最新消息
Latest News
亮點成就
Highlight Achievement
  • [碩士論文][2024/03]整合AI集成學習應用於Kinase藥物設計與抑制劑預測 - 恭喜林韋霖、藍靖涵通過口試
  • [計畫申請][2024/02]藉由生成式AI(GPT)改良固碳酵素的結合位點以提高固碳效率 [淨零計畫]
  • [碩士論文][2024/01]CRISPR技術整合人工智慧剖析泛癌核心及必需基因組應用於二十七種癌症 - 恭喜周治瑗通過口試
  • [2023/12/29]本實驗室以「AI老藥新用平台發現超越瑞德西韋的多效型新冠解方」獲得「2023國家新創獎-新創精進獎」[新聞連結]
  • [國際交流][2023/11/23]本實驗室徐子淳、陳澤昕與童政瑜共計3名學生於11月至日本京都大學交換學生,促進研究交流
  • [獲獎][2023/11/12]恭喜陳澤昕於「2023多體學與精準醫學聯合會議」參展海報"Drug-target interaction building modules by the synergy of evolutionary biochemistry and transformer models"獲頒海報展示獎佳作
  • [2023/10/04]「藥物–蛋白質–生化途徑–疾病解卷積應用於藥物作用機制和癌症藥物發展」獲得國家衛生研究院113年度整合性醫藥衛生科技研究計畫審查通過[通過計畫一覽表]
  • [2023/07]歡迎碩班新生:李春香、王之炫、侯亦珊、李威成與陳爰媛加入BioXGEM研究團隊!
  • [生科院體育週][2023/05/11]實驗室參與排球賽
  • [實驗室尾牙出遊][2023/01/13]海屋Cafe披薩+南寮自行車半日遊
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  • [畢業生出路]在教學及人才培育上,培育21位博士及60位碩士,其中7位在大學擔任教職(如國立台灣大學、國立陽明交通大學、國立中興大學、國立中山大學、台北醫學大學、輔仁大學及國防醫學大學)
  • [獲獎][2023/11/27]恭喜陳筠媞論文「以AI老藥新用平台發現甲氨蝶呤的抑制SARS-CoV-2入侵、複製及發炎」榮獲「2023鴻海科技獎」,喜提獎金新台幣25萬元![得獎名單]
  • [獲獎][2023/11/12]恭喜童政瑜於「2023多體學與精準醫學聯合會議」參展海報"Infer Precision Cancer Targets and Drug Responses by Encoding Omics-Drug-Protein-Pathway Associations"獲頒海報展示獎佳作
  • [獲獎][2023/10/28]恭喜陳筠媞論文「研究同源結構靈活性及藥物調控網路的老藥新用策略」參加「2023崇越論文大賞競賽」榮獲博士組佳作論文獎[得獎名單]
  • [學術發表][2023/08/23]本實驗室研究成果Identification of the HNSC88 Molecular Signature for Predicting Subtypes of Head and Neck Cancer發表於International Journal of Molecular Sciences
  • [學術發表][2023/06/10]本實驗室與紐約大學合作研究成果Transcriptomic analysis of World Trade Center particulate Matter-induced pulmonary inflammation and drug treatments發表於Environment International
  • [2022/03]本實驗室主持人楊進木教授榮獲110年度科技部傑出研究獎[獲獎名單連結]
  • [2022/11/30]恭喜博士候選人陳筠媞榮獲國科會核定112年度「補助博士生赴國外研究」(千里馬專案)補助將赴美國哈佛大學研究,補助12個月(NT$900,000)[相關連結]
  • [2021/10/27]本實驗室以「AI老藥新用平台發現超越瑞德西韋的多效型新冠解方」獲得「第18屆國家新創獎-學研新創獎」[新聞連結]
  • [2021/08/03]Congratulations to Yun-Ti Chen for approving the Fellowship Certification of the United Kingdom Higher Education Academy. 恭喜博士生陳筠媞通過英國高等教育學會的會士認證
  • [2021/05/28]恭喜本實驗室主持人楊進木教授榮獲『第十九屆有庠科技獎生技醫藥類』[新聞連結]
  • [記者會][2021/02/23]「AI算出新冠解方-陽明交大發現比瑞德西韋強數十倍的潛力藥」:5家實體報紙、超過10家電視台及超過20家網路媒體報導 [中央社] [自由時報] [中時新聞網] [蘋果即時] [Digitimes] [關鍵評論] [工商時報] [勁報] [科技新報] [央廣新聞]
  • [2020/11/26]恭喜本實驗室主持人楊進木教授榮獲「第三十屆王民寧獎」-學術研究成果對醫藥科技發展、國民健康和國家社會傑出貢獻獎:藥學類
  • [2020/05/08]恭賀本實驗室主持人楊進木教授榮獲中國工程師學會109年度傑出工程教授獎[獲獎公告連結]
  • [2019/08/30]本實驗室受邀TechNews科技新報媒體專訪,報導專題「串聯起基因和藥物,華佗精算的精準醫療新篇章」刊載於TechNews科技新報[新聞連結]
  • [科技部計畫]本實驗室結合計算生物與AI技術,以「智慧計算精準醫藥平台」通過科技部5年50億「AI創新研究中心專案計畫」
  • [科技部展覽]本實驗室發展之「華陀精算」於「2018未來科技展」榮獲「最佳媒體關注獎 (五個獲獎單位,從81未來科技突破獎選出)」及「未來科技突破獎(81團隊,從~400研究團隊選出)」,且受科技部陳良基部長於臉書公開肯定 (唯一研究團隊)[部長臉書連結][新聞連結]
  • [國際合作計劃]賀!本實驗室與京都大學Prof.Akustu合作通過「高等教育深耕計畫」108年深化國際研究合作方案以及京都大學2019國際合作計畫(2019 International Collaborative Research Program of ICR, Kyoto University),後者獲補助經費約1,280,000日圓
  • [創業競賽]賀!本實驗室以「華陀精算」參加BTSC第三屆京台青年創新創業大賽獲得台灣前10強[新聞連結]
  • [國際交流]碩士生蔡宜君透過校內國際處姊妹校交換學生至比利時布魯塞爾自由大學(ULB)
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學術與獲獎
Academic Achievements & Awards
產學與專利
Industry-Academia Collaboration & Patents
國際交流與人才培育
International Exchange & Talent Education
  • [學術發表][2023/01/11]本實驗室與台大醫院、高雄醫學大學等合作腸道菌與糖尿病研究成果Gut microbiota composition can reflect immune responses of latent tuberculosis infection in patients with poorly controlled diabetes發表於Respiratory Research
  • [學術發表][2022/12/21]本實驗室與國防預醫所、清大生科等合作COVID-19相關研究成果Methotrexate inhibition of SARS-CoV-2 entry, infection and inflammation revealed by bioinformatics approach and a hamster model發表於Frontiers in Immunology
  • [學術發表][2022/06/22]本實驗室AI相關研究成果Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties發表於BMC Bioinformatics
  • [學術發表][2022/06/20]本實驗室AI相關研究成果Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations發表於BMC Bioinformatics
  • [學術發表][2022/04/15]本實驗室AI相關研究成果Discovery of moiety preference by Shapley value in protein kinase family using random forest models發表於BMC Bioinformatics
  • [學術發表][2022/01/07]本實驗室與京都大學合作AI GCN相關研究成果A novel graph convolutional neural network for predicting interaction sites on protein kinase inhibitors in phosphorylation,發表於Scientific Reports
  • [學術發表][2022/01/05]本實驗室與台大、高醫合作TB用藥相關研究成果Whole-blood 3-gene Signature as a Decision Aid for Rifapentine-based TB Preventive Therapy,發表於Clinical Infectious Diseases
  • [學術發表][2021/10/19]本實驗室AI相關研究成果Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data發表於Scientific Reports
  • [學術發表][2020/12/29]本實驗室與陽明大學、中研院及國防預醫所共同研究成果Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing,榮登國際頂級期刊[ACS Nano, IF: 14.588]
  • [學術發表][2020/08/12]恭喜本實驗室吳承軒同學研究成果Configurational differences and binding mechanisms of Interleukin-1 receptor-associated kinase 1獲IEEE-BioInformatics And BioEngineering (BIBE) 國際研討會接受發表
  • [學術發表][2020/08/12]恭喜本實驗室林楚芸同學研究成果FooDisNET: a database of food-compound-protein-disease associations 獲IEEE-BioInformatics And BioEngineering (BIBE) 國際研討會接受發表
