for Biomedical Informatics (NYCU)
2021 Fall | 2022 Fall | 2023 Fall - 量化數據分析(國立陽明交通大學)
Quantitative data analysis (NYCU)
2020 Spring | 2021 Spring | 2022 Spring | 2023 Spring | 2024 Spring - 生醫資訊新知(國立陽明大學)
This Week in Biomedical Informatics (NYMU)
2019 Fall - 晝夜節律概論(國立陽明大學)
Introduction to Circadian Rhythms (NYMU)
2019 Fall - 計算與數據科學程式設計基礎(國立陽明大學)
Fundamental Programming for Data Science (NYMU)
2018 Fall - 計算與數據科學實驗(國立陽明大學)
Laboratory for Computation and Data Science (NYMU)
2018 Spring | 2019 Spring - 計算機概論與程式設計(國立陽明交通大學)
Introduction to Computer Science & Programming (NYCU)
2017 Fall | 2018 Spring | 2018 Fall | 2019 Spring | 2019 Fall | 2020 Spring | 2020 Fall | 2021 Spring | 2021 Fall | 2022 Fall | 2023 Fall - 生物資訊學原理(國立陽明大學)
Principles of Bioinformatics (NYMU)
2017 Fall | 2018 Fall | 2019 Fall | 2020 Fall - 生物資訊學實習(國立臺灣大學)
Bioinformatics Laboratory, TA (NTU)
2012 Spring | 2013 Spring - 生物資訊程式設計(國立陽明大學)
Bioinformatics Programming, Instructor (NYMU)
2011 Summer | 2012 Summer | 2013 Summer
Academic Society
- 台灣演化與計算生物學會.創社會員
Founding member, Taiwan Society of Evolution and Computational Biology (TaiwanSECB)
Reviewer/Referee
Conference
- 第36屆生物醫學聯合學術年會
JACBS 2022, the 36th Joint Annual Conference of Biomedical Science - APBC 2021, the 19th Asia Pacific Bioinformatics Conference
- APBC 2020, the 18th Asia Pacific Bioinformatics Conference
- APBC 2019, the 17th Asia Pacific Bioinformatics Conference
- IEEE BIBE 2018, the 18th IEEE International Conference on Bioinformatics and Bioengineering
- APBC 2018, the 16th Asia Pacific Bioinformatics Conference
- GIW/BIOINFO 2017, the 28th International Conference on Genome Informatics
- APBC 2017, the 15th Asia Pacific Bioinformatics Conference
- GIW 2013, the 24th International Conference on Genome Informatics
Journal
- Bioinformatics, Oxford Journals
- Biomedicines, MDPI
- BMC Cardiovascular Disorders, BioMed Central
- BMC Genomics, BioMed Central
- BMC Systems Biology, BioMed Central
- Communications Biology, Nature Portfolio
- Data in Brief, Elsevier
- Frontiers in Psychiatry, Frontiers Media
- International Journal of Molecular Sciences, MDPI
- Journal of Gastroenterology and Hepatology, Wiley
- Journal of Personalized Medicine, MDPI
- Nucleic Acids Research, Oxford Journals
- PLoS ONE, the Public Library of Science
- Scientific Reports, Nature Portfolio
- Transactions on Knowledge and Data Engineering, IEEE Computer Society
Book
- R Bioinformatics Cookbook, Packt Publishing Ltd.
- Hands-On Bioinformatics with Python, Packt Publishing Ltd.
- Bioinformatics with Python Cookbook, 2nd edition, Packt Publishing Ltd.
- Bioinformatics with Python Cookbook, Packt Publishing Ltd.
Conference/Workshop
- 2022演化基因體學與生物資訊學國際研討會(受邀演講)
ISEGB 2022 (Coordinator/Speaker) - 2022國立臺灣大學生物資訊營.台北(受邀授課)
NTU Bioinformatics Camp (Invited Instructor), Taipei, Taiwan - 2021國立清華大學生醫產業與新農業創新創業人才培育計畫.新竹(受邀授課)
Program for Quantitative Data Analysis (Invited Instructor)
2021 Training Program for Interdisciplinary Talents of Biomedicine and New Agriculture, NTHU, Hsinchu, Taiwan - 2020陽明交大生物科技與藥物發展研討會.新竹(受邀演講)
NYCUS 2020 (Invited Speaker)
2020 Symposium for Biological Technology and Therapeutic Development, NYCU, Hsinchu, Taiwan - 2020國立清華大學生醫產業與新農業創新創業人才培育計畫.新竹(受邀授課)
Program for Quantitative Data Analysis (Invited Instructor)
2020 Training Program for Interdisciplinary Talents of Biomedicine and New Agriculture, NTHU, Hsinchu, Taiwan - 第27屆細胞及分子生物新知研討會.墾丁(受邀演講)
CSCMB 2020 (Invited Speaker)
The 27th Symposium on Recent Advances in Cellular and Molecular Biology, Kenting, Taiwan - 2019中央大學生醫工程與數據科學工作坊.桃園(受邀授課)
NCU 2019 Bio & DS Workshop (Invited Instructor)
2019 Bioinformatics & Data Science Workshop, NCU, Taoyuan, Taiwan - 2018演化基因體學與生物資訊學國際研討會.中央研究院(受邀演講)
ISEGB 2018 (Invited Speaker)
2018 International Symposium on Evolutionary Genomics and Bioinformatics, Academia Sinica, Taipei, Taiwan - 2017基因體流行病學研習營.中央研究院(受邀授課)
GEW 2017 (Invited Instructor)
2017 Genomic Epidemiology Workshop, Academia Sinica, Taipei, Taiwan - 2015年新興資訊科技青年學人研討會.美國麻州劍橋 (口頭發表)
EITA 2015 (Oral Presentation)
The 4th EITA Young Investigator Conference, Cambridge, MA, USA. - 第15屆國際系統生物學會議.澳大利亞墨爾本(海報發表.大會旅行獎助)
ICSB 2014 (Poster Presentation; Student Travel Fellowship)
The 15th International Conference on Systems Biology, Melbourne, Australia. - 2014年新興資訊科技研討會:新媒體與生醫研究.美國麻州劍橋 (口頭發表)
EITA 2014 (Oral Presentation)
The 2014 EITA Conference on New Media and Biomedical Research, Cambridge, MA, USA. - 第7屆亞洲青年學人生物資訊和生物體學會議.日本東京 (口頭發表.大會旅行獎助)
AYRCOB 2013 (Oral Presentation; Travel Fellowship)
The 7th Asian Young Researchers Conference on Computational and Omics Biology, Tokyo, Japan. - 第9屆亞太生物資訊學會議.韓國仁川 (口頭發表.國科會獎助)
APBC 2011 (Oral Presentation; NSC Sponsorship)
The 9th Asia Pacific Bioinformatics Conference, Incheon, Korea. - 第24/26屆生物醫學聯合學術年會.台北 (口頭/海報發表)
JACBS 2009/2011 (Oral/Poster Presentation)
The 24th/26th Joint Annual Conference of Biomedical Science, Taipei, Taiwan.
Talk/Lecture/TV Interview
- Dec. 2023
受邀演講:《醫學科技產程轉譯特論》.台北醫學大學.醫學科技學院
Invited talk: Data Mining in Genomics—Applications in Circadian Medicine
College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan - Dec. 2023
受邀演講:《人工智慧技巧於智慧醫療之應用》.馬偕醫學院
Invited talk: Network Medicine in the Age of Biomedical Big Data
The AI Class, Department of Medicine, MacKay Medical College, Taipei, Taiwan - Oct. 2023
受邀演講:《生醫大數據時代下的網路醫學》.台北醫學大學.醫學資訊研究所
Invited talk: Network Medicine in the Age of Biomedical Big Data
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan - Nov. 2022
受邀演講:《基因體資料探勘》.國立清華大學.智慧生醫博班學程
Invited talk: Data Mining in Genomics
Ph.D. Program in Biomedical Artificial Intelligence, National Tsing Hua University, Taiwan - Nov. 2021
受邀演講:《基因體資料探勘》.國立陽明交通大學.生物科技學院
Invited talk: Data Mining in Genomics
College of Biological Science and Technology, National Yang Ming Chiao Tung University, Taiwan - Sept. 2021
受邀演講:《生醫資料科學與智慧計算—數位醫學應用》.台北榮民總醫院.醫研部
Invited talk: Biomedical Data Science & Intelligent Informatics for Digital Medicine
Department of Medical Research, Taipei Veterans General Hospital, Taiwan - Apr. 2021
受邀座談:《如何規劃學習歷程—大學端評審老師的觀點 & 生醫資訊跨領域導航》.基隆市私立二信高級中學
Invited talk: How to prepare your E-Portfolio: Professor’s perspectives
Er Xin High School, Keelung, Taiwan - Mar. 2021
受邀演講:《生醫資料科學與智慧計算—神經科學應用》.台北榮民總醫院.神經內科
Invited talk: Biomedical Data Science & Intelligent Informatics for Neuroscience
Department of Neurology in the Neurological Institute, Taipei Veterans General Hospital, Taiwan - Dec. 2020
受邀演講:《生醫大數據時代下的網路醫學》.台北醫學大學.醫學科技學院
Invited talk: Network Medicine in the Age of Biomedical Big Data