  • [學術發表][2020/05/22]本實驗室與北醫李嘉華副教授合作研究成果An Integrated Genomic Strategy to Identify CHRNB4 as a Diagnostic/Prognostic Biomarker for Targeted Therapy in Head and Neck Cancer,發表於Cancers
  • [學術發表][2019/11/28]本實驗室與國衛院喻秋華研究員合作研究成果Omics-based Investigation of Diet-induced Obesity Synergized with HBx, Src, and p53 Mutation Accelerating Hepatocarcinogenesis in Zebrafish Model,發表於Cancers
  • [學術發表][2019/07/16]本實驗室研究成果Membrane protein-regulated networks across human cancers(癌症膜蛋白調節網路),榮登國際頂級期刊[Nature Communications]
  • [演講專題][2019/01/25]楊進木教授受邀至「中華民國細胞及分子生物學學會(CSCMB)」第26屆細胞及分子生物新知研討會演講,講題為Molecular interaction family for systems biology and drug design
  • [演講專題][2018/10/09]楊進木教授受邀至國家衛生研究院分子與基因醫學研究所演講,講題為Molecular interaction family for systems biology and drug design
  • [科技部計畫][2017/12]賀!本實驗室結合計算生物與AI技術,以「智慧計算精準醫藥平台」通過科技部5年50億「AI創新研究中心專案計畫」[新聞連結]
  • [科技部計畫][2016/08~2018/07]三總李日清主任獲得二年期科技部計畫
  • [院內計畫][2016/08]MD. Ph.D.學生賴文森醫師獲得 2017 年院內計畫
  • [院內計畫][2016/08]三總李日清主任獲得 2017 年院內計畫
  • [國衛院計畫][2016~2020]獲得五年期國衛院計畫
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  • [專利][2023/10/17]發明人:Jinn-Moon Yang, Po-Shiuan HSIEH, Chih-Heng Huang, Yu-Hsiu Chang, Nikhil PATHAK, Yen-Chao HSU, Yun-Ti Chen, Nung-Yu HSU。名稱:Method against severe acute respiratory syndrome coronavirus 2 infection。美國專利:公告號US11786530B2,公告日2023/10/17。
  • [專利][2023/09/11]發明人:楊進木、謝博軒、黃志恒、張聿秀、倪 齊歐、許彥超、陳筠媞、許農育。名稱:對抗嚴重急性呼吸道症候群冠狀病毒2型感染的方法。中華民國專利:發明第I815341號,公告日2023/09/11。
  • [專利][2020/12/21]楊進木、林峻宇、邱一原、李容羽、何元順、李嘉華。安非他酮和醫藥組合物在製備治療癌症之藥物的用途及抑制腫瘤細胞遷移的方法。中華民國專利:發明第 I713875號,2020/12/21。
  • [產學研合作][2020/05]本實驗室與國防醫學院簽署MOU,合作研發
  • [產學研合作][2020/02]本實驗室與工研院生醫所簽署MOU,合作研發癌症新藥開發
  • [科技部展覽][2019/10/07]本實驗室獲邀參展科技部舉辦,2019 AI創新研究專案國際研討會暨聯合成果展。[網頁連結]
  • [2019/09/16]中華民國經濟部智慧財產局核定「華陀精算」和「BioXGEM」商標註冊通過。[商標註冊證]
  • [2019/05/10]計畫主持人楊進木團隊參與水狸工作室姚南光執行長主辦的「人工智慧與生技醫療產品專利策略布局與攻防」交流會
  • [科技部展覽][2018/12/15]本實驗室發展之「華陀精算」於「2018未來科技展」榮獲「最佳媒體關注獎 (五個獲獎單位,從81未來科技突破獎選出)」及「未來科技突破獎(81團隊,從~400研究團隊選出)」,且受科技部陳良基部長於臉書公開肯定 (唯一研究團隊)[部長臉書連結][新聞連結]
  • [科技部展覽][2018/12/13~15]本實驗室以「華陀精算」參展2018未來科技展並獲選掘金22項獨家亮點技術搶先曝光[新聞連結][技術介紹]
  • [科技部展覽][2018/09]本實驗室以「華陀精算」,自近400件報名技術中脫穎而出為具有「產業應用性」、「科學突破性」之科研成果,獲選參展2018未來科技展(12/13-12/15)
  • [科技部展覽][2018/08]本實驗室以「華陀精算」參展2018 AIslanders' Show AI創新研發成果展
  • [創業競賽][2018/07]賀!本實驗室以「華陀精算」參加BTSC第三屆京台青年創新創業大賽獲得台灣前10強[新聞連結]
  • [US Patent](US20160096848A1)Selective inhibitors for protein kinases and pharmaceutical composition and use thereof
  • [US Patent](US20160068495A1)Compound for promoting apoptosis of cancer cells and a pharmaceutical composition containing the same and uses thereof
  • [Patent][2016/06/21]取得中華民國專利:發明第 I538914 號 蛋白質激酶之選擇性抑制劑、其醫藥組成物及其用途
  • [Patent][2016/06/11]取得中華民國專利:發明第 I536987 號 一種專一性表皮生長因子接受器之選擇性抑制劑、其醫藥組成物及其用途
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  • [碩士學位][2024/03]恭喜藍靖涵獲得碩士學位
  • [碩士學位][2024/03]恭喜林韋霖獲得碩士學位
  • [碩士學位][2024/01]恭喜周治瑗獲得碩士學位
  • [博士學位][2023/07]恭喜李容羽獲得博士學位
  • [博士學位][2023/07]恭喜莊佾軒獲得博士學位
  • [碩士學位][2023/01]恭喜張振寧獲得碩士學位
  • [2023]恭喜專題生李柏毅、魏士閎獲得USC入學
  • [2022/11/30]恭喜博士候選人陳筠媞榮獲國科會核定112年度「補助博士生赴國外研究」(千里馬專案)補助將赴美國哈佛大學研究
  • [碩士學位][2022/07]恭喜楊欣儒獲得碩士學位
  • [碩士學位][2021/08]恭喜陳宜群獲得碩士學位
  • [碩士學位][2020/12]恭喜黃宇薇獲得碩士學位
  • [碩士學位][2020/09]恭喜范祐瑋、林庠豫獲得碩士學位
  • [2019/06]恭賀實驗室畢業學長許凱程升等副教授(臺北醫學大學)
  • [碩/博士學位][2020/07]恭喜Nikhil Pathak獲得博士學位;林楚芸及吳承軒獲得碩士學位
  • [國際交流][2019/11/18]本實驗室2博士生1碩士生共計3名學生將於11月至日本京都大學交換學生,促進研究交流
  • [國際交流][2019/10/07]本實驗室與日本京都大學簽署MOU,進一步促進與京都大學之間的交流合作
  • [國際合作計劃][2019/03]賀!本實驗室與京都大學Prof.Akustu合作通過京都大學2019國際合作計畫(2019 International Collaborative Research Program of ICR, Kyoto University),獲補助經費約1,280,000日圓
  • [國際合作計劃][2019/03]賀!本實驗室與京都大學Prof.Akustu合作通過「高等教育深耕計畫」108年深化國際研究合作方案
  • [碩士學位][2019/03]趙千嫣、李力渝、劉威廷及郭超望獲得碩士學位
  • [碩士學位][2019/03]洪慈懋獲得碩士學位
  • [2019/01]蔡宜君獲得碩士學位
  • [國際交流][2019/02]碩士生蔡宜君透過校內國際處姊妹校交換學生至比利時布魯塞爾自由大學(ULB)
  • [演講專題][2018/11/02]邀請日本京都大學生物資訊中心教授Tatsuya Akutsu演講,講題為Two Approaches for Integrating Omics Data for Analysis of Biological Data
  • [演講專題][2018/11/02]邀請JSPS Post-Doctoral Research Fellow/Guest Research Associate(JSPS外国人特別研究員)林峻宇博士演講,講題為Life as a researcher in Japan - JSPS International Fellowships for Research in Japan
  • [2018/08]陳筠媞獲得碩士學位
  • [2018/06]MD. Ph.D.學生國軍臺中總醫院賴文森醫師獲得博士學位
  • [2017/10]黃星翰獲得博士學位
  • [2017/10]本實驗室畢業學長林峻宇博士獲聘JSPS Post-Doctoral Research Fellow/Guest Research Associate(JSPS外国人特別研究員)
  • [2017/07]李容羽、巫思穎、林思妤獲得碩士學位
  • 恭賀三總李日清主任升等副教授
  • [2016/06]MD. Ph.D.學生三總李日清主任獲得博士學位
  • [2016/07]許元綸、楊方琪、顏佳儀、李哲勳獲得碩士學位
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楊進木 (Jinn-Moon Yang)

Dean
College of Biological Science and Technology

Professor
Drug Design and Systems Biology Laboratory
Department of Biological Science and Technology
Institute of Bioinformatics & Systems Biology, National Yang Ming Chiao Tung University

Address: 75 Po-Ai Street, Hsinchu, Taiwan, 30068
Office & Lab : 415-1 and 404 (Lab) in Jan Qi Biomedical Engineering Building
Tel: 886-3-5712121 ext.56942; Fax: 886-3-5729288