College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan - Dec. 2020
受邀演講:《生醫大數據時代下的網路醫學》.國立陽明大學牙醫學院
Invited talk: Network Medicine in the Age of Biomedical Big Data
School of Dentistry, National Yang-Ming University, Taipei, Taiwan - Dec. 2019
受邀演講:《「選擇」:職涯規劃經驗分享》.國立臺灣⼤學與中央研究院基因體與系統生物學學程
Invited talk: Career Planning and Development for Young Researchers
The 2019 NTU-Academia Sinica Genome and Systems Biology (GSB) Program Retreat, Yilan, Taiwan - Nov. 2019
受邀演講:《從基因體數據中挖掘資訊:以偵測生理時鐘基因表現為例》.亞洲大學
Invited talk: Data Mining in Genomics: Detecting Circadian Gene Expression
Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan - Oct. 2019
受邀演講:《基因表現約日節律於人類疾病與健康之探究》.中央研究院資訊所
Invited talk: Circadian gene expression in human health and diseases
Bioinformatics Program Seminar, Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei, Taiwan - Aug. 2019
受邀演講:《基因表現約日節律於人類疾病與健康之探究》.中央研究院分子細胞研究所
Invited talk: Circadian gene expression in human health and diseases
Institute of Molecular Biology, Computational Biology & Bioinformatics Seminar Series, Academia Sinica, Taipei, Taiwan - May 2019
受邀演講:《基因表現約日節律於人類疾病與健康之探究》.台北醫學大學
Invited talk: Circadian gene expression in human health and diseases
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan - Sept. 2018
受邀演講:《探究老化對於人類大腦前額葉皮質基因表達晝夜節律之影響》.中央研究院分子醫學博士學位學程
Invited Talk: Effects of aging on circadian patterns of gene expression in the human prefrontal cortex
Taiwan International Graduate Program (TIGP) Molecular Medicine Program Retreat 2018, Fullon, New Taipei City, Taiwan - Mar. 2018
受邀演講:《探究老化對於人類大腦前額葉皮質基因表達晝夜節律之影響》.高雄醫學大學
Invited Talk: Effects of aging on circadian patterns of gene expression in the human prefrontal cortex
Ph.D. Program in Toxicology, Kaohsiung Medical University, Kaohsiung, Taiwan - Mar. 2017
受邀演講:《探究老化對於人類大腦前額葉皮質基因表達晝夜節律之影響》.國立陽明大學
Invited Talk: Effects of aging on circadian patterns of gene expression in the human prefrontal cortex
Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan - Feb. 2017
受邀演講:《人類組織基因表達與調控網絡之性別差異》.國立陽明大學
Invited Talk: Sexual dimorphism in gene expression and regulatory networks across human tissues
Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan - Dec. 2016
受邀演講:《以後設分析法偵測基因共表現網路差異模組》.哈佛醫學院
Invited Talk: Meta-analysis Framework for Differential Co-expression Network Detection
Channing Division of Network Medicine, Harvard Medical School, Boston, USA - May 2016
受邀演講:《分子生物多體學網路整合分析》.哈佛醫學院
Invited Talk: Multi-omic Network-based Analyses of GTEx Data
Channing Division of Network Medicine, Harvard Medical School, Boston, USA - Dec. 2014
受邀授課:《癌症基因體體細胞突變組合分析》.台北醫學大學
Invited Lecture: Analyzing Combinations of Somatic Mutations in Cancer Genomes
Ph.D. Program for Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan. - Nov. 2014
受邀演講:《3端非轉錄體與微核醣核酸重編程之探索》.德國馬克斯普朗克學會
Invited Talk: Exploring the Programming of 3’UTRome and MicroRNA Regulatory Network
Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Dresden, Germany. - May 2013
受邀授課:《癌症生物學之微核醣核酸研究:資料庫與工具》.國立台灣大學
Invited Lecture: MicroRNA Research in Cancer Biology: Databases and Tools
Department of Life Science, National Taiwan University, Taipei, Taiwan. - Nov. 2012
受邀座談:《大專院校運動績優生生涯規劃與挑戰》.國立台灣大學
Invited Talk: Student-Athlete Success: Meeting the Challenges of College Life
Physical Education Office, National Taiwan University, Taipei, Taiwan. - Mar. 2012
受邀授課:《基因類別富集分析方法》.國立台灣大學
Invited Lecture: Gene Category Over-representation Analysis
Department of Life Science, National Taiwan University, Taipei, Taiwan. - Dec. 2011
電視訪問.台灣公共電視
TV Interview, TAIWAN PUBLIC TV, Taiwan. - Jan. 2011
受邀授課:《轉錄因子與微核醣糖核酸於人類調控網路之共調控預測》.國立台灣大學
Invited Lecture: Coregulation of Transcription Factors and MicroRNAs in Human Transcriptional Regulatory Network
Department of Life Science, National Taiwan University, Taipei, Taiwan. - May. 2009
電視訪問.台灣民視
TV Interview, FORMOSA TV, Taiwan.