E-mail: moon@nycu.edu.tw

Research Overview

    We have extensively explored new models of computational systems biology and computer-aided drug design to study fundamental theories of molecular interactions (e.g., Molecular Interaction Family) in cells. Our goal is to study drug-protein-pathway-cellular processes-disease relationships, and to establish the links from basic research to translational medicine. To achieve these goals, our team has been committed to integrate artificial intelligence, big data, physico-chemical concepts, and biology for exploring relationships among "molecular interactions", "cell behavior" and "drug discovery principles". To validate our models, we have rigorously collaborated with biological/clinical teams and their bioassay/clinical results support and demonstrate that our models are able to address the challenges and achieve our goals. We have continuously collaborated with researchers from various universities and institutes like NHRI, Academic Sinica, research hospitals (e.g., NTUH, TMU, and KMU) and international institutes (e.g., Kyoto University and Harvard University) for resolving unmet clinical needs and important biological issues.


Achievement

  1. According to Essential Science Indicators (ESI), I have three highly cited papers
  2. Published over 100 papers and I am the corresponding authors for some top journals as follows:
    (1) Genome Biology (IF=18.011)
    (2) 10 papers in Nucleic Acids Research (IF=19.16)
    (3) Nature Communications (IF=17.694)
    (4) ACS Nano (IF=18.027)
    (5) Clinical Infectious Diseases (IF=20.999)
  3. We have over 10 patents and discovered more than 30 lead drugs
  4. My h-index is 36 and the number of citations is over 5,300 (Google scholar)

Awards

  • 2022: 獲科技部傑出研究獎
  • 2021: 獲第18屆國家新創獎-學研新創獎
  • 2021: 獲第十九屆有庠科技講座-生技醫藥類
  • 2021: 獲第三十屆王民寧獎-藥學類傑出貢獻獎
  • 2020: 獲中國工程師學會-傑出工程教授獎,獲總統接見。
  • 2020: 獲科技部「未來科技突破獎」及「最佳媒體關注獎」
  • 2018: 獲國衛院三次執行整合性醫藥衛生科技研究計畫獎牌
  • 2015: 獲科技科技部「績優產學小聯盟」

    Our main research works and achievements can be briefly summarized as follows:
  1. We published Taiwan's first molecular docking paper in top-rank journal and developed it as iGEMDOCK (BMC Bioinformatics, selected as highly cited paper), which is one of widely used docking tools in the world. iGEMDOCK has been downloaded more than 100,000 times and has won the National Innovation Award. Furthermore, aiming to solve the low accuracy of virtual drug screening, we have proposed homopharma (protein-ligand interface family) and SiMMap to greatly improve the accuracy, hit rate of drug discovery, and for investigating drug binding and inhibition mechanisms supported by experimental verification. These results have been published in Genome Biology and Nucleic Acids Research, and we have obtained a US patent.
  2. In computational systems biology, we pioneered innovative theories and tools of protein-protein interaction family and protein module family, and published five papers in Nucleic Acids Research. Through interdisciplinary cooperation and experimental validation, we have successfully discovered biomarkers and identified disease subtypes for the diagnosis and treatment of several cancers (e.g., head and neck cancer and triple-negative breast cancer). Some of these results have been published in Nature Communications (2019) and Cancers (2020).
  3. For cancer precision medicine, we established Cancer Membrane Protein-regulated Networks (CaMPNets) comprising of nearly 2,000 membrane proteins (MP) in 15 diverse cancers to explore their roles in cancers, and then applied CaMPNets to clinical prognostic biomarkers identification and drug development. The cell and animal results validated our models, discovered the target MP and its FDA drug in triple-negative breast cancer. These results were published in Nature Communications (2019) and we obtained two ROC patents (2021) and filed a U.S. patent application.
  4. For COVID-19 drug repurposing, we have integrated pharmacophore-based models and site-moiety maps to uncover flexible active site conformations of SARS-CoV-2 3CL Proteases. Our model discovered Boceprevir (IC50=1.42 μM and EC50=49.89 μM) and Telaprevir (both HCV drugs) and Nelfinavir (HIV drug) as potential COVID-19 drugs (ACS Nano, 2021). Furthermore, we have developed a NetPharma framework, combining homopharma and evolution-based systems biology, to discover a multi-target FDA drug (JMY206, better than Remdesivir) of COVID-19. JMY206 in infected hamster model (validation by Taiwan's only P4 laboratory, National Defense Medical Center) can prevent lung damage and inflammation by modulating neutrophil infiltration and innate/ adaptive immune responses. Based on these results, we prepared papers for publication, applied two U.S. provisional patent applications (ID: 63160507 and 63160518) and clinical applications.

Selected Papers

  1. Huang, H. L., Lee, J. Y., Lo, Y. S., Liu, I. H., Huang, S. H., Huang, Y. W., Lee, M. R., Lee, C. H., Cheng, M. H., Lu, P. L., Wang, J. Y.*, Yang, J. M.*, Chong, I.W. (2022) Whole-blood 3-gene signature as a decision sid for rifapentine-based TB preventive therapy, Clinical Infectious Diseases, doi: 10.1093/cid/ciac003. (IF=20.999)
  2. Huang, Y. W., Hsu, Y. C., Chuang, Y. H., Chen, Y. T., Lin, X. Y., Fan, Y. W., Pathak, N., Yang, J. M.* (2022) Discovery of moiety preference by Shapley value in protein kinase family using random forest models, BMC Bioinformatics, 23, doi: 10.1186/s12859-022-04663-5.
  3. Pathak, N., Chen, Y. T., Hsu, Y. C., Hsu, N. Y., Kuo, C. J., Tsai, H. P., Kang, J. J., Huang, C. H., Chang, S. Y., Chang, Y. H., Liang, P. H. and Yang, J. M.* (2020) Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing, ACS nano, 15(1), 857-872, doi: 10.1021/acsnano.0c07383.
  4. Chuang, Y. H., Huang, S. H., Hung, T. M., Lin, X. Y., Lee, J. Y., Lai, W. S. and Yang, J. M.* (2021) Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data, Scientific Reports, 11:20691.
  5. Lin, C. Y., Lee, C. H., Chuang, Y. H., Lee, J. Y., Chiu, Y. Y., Lee, Y. H. W., Jong, Y. J., Hwang, J. K., Huang, S. H., Chen, L. C., Wu, C. H., Tu, S. H., Ho, Y. S., Yang, J. M.* (2019) Membrane protein-regulated networks across human cancers, Nature Communications, 10(1):3131.
  6. Chiu, Y. Y., Lin, C. T., Huang, J. W., Hsu, K. C., Tseng, J. H., You, S. R., and Yang, J. M.* (2013) KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms, Nucleic Acids Research, 41(Database issue):D430-40.
  7. Hsu, K. C., Cheng, W. C., Chen, Y. F., Wang, W. C., and Yang, J. M.* (2013) Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways, PLOS Computational Biology, 9(7):e1003127.
  8. Lin, C. Y., Lin, Y. W., Yu, S. W., Lo, Y. S., and Yang, J. M.* (2012) MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates, Nucleic Acids Research, 40(Web Server issue):W263-70.
  9. Chu, C. H., Wang, L. Y., Hsu, K. C., Chen, C. C., Cheng, H. H., Wang, S. M., Wu, C. M., Chen, T. J., Li, L. T., Liu, R. Hung, C. L., Yang, J. M.*, Kung, H. J.*, and Wang, W. C.* (2014) KDM4B as a target for prostate cancer: structural analysis and selective inhibition by a novel inhibitor, Journal of Medicinal Chemistry, 57(14):5975-85.
  10. Hsu, K. C., Chen, Y. F., Lin, S. R., and Yang, J. M.* (2011) iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis, BMC Bioinformatics, 12 Suppl 1:S33.
  11. Tung, C. H., Huang, J. W., and Yang, J. M.* (2007) Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database, Genome Biology, 8(3):R31.
  12. Chen, Y. C., Lo, Y. S., Hsu, W. C., and Yang, J. M.* (2007) 3D-partner: a web server to infer interacting partners and binding models, Nucleic Acids Research, 35(Web Server issue):W561-7.
  13. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2006) (PS)(2): protein structure prediction server, Nucleic Acids Research, 34(Web Server issue):W152–7.
  14. Yang, J. M.*, Chen, Y. F., Shen, T. W., Kristal, B. S., and Hsu, D. F. (2005) Consensus scoring criteria for improving enrichment in virtual screening, Journal of Chemical Information and Modeling, 45(4):1134-46.
  15. Yang, J. M.*, and Chen, C. C. (2004) GEMDOCK: A generic evolutionary method for molecular docking, Proteins-Structure Function and Bioinformatics, 55(2):288-304.

Complete Journal Papers

  1. Chen, Y. T., Li, J., Chang, J. N., Luo, Y. C., Yu, W., Chen, L. C. and Yang, J. M.* (2023) Transcriptomic analysis of World Trade Center particulate Matter-induced pulmonary inflammation and drug treatments, Environment International 108027.
  2. Chen, Y. T., Chang, Y. H., Pathak, N., Tzou, S. C., Luo, Y. C., Hsu, Y. C., Li, T. N., Lee, J. Y., Chen, Y. C., Huang, Y. W., Yang, H. J., Hsu, N. Y., Tsai, H. P., Chang, T. Y., Hsu, S. C., Liu, P. C., Chin, Y. F., Lin, W. C., Yang, C. M., Wu, H. L., Lee, C. Y., Hsu, H. L., Liu, Y. C., Chu, J. W., Wang, L. H. C., Wang, J. Y., Huang, C. H., Lin, C. H., Hsieh, P. S., Wu Lee, Y. H., Hung, Y. J. and Yang, J. M.* (2022) Methotrexate inhibition of SARS-CoV-2 entry, infection and inflammation revealed by bioinformatics approach and a hamster model, Frontiers in Immunology 13: 7590.
  3. Huang, H. C., Chen, Y. T., Lin, H. H., Li, Z. Q., Yang, J. M. and Tzou, S. C. (2022) Inhibition of IRAK1 Is an Effective Therapy for Autoimmune Hypophysitis in Mice, International Journal of Molecular Sciences 23.23: 14958.
  4. Li, R., Lee, J. Y., Yang, J. M. and Akutsu, T. (2022) Densest subgraph-based methods for protein-protein interaction hot spot prediction, BMC Bioinformatics 23.1: 1-12.
  5. Li, L. Y. J., Wang, S. Yi., Yang, J. M., Chen, C. J., Tsai, C. Y., Wu, L. Y. Y., Wu, T. F., Wu, C. J. (2022) The Development and Evaluation of a Smartphone-Aided Diagnosis Application to Measure Tympanic Membrane Perforations, Ear, Nose & Throat Journal, 01455613221123361.
  6. Fan, Y. W., Liu, W. H., Chen, Y. T., Hsu, Y. C., Pathak, N., Huang, Y. W., and Yang, J. M.* (2022) Exploring kinase family inhibitors and their moiety preferences using deep SHapley additive exPlanations, BMC Bioinformatics, 23(4), 1-18.
  7. Lin, X. Y., Huang, Y. W., Fan, Y. W., Chen, Y. T., Pathak, N., Hsu, Y. C. and Yang, J. M.* (2022) Identification of pan-kinase-family inhibitors using graph convolutional networks to reveal family-sensitive pre-moieties, BMC Bioinformatics, 23(4), 1-13.
  8. Huang, Y. W., Hsu, Y. C., Chuang, Y. H., Chen, Y. T., Lin, X. Y., Fan, Y. W., Pathak, N. and Yang, J. M.* (2022) Discovery of moiety preference by Shapley value in protein kinase family using random forest models, BMC Bioinformatics, 23(4), 1-14.
  9. Wang, F., Chen, Y. T., Yang, J. M. and Akutsu, T. (2022) A novel graph convolutional neural network for predicting interaction sites on protein kinase inhibitors in phosphorylation, Scientific Reports, 12:229.
  10. Huang, H. L., Lee, J. Y., Lo, Y. S., Liu, I. H., Huang, S. H., Huang, Y. W., Lee, M. R., Lee, C. H., Cheng, M. H., Lu, P. L., Wang, J. Y., Yang, J. M. and Chong, I. W. (2022) Whole-blood 3-gene Signature as a Decision Aid for Rifapentine-based TB Preventive Therapy, Clinical Infectious Diseases.
  11. Chuang, Y. H., Huang, S. H., Hung, T. M., Lin, X. Y., Lee, J. Y., Lai, W. S. and Yang, J. M.* (2021) Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data, Scientific Reports, 11:20691.
  12. Chiou, W. C., Hsu, M. S., Chen, Y. T., Yang, J. M., Tsay, Y. G., Huang, H. C., and Huang, C. (2021) Repurposing existing drugs: identification of SARS-CoV-2 3C-like protease inhibitors, Journal of Enzyme Inhibition and Medicinal Chemistry, 36(1), 147-153.
  13. Chiou, W. C., Chen, J. C., Chen, Y. T., Yang, J. M., Hwang, L. H., Lyu, Y. S., Yang, H. Y. and Huang, C. (2021) The inhibitory effects of PGG and EGCG against the SARS-CoV-2 3C-like protease, Biochemical and biophysical research communications.
  14. Pathak, N., Chen, Y. T., Hsu, Y. C., Hsu, N. Y., Kuo, C. J., Tsai, H. P., Kang, J. J., Huang, C. H., Chang, S. Y., Chang, Y. H., Liang, P. H. and Yang, J. M.* (2020) Uncovering Flexible Active Site Conformations of SARS-CoV-2 3CL Proteases through Protease Pharmacophore Clusters and COVID-19 Drug Repurposing, ACS nano, 15(1), 857-872, doi: 10.1021/acsnano.0c07383.
  15. Hsu, K. C., HuangFu, W. C., Lin, T. E., Chao, M. W., Sung, T. Y., Chen, Y. Y., Pan, S. L., Lee, J. C., Tzou, S. C., Sun, C. M. and Yang, J. M.* (2020) A site-moiety map and virtual screening approach for discovery of novel 5-LOX inhibitors, Scientific reports, 10(1), 1-12.
  16. Chuang, Y. H., Lee, C. H., Lin, C. Y., Liu, C. L., Huang, S. H., Lee, J. Y., Chiu, Y. Y., Lee, J. C., Yang, J. M.* (2020) An Integrated Genomic Strategy to Identify CHRNB4 as a Diagnostic/Prognostic Biomarker for Targeted Therapy in Head and Neck Cancer, Cancers, 12(5), 1324.
  17. Hengphasatporn, K., Plaimas, K., Suratanee, A., Wongsriphisant, P., Yang, J. M., Shigeta, Y., Chavasiri, W., Boonyasuppayakorn, S., Rungrotmongkol, T. (2020) Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells, Molecules, 25(8), 1883.
  18. Yang, W. Y., Rao, P. S., Luo, Y. C., Lin, H. K., Huang, S. H., Yang, J. M.*, Yuh, C. H.* (2019) Omics-based Investigation of Diet-induced Obesity Synergized with HBx, Src, and p53 Mutation Accelerating Hepatocarcinogenesis in Zebrafish Model, Cancers, 11(12), 1899.
  19. Simak, M., Lu, H. H. S., Yang, J. M. (2019) Boolean function network analysis of time course liver transcriptome data to reveal novel circadian transcriptional regulators in mammals, Journal of the Chinese Medical Association, 82(11), 872-880.
  20. Lin, C. Y., Lee, C. H., Chuang, Y. H., Lee, J. Y., Chiu, Y. Y., Lee, Y. H. W., Jong, Y. J., Hwang, J. K., Huang, S. H., Chen, L. C., Wu, C. H., Tu, S. H., Ho, Y. S., Yang, J. M.* (2019) Membrane protein-regulated networks across human cancers, Nature Communications, 10(1):3131.
  21. Lee, J. Y., Lin, S. Y., Lin, C. Y., Chuang, Y. H., Huang, S. H., Tseng, Y. Y., Wang, H. J., Yang, J. M.* (2019) Identification of the PCA29 gene signature as a predictor in prostate cancer, Journal of Bioinformatics and Computational Biology, 17(3):1940006.
  22. Lin, C. Y., Ruan, P. Y., Li, R. M., Yang, J. M., See, S., Song, J. N., Akutsu, T. (2019) Deep learning with evolutionary and genomic profiles for identifying cancer subtypes, Journal of Bioinformatics and Computational Biology, 17(3):1940005.
  23. Lee, C. C., Chang, W. H., Chang, Y. S., Yang, J. M., Chang, C. S., Hsu, K. C., Chen, Y. T., Liu, T. Y., Chen, Y. C., Lin, S. Y., Wu, Y. C., Chang, J. G. (2019) Alternative splicing in human cancer cells is modulated by the amiloride derivative 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxide, Molecular Oncology, 13(8):1744-1762.
  24. Huang, L. C., Tam, K. W., Liu, W. N., Lin, C. Y., Hsu, K. W., Hsieh, W. S., Chi, W. M., Lee, A. W., Yang, J. M., Lin, C. L., Lee, C. H. (2018) CRISPR/Cas9 Genome Editing of Epidermal Growth Factor Receptor Sufficiently Abolished Oncogenicity in Anaplastic Thyroid Cancer, Disease Markers, 3835783.
  25. Huang, S. H., Lo, Y. S., Luo, Y. C., Tseng, Y. Y., Yang, J. M.* (2017) A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations, BMC Systems Biology, 12(2):13.
  26. Pathak, N., Lai, M. L., Chen, W. Y., Hsieh, B. W., Yu, G. Y., Yang, J. M.* (2017) Pharmacophore anchor models of flaviviral NS3 proteases lead to drug repurposing for DENV infection, BMC Bioinformatics, 18(16):548.
  27. Lai, W. S., Cheng, S. Y., Lin, Y. Y., Yang, P. L., Lin, H. C., Cheng, L. H., Yang, J. M., Lee, J. C. (2017) Clinical assessment of diode laser-assisted endoscopic intrasphenoidal vidian neurectomy in the treatment of refractory rhinitis, Lasers in Medical Science, 32(9):2097-104.
  28. Huang, L. C., Lin, C. L., Qiu, J. Z., Lin, C. Y., Hsu, K. W., Tam, K. W., Lee, J. Y., Yang, J. M., Lee, C. H. (2017) Nicotinic Acetylcholine Receptor Subtype Alpha-9 Mediates Triple-Negative Breast Cancers Based on a Spontaneous Pulmonary Metastasis Mouse Model, Frontiers in Cellular Neuroscience, 11:336.
  29. Hsu, K. C., Hung, H. C., HuangFu, W. C., Sung, T. Y., Lin, T. E., Fang, M. Y., Chen, I. J., Pathak, N., Hsu, J. T. A., Yang, J. M.* (2017) Identification of neuraminidase inhibitors against dual H274Y/I222R mutant strains, Scientific Reports, 7(1):12336.
  30. Lin, H. C., Huan, Y. S., Chu, Y. H., Liu, S. C., Shangkuan, W. C., Lai, W. S., Yang, J. M., Lin, Y. S., Ma, K. H., Lee, J. C. (2017) Vascular anatomy is a determining factor of successful submental flap raising: a retrospective study of 70 clinical cases, PeerJ, 5:e3606.
  31. Hsu, H. H., Hsu, Y. C., Chang, L. J., Yang, J. M.* (2017) An integrated approach with new strategies for QSAR models and lead optimization, BMC Genomics, 18(Suppl 2):104.
  32. Hsu, K. C., Liu, C. Y., Lin, T. E., Hsieh, J. H., Sung, T. Y., Tseng, H. J., Yang, J. M., Huang, W. J. (2017) Novel Class IIa-Selective Histone Deacetylase Inhibitors Discovered Using an in Silico Virtual Screening Approach, Scientific Reports, 7(1):3228.
  33. Lai, W. S., Lin, Y. Y., Shih, C. P., Chen, H. C., Yang, P. L., Chu, Y. H., Yang, J. M., Lee, J. C. (2017) Clinical application of suction-tube-assisted septal submucosal dissection for endoscopic septoplasty, European Archives of Oto-rhino-laryngology, 274(3):1471-1475.
  34. Das, A., Adak, A. K., Ponnapalli, K., Lin, C. H., Hsu, K. C., Yang, J. M., Hsu, T. A., Lin, C. C. (2016) Design and synthesis of 1,2,3-triazole-containing N-acyl zanamivir analogs as potent neuraminidase inhibitors, European Journal of Medicinal Chemistry, 123:397-406.
  35. Huang, K. W., Hsu, K. C., Chu, L. Y., Yang, J. M., Yuan, H. S., Hsiao, Y. Y. (2016) Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES), Journal of Medicinal Chemistry, 59(17):8019-29.
  36. Lin, C. H., Wu, Y. R., Yang, J. M., Chen, W. L., Chao, C. Y., Chen, I. C., Lin, T. H., Wu, Y. C., Hsu, K. C., Chen, C. M., Lee, G. C., Hsieh-Li, H. M., Lee, C. M., Lee-Chen, G. J., (2016) Novel Lactulose and Melibiose Targeting Autophagy to Reduce PolyQ Aggregation in Cell Models of Spinocerebellar Ataxia 3, CNS & Neurological Disorders - Drug Targets, 15(3):351-9.
  37. Tsai, W. C., Yang, J. M., Liu, S. C., Chu, Y. H., Lai, W. S., Lin, Y. S., and Lee, J. C. (2015) Management of different kinds of head and neck defects with the submental flap for reconstruction, European Archives of Oto-Rhino-Laryngology, 272(12):3815-9.
  38. Hsu, K. C., Sung, T. Y., Lin, C. T., Chiu, Y. Y., Hsu, J. T., Hung, H. C., Sun, C. M., Barve, I., Chen, W. L., Huang, W. C., Huang, C. T., Chen, C. H., and Yang, J. M.* (2015) Anchor-based classification and type-C inhibitors for tyrosine kinases, Scientific Reports, 5:10938.
  39. Lee, G. C., Lin, C. H., Tao, Y. C., Yang, J. M. , Hsu, K. C., Huang, Y. J., Huang, S. H., Kung, P. J., Chen, W. L., Wang, C. M., Wu, Y. R., Chen, C. M., Lin, J. Y., Hsieh-Li, H. M., and Lee-Chen, G. J. (2015) The potential of lactulose and melibiose, two novel trehalase-indigestible and autophagy-inducing disaccharides, for polyQ-mediated neurodegenerative disease treatment, Neurotoxicology, 48:120-30.
  40. Chao, J. I., Wang, S. P., Wu, Y. H., Yang, J. M., Chen, CPA (2015) A novel EGFR inhibitor SP101 blocks survivin and tumor growth in the human non-small cell lung carcinoma, FASEB Journal, vol. 29 no. 1 Supplement LB113.
  41. Lin, C. Y., Lee, T. L., Chiu, Y. Y., Lin, Y. W., Lo, Y. S., Lin, C. T., and Yang, J. M.* (2015) Module organization and variance in protein-protein interaction networks, Scientific Reports, 5:9386.
  42. Lee, J. C., Lai, W. S., Ju, D. T., Chu, Y. H., and Yang, J. M. (2015) Diode laser assisted minimal invasive sphenoidotomy for endoscopic transphenoidal pituitary surgery: Our technique and results, Lasers in Surgery and Medicine, 47(3):239-42.
  43. Lo, Y. S., Huang, S. H., Luo, Y. C., Lin, C. Y., and Yang, J. M.* (2015) Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping, Plos One, 10(1):e0116347.
  44. Chiu, Y. Y., Tseng, J. H., Liu, K. H., Lin, C. T., Hsu, K. C. and Yang, J. M.* (2014) Homopharma: A new concept for exploring the molecular binding mechanisms and drug repurposing, BMC Genomics, 15 Suppl 9:S8. (Best paper award in The 13th International Conference on Bioinformatics)
  45. Lee, C. C., Maestre‐Reyna, M., Hsu, K. C., Wang, H. C., Liu, C. I., Jeng, W. Y., Lin, L. L., Wood, R., Chou, C. C., Yang, J. M., and Wang, A. H. (2014) Crowning Proteins: Modulating the Protein Surface Properties using Crown Ethers, Angewandte Chemie International Edition, 53(48):13054-8.
  46. Ma, N., Lai, C.-S., Chung, C.-H., Yang, J.-M., Hsu, K.-C., Chen, C.-Y., Chung, T.-S., Li, S., Ho, C.-T., and Pan, M.-H. (2014) 5-Demethyltangeretin is more potent than tangeretin in inhibiting dimethylbenz(a)anthracene (DMBA)/12-O-tetradecanoylphorbol-13-acetate (TPA)-induced skin tumorigenesis, Journal of Functional Foods, 11:528-37.
  47. Chu, C. H., Wang, L. Y., Hsu, K. C., Chen, C. C., Cheng, H. H., Wang, S. M., Wu, C. M., Chen, T. J., Li, L. T., Liu, R. Hung, C. L., Yang, J. M.*, Kung, H. J.*, and Wang, W. C.* (2014) KDM4B as a target for prostate cancer: structural analysis and selective inhibition by a novel inhibitor, Journal of Medicinal Chemistry, 57(14):5975-85.
  48. Wang, H. C., Ho, C. H., Hsu, K. C., Yang, J. M. and Wang, A.H. (2014) DNA mimic proteins: functions, structures, and bioinformatic analysis, Biochemistry, 53(18):2865-74.
  49. Wang, H. C., Hsu, K. C., Yang, J. M.Wu, M. L., Ko, T. P., Lin, S. R. and Wang, A. H. (2014) Staphylococcus aureus protein SAUGI acts as a uracil-DNA glycosylase inhibitor, Nucleic Acids Research, 42(2):1354-64.
  50. Liu, I. H., Lo, Y. S., and Yang, J. M.* (2013) Genome-wide structural modelling of TCR-pMHC interactions, BMC Genomics, 14 Suppl 5:S5.
  51. Chen, S. H., Lin, S. W., Lin, S. R., Liang, P. H., and Yang, J. M.* (2013) Moiety-Linkage Map Reveals Selective Nonbisphosphonate Inhibitors of Human Geranylgeranyl Diphosphate Synthase, Journal of Chemical Information and Modeling, 53(9):2299-311.
  52. Hsu, K. C., Cheng, W. C., Chen, Y. F., Wang, W. C., and Yang, J. M.* (2013) Pathway-based screening strategy for multitarget inhibitors of diverse proteins in metabolic pathways, PLOS Computational Biology, 9(7):e1003127.
  53. Chen, Y. J., Kay, N., Yang, J. M., Lin, C. T., Chang, H. L., Wu, Y. C., Fu, C. F., Chang, Y., Lo, S., Hou, M. F., Lee, Y. C., Hsieh, Y. C., and Yuan, S. S. (2013) Total Synthetic Protoapigenone WYC02 Inhibits Cervical Cancer Cell Proliferation and Tumour Growth through PIK3 Signalling Pathway, Basic & Clinical Pharmacology & Toxicology, 113(1):8-18.
  54. Hsu, K. C., Hung, H. C., Horng, J. T., Fang, M. Y., Chang, C. Y., Li, L. T., Chen, I. J., Chen, Y. C., Chou, D. L., Chang, C. W., Hsieh, H. P., Yang, J. M.*, and J. T., Hsu*. (2013) Parallel screening of wild-type and drug-resistant targets for anti-resistance neuraminidase inhibitors, PLoS ONE, 8(2):e56704.
  55. Lin, C. Y., Chen, Y. C., Lo, Y. S., and Yang, J. M.* (2013) Inferring homologous protein-protein interactions through pair position specific scoring matrix, BMC Bioinformatics, 14 Suppl 2:S11.
  56. Liu, I. H., Lo, Y. S. and Yang, J. M.* (2013) Template-based scoring functions for visualising biological insights of H-2K(b)-peptide-TCR complexes, International Journal of Data Mining and Bioinformatics, 8(3):326-37.
  57. Lin, C. H., Chang, T. C., Das, A., Fang, M. Y., Hung, H. C., Hsu, K. C., Yang, J. M., M, v. I., Mong, K. K., Hsu, T. A., and Lin, C. C. (2013) Synthesis of acylguanidine zanamivir derivatives as neuraminidase inhibitors and the evaluation of their bio-activities, Organic & Biomolecular Chemistry, 11(24):3943-8.
  58. Chiu, Y. Y., Lin, C. T., Huang, J. W., Hsu, K. C., Tseng, J. H., You, S. R., and Yang, J. M.* (2013) KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms, Nucleic Acids Research, 41(Database issue):D430-40.
  59. Chiu, Y. Y., Lin, C. Y., Lin, C. T., Hsu, K. C., Chang, L. Z., and Yang, J. M.* (2012) Space-related pharma-motifs for fast search protein binding motifs and polypharmacological targets, BMC Genomics, 13 Suppl 7:S21.
  60. Huang, J. W., Lin, W. F., and Yang, J. M.* (2012) Antigenic sites of H1N1 influenza virus hemagglutinin revealed by natural isolates and inhibition assays, Vaccine, 30(44):6327-37.
  61. Lin, C. Y., Lin, Y. W., Yu, S. W., Lo, Y. S., and Yang, J. M.* (2012) MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates, Nucleic Acids Research, 40(Web Server issue):W263-70.
  62. Hsu, S. C., Chang, C. P., Tsai, C. Y., Hsieh, S. H., Wu-Hsieh, B. A., Lo, Y. S., and Yang, J. M. (2012) Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes, Immunology, 136(2):139-52.
  63. Chang, K. M., Chen, S. H., Kuo, C. J., Chang, C. K., Guo, R. T., Yang, J. M., and Liang, P. H. (2012) Roles of amino acids in the Escherichia coli octaprenyl diphosphate synthase active site probed by structure-guided site-directed mutagenesis, Biochemistry, 51(16):3412-9.
  64. Cheng, W. C., Chen, Y. F., Wang, H. J., Hsu, K. C., Lin, S. C., Chen, T. J., Yang, J. M.*, and Wang, W. C. (2012) Structures of Helicobacter pylori shikimate kinase reveal a selective inhibitor-induced-fit mechanism, PLoS ONE, 7(3):e33481.
  65. Hsu, K. C., Cheng, W. C., Chen, Y. F., Wang, H. J., Li, L. T., Wang, W. C., and Yang, J. M.* (2012) Core site-moiety maps reveal inhibitors and binding mechanisms of orthologous proteins by screening compound libraries, PLoS ONE, 7(2):e32142.
  66. Hsu, K. C., Chen, Y. F., and Yang, J. M.* (2012) GemAffinity: a scoring function for predicting binding affinity and virtual screening, International Journal of Data Mining and Bioinformatics, 6(1):27-41.
  67. Clinciu, D. L., Yang, J. M., Hsu, K. C., Lo, C. C., Wallace, S., and Yu, H. C. (2011) The relevance of protein-ligand interaction profiles in computer-aided novel compound design and applications, Current Bioinformatics, 6(3):383-8.
  68. Liu, I. H., Lo, Y. S., and Yang, J. M.* (2011) PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes, Nucleic Acids Research, 39(Web Server issue):W254-60.
  69. Tsai, C. C., Liu, H. F., Hsu, K. C.,Yang, J. M., Chen, C. P., Liu, K. K., Hsu, T. S., and Chao, J. I. (2011) 7-Chloro-6-piperidin-1-yl-quinoline-5,8-dione (PT-262), a novel ROCK inhibitor blocks cytoskeleton function and cell migration, Biochemical Pharmacology, 81(7):856-65.
  70. Hsu, K. C., Chen, Y. F., Lin, S. R., and Yang, J. M.* (2011) iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis, BMC Bioinformatics, 12 Suppl 1:S33.
  71. Huang, J. W., and Yang, J. M.* (2011) Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses, BMC Bioinformatics, 12 Suppl 1:S31.
  72. Clinciu, D. L., Chen, Y. F., Ko, C. N., Lo, C. C., and Yang, J. M.* (2010) TSCC: Two-Stage Combinatorial Clustering for virtual screening using protein-ligand interactions and physicochemical features, BMC Genomics, 11 Suppl 4:S26.
  73. Lo, Y. S., Chen, Y. C., and Yang, J. M.* (2010) 3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes, BMC Genomics, 11 Suppl 3:S7.
  74. Chen, Y. F., Hsu, K. C., Lin, S. R., Wang, W. C., Huang, Y. C., and Yang, J. M.* (2010) SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties, Nucleic Acids Research, 38(Web Server issue):W424-30.
  75. Lo, Y. S., Lin, C. Y., and Yang, J. M.* (2010) PCFamily: a web server for searching homologous protein complexes, Nucleic Acids Research, 38(Web Server issue):W516-22.
  76. Liu, K. P., Hsu, K. C., Huang, J. W., Chang, L. S., and Yang, J. M.* (2010) ATRIPPI: An atom-residue preference scoring function for protein-protein interactions, International Journal on Artificial Intelligence Tools, 19(3):251-66.
  77. Chin, K. H., Lee, Y. C., Tu, Z. L., Chen, C. H., Tseng, Y. H., Yang, J. M.*, Ryan, R. P., McCarthy, Y., Dow, J. M., Wang, A. H. J., and Chou, S. H. (2010) The c-AMP receptor-like protein clp is a novel c-di-gmp receptor linking cell-cell signaling to virulence gene expression in xanthomonas campestris, Journal of Molecular Biology, 396(3):646-62.
  78. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2009) (PS)(2)-v2: template-based protein structure prediction server, BMC Bioinformatics, 10:366.
  79. Lin, F. K., Pan, C. L., Yang, J. M., Chuang, T. J., and Chen, F. C. (2009) CAPIH: A web interface for comparative analyses and visualization of host-HIV protein-protein interactions, BMC Microbiology, 9:164
  80. Chen, C. C., Lin, C. Y., Lo, Y. S., and Yang, J. M.* (2009) PPISearch: a web server for searching homologous protein-protein interactions across multiple species, Nucleic Acids Research, 37(Web Server issue):W369-75.
  81. Hung, H. C., Tseng, C. P., Yang, J. M., Ju, Y. W., Tseng, S. N., Chen, Y. F., Chao, Y. S., Hsieh, H. P., Shih, S. R., and Hsu, J. T. A. (2009) Aurintricarboxylic acid inhibits influenza virus neuraminidase, Antiviral Research, 81(2):123-31.
  82. Huang, J. W., King, C. C., and Yang, J. M.* (2009) Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses, BMC Bioinformatics, 10 Suppl 1:S41.
  83. Yao, Y. Y., Shrestha, K. L., Wu, Y. J., Tasi, H. J., Chen, C. C., Yang, J. M., Ando, A., Cheng, C. Y., and Li, Y. K. (2008) Structural simulation and protein engineering to convert an endo-chitosanase to an exo-chitosanase, Protein Engineering Design & Selection, 21(9):561-6.
  84. Yang, M. C., Guan, H. H., Yang, J. M., Ko, C. N., Liu, M. Y., Lin, Y. H., Huang, Y. C., Chen, C. J., and Mao, S. J. T. (2008) Rational design for crystallization of beta-lactoglobulin and Vitamin D(3) complex: revealing a secondary binding site, Crystal Growth & Design, 8(12):4268-76.
  85. Yang, M. C., Guan, H. H., Liu, M. Y., Lin, Y. H.,Yang, J. M., Chen, W. L., Chen, C. J., and Mao, S. J. T. (2008) Crystal structure of a secondary vitamin D(3) binding site of milk beta-lactoglobulin, Proteins-Structure Function and Bioinformatics, 71(3):1197-210.
  86. Yang, C. Y., Chang, C. H., Yu, Y. L., Lin, T. C. E., Lee, S. A., Yen, C. C., Yang, J. M., Lai, J. M., Hong, Y. R., Tseng, T. L., Chao, K. M., and Huang, C. Y. F. (2008) PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database, Bioinformatics, 24(16):i14-20.
  87. Chiu, Y. Y., Hwang, J. K., and Yang, J. M.* (2008) Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformations, Journal of Computational Chemistry, 29(9):1364-73.
  88. Chang, Y. L., Tsai, H. K., Kao, C. Y., Chen, Y. C., Hu, Y. J., and Yang, J. M.* (2008) Evolutionary conservation of DNA-contact residues in DNA-binding domains, BMC Bioinformatics, 9 Suppl 6:S3.
  89. Yang, J. M., Chen, Y. F., Tu, Y. Y., Yen, K. R., and Yang, Y. L. (2007) Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors, PLoS ONE, 2(5):e428.
  90. Tung, C. H., and Yang, J. M.* (2007) fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies, Nucleic Acids Research, 35(Web Server issue):W438-43.
  91. Tung, C. H., Huang, J. W., and Yang, J. M.* (2007) Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database, Genome Biology, 8(3):R31.
  92. Chen, Y. C., Lo, Y. S., Hsu, W. C., and Yang, J. M.* (2007) 3D-partner: a web server to infer interacting partners and binding models, Nucleic Acids Research, 35(Web Server issue):W561-7.
  93. Yang, J. M.*, and Tung, C. H. (2006) Protein structure database search and evolutionary classification, Nucleic Acids Research, 34(13):3646-59.
  94. Chen, C. C., Hwang, J. K., and Yang, J. M.* (2006) (PS)(2): protein structure prediction server, Nucleic Acids Research, 34(Web Server issue):W152–7.
  95. Yang, J. M.*, and Shen, T. W. (2005) A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators, Proteins-Structure Function and Bioinformatics, 59(2):205-20.
  96. Yang, J. M.*, Chen, Y. F., Shen, T. W., Kristal, B. S., and Hsu, D. F. (2005) Consensus scoring criteria for improving enrichment in virtual screening, Journal of Chemical Information and Modeling, 45(4):1134-46.
  97. Yang, J. M.*, and Chen, C. C. (2004) GEMDOCK: A generic evolutionary method for molecular docking, Proteins-Structure Function and Bioinformatics, 55(2):288-304.
  98. Yang, J. M.* (2004) Development and evaluation of a generic evolutionary method for protein-ligand docking, Journal of Computational Chemistry, 25(6):843-57.
  99. Tsai, H. K., Yang, J. M., Tsai, Y. F., and Kao, C. Y. (2004) Some issues of designing genetic algorithms for traveling salesman problems, Soft Computing, 8(10):689-97.
  100. Tsai, H. K., Yang, J. M., Tsai, Y. F., and Kao, C. Y. (2004) An evolutionary algorithm for large traveling salesman problems, IEEE Transactions on Systems Man and Cybernetics Part B-Cybernetics, 34(4):1718-29.
  101. Tsai, H. K., Yang, J. M.*, Tsai, Y. F., and Kao, C. Y. (2004) An evolutionary approach for gene expression patterns, IEEE Transactions on Information Technology in Biomedicine, 8(2):69-78.
  102. Yu, C. S., Wang, J. Y., Yang, J. M., Lyu, P. C., Lin, C. J., and Hwang, J. K. (2003) Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets, Proteins-Structure Function and Bioinformatics, 50(4):531-6.
  103. Tsai, H. K., Yang, J. M., Tsai, Y. F., and Kao, C. Y. (2003) Heterogeneous selection genetic algorithms for traveling salesman problems, Engineering Optimization, 35(3):297-311.
  104. Lin, E. S., Yang, J. M., and Yang, Y. S. (2003) Modeling the binding and inhibition mechanism of nucleotides and sulfotransferase using molecular docking, Journal of the Chinese Chemical Society, 50(3B):655-63.
  105. Chuang, C. C., Chen, C. Y., Yang, J. M., Lyu, P. C., and Hwang, J. K. (2003) Relationship between protein structures and disulfide bonding patterns, Proteins-Structure Function and Genetics, 53(1):1-5.
  106. Chu, Y. W., and Yang, J. M.* (2003) Finding regularity in various types of secondary protein structures, Journal of Information Science and Engineering, 19:943-952.
  107. Yang, J. M.*, Tsai, C. H., Hwang, M. J., Tsai, H. K., Hwang, J. K., and Kao, C. Y. (2002) GEM: A Gaussian evolutionary method for predicting protein side-chain conformations, Protein Science, 11(8):1897-907.
  108. Yang, J. M.*, Lin, C. J., and Kao, C. Y. (2002) A robust evolutionary algorithm for global optimization, Engineering Optimization, 34(5):405-425.
  109. Yang, J. M.*, and Kao, C. Y. (2001) Efficient evolutionary algorithm for the thin-film synthesis of inhomogeneous optical coatings, Applied Optics, 40(19):3256-67.
  110. Yang, J. M.*, and Kao, C. Y. (2001) An evolutionary algorithm for the synthesis of multilayer coatings at oblique light incidence