Team & Club
- 2003~2009, 2010~2013:
國立臺灣大學游泳代表隊隊員
Member of NTU Swimming Team - 2007~2008:
國立臺灣大學游泳代表隊隊長
Captain of NTU Swimming Team - 1994~2013:
基隆市游泳代表隊隊員
Member of Keelung Swimming Club - 2010~2012:
Speedo® 臺灣區運動員代言人
Athlete Endorser of Speedo® Taiwan - 2005~2006:
Mizuno Swim® 臺灣區契約選手
Sponsored Athlete of Mizuno Swim® Taiwan - 2001~2004:
Arena® 臺灣區贊助選手
Sponsored Athlete of Arena® Taiwan
Sports Competition
- 2011年短水道世界盃新加坡分站
FINA/ARENA Swimming World Cup 2011, Singapore
50公尺蛙式:決賽第8名
50m Breaststroke, finalist - 2010年杜拜世界游泳短水道錦標賽
10th FINA Short Course World Swimming Championships, Dubai, United Arab Emirates, 2010
50公尺蛙式:總排名第45名(參賽人數92名)
50m Breaststroke, overall ranking: 45 / 92 - 2010年廣州亞運會
16th Asian Games, Guangzhou, China, 2010
50公尺蛙式:總排名第16名(參賽人數34名)
50m Breaststroke, overall ranking: 16 / 34 - 2004年雅典奧運會
28th Olympic Games, ATHENS, Greece, 2004
100公尺蛙式:總排名第35名(參賽人數60名)
100m Breaststroke, overall ranking: 35 / 60 - 2002年釜山亞運會
14th Asian Games, BUSAN, South Korea, 2002
100公尺蛙式:總排名第4名
100m Breaststroke, overall ranking: 4 - 2002年法國世界中學生運動會
ISF World Gymnasiade, CAEN, France, 2002
(34 countries with 2000 high school athletes)
100公尺蛙式:金牌
Won gold in the 100m breaststroke
200公尺蛙式:金牌
Won gold in the 200m breaststroke - 2002年莫斯科世界游泳短水道錦標賽
6th FINA Short Course World Swimming Championships, MOSCOW, Russia, 2002
100公尺蛙式:總排名第35名(參賽人數59名)
100m Breaststroke, overall ranking: 35 / 59
200公尺蛙式:總排名第23名(參賽人數41名)
200m Breaststroke, overall ranking: 23 / 41 - 2001年福岡世界游泳錦標賽
9th FINA World Swimming Championships, FUKUOKA, Japan, 2001
100公尺蛙式:總排名第39名(參賽人數62名)
100m Breaststroke, overall ranking: 39 / 62
200公尺蛙式:總排名第27名(參賽人數40名)
200m Breaststroke, overall ranking: 27 / 40 - 2001年大阪東亞運
3rd East Asian Games, OSAKA, Japan, 2001
200公尺蛙式:決賽第4名
Finished 4th in the final of the 200m breaststroke - 2000年雪梨奧運選拔賽
2000 Olympic Trials, KAOHSIUNG, Taiwan, 2000
200公尺蛙式:通過奧運參賽標準B
Qualified for Olympic athlete candidate in 200m breaststroke B standard
Career Records
- 前任200公尺蛙式全國紀錄保持:2001/4 ~ 2005/6
Former 200m Breaststroke National Record holder in Taiwan - 前任50公尺蛙式全國短水道紀錄保持:2009/12 ~ 2009/12
Former 50m Breaststroke Short Course National Record holder in Taiwan - 前任200公尺蛙式全國短水道紀錄保持:2001/12 ~ 2004/12
Former 200m Breaststroke Short Course National Record holder in Taiwan - 前任4×100公尺混合式接力全國短水道紀錄保持:2010/12 ~
Current 4x100m Medley Relay Short Course National Record holder in Taiwan - 前任200公尺蛙式全國運動會大會紀錄保持:2001/10 ~ 2005/10
Former 200m Breaststroke Meet Record holder of National Athletic Games in Taiwan - 前任200公尺蛙式全國中等學校運動會大會紀錄保持:2001/4 ~ 2013/4
Current 200m Breaststroke Meet Record holder of National High School Athletic Games in Taiwan - 前任200公尺蛙式亞洲分齡紀錄保持(18歲以上組):2003/8 ~ 2007/8
Former 200m Breaststroke Asian Age Group Record holder (above 18) - 前任200公尺蛙式亞洲分齡紀錄保持(15-17歲組):2002/8 ~ 2009/8
Former 200m Breaststroke Asian Age Group Record holder (U18) - 前任100公尺蛙式亞洲分齡紀錄保持(15-17歲組):2002/8 ~ 2009/8
Former 100m Breaststroke Asian Age Group Record holder (U18) - 前任50 公尺蛙式亞洲分齡紀錄保持(15-17歲組):2002/8 ~ 2009/8
Former 50m Breaststroke Asian Age Group Record holder (U18) - 前任200公尺蛙式亞洲分齡紀錄保持(13-14歲組):2000/8 ~ 2002/8
Former 200m Breaststroke Asian Age Group Record holder (U15)
Awards & Honors
- 一一一學年國立陽明交通大學教學優良獎
22/23 Excellence in Teaching Award, National Yang Ming Chiao Tung University - 一〇八學年國立陽明大學教學傑出教師
19/20 Excellence in Teaching Award, National Yang-Ming University - 一〇七年科技部愛因斯坦年輕學者
2018 MOST Einstein Young Scholar Fellowship - 第15屆國際系統生物學會議學生旅行獎學金
Student Travel Fellowship, the 15th International Conference on Systems Biology (ICSB 2014) - 國科會公費補助赴國外研究
Study Abroad Grant, National Science Council, Taiwan - 第七屆亞洲青年學人計算生物組學會議旅行獎學金
Travel Fellowship, the 7th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB 2013) - 一〇〇年全國大專校院運動會運動精神獎
Sportsmanship Award Winner in 2011 National Intercollegiate Athletic Games (3 winners per year among 9,200 athletes from 164 colleges in Taiwan) - 國科會出席國際學術會議全額補助
Full Sponsorship for Attending International Conference, National Science Council, Taiwan (NSC-100-2922-I-002-025) - 國立臺灣大學生醫電子與資訊學研究所碩士班第一名畢業
Graduated summa cum laude from NTU BEBI - 九十六年大專優秀青年
2007 Outstanding College Youth of the Republic of China - 九十六年國立臺灣大學優秀青年楷模
2007 National Taiwan University Outstanding College Youth (15 winners per year from 32,791 NTU students) - 國立臺灣大學資訊工程學系第七名畢業
Ranked 7th among 108 graduates in NTU CSIE (top 6%) (GPA 3.94) - 三屆國立臺灣大學書卷獎
Three-time Presidential Award Winner (top 5%) in Dept. of Computer Science and Information Engineering (CSIE) of National Taiwan University (NTU) - 九十五年國立臺灣大學傑出表現獎
2006 National Taiwan University Scholarship for Outstanding Performance (15 winners per year from 32,233 NTU students) - 九十四年中華嘉新體育獎學金(大專組)
2005 Chinese Chia-Hsin Sports Scholarship (College Group) - 美國大學委員會學術評估測試(SAT)數理科滿分(800)
Earned a full score (800) on SAT Reasoning Test, Mathematics - 中華民國國光體育獎章
Guo Guang Sports Medal recipient decorated by the President of the Republic of China (athletes’ most prestigious award in Taiwan) - 九十三年基隆市傑出運動員
2004 Outstanding Athlete of Keelung City - 九十二年中華嘉新體育獎學金(高中組)
2003 Chinese Chia-Hsin Sports Scholarship (High School Group) - 九十二年基隆市中等學校優秀青年代表
2003 Outstanding High School Youth of Keelung City - 九十年基隆市十大傑出運動員
2001 Top-Ten Outstanding Athlete of Keelung City - 八十九年末代聯招省聯基隆區榜首
2000 Ranked 1st in the Joint High School Entrance Exam in Taiwan (Area of Keelung City) - 八十九年基隆市中等學校優秀青年代表
2000 Outstanding High School Youth of Keelung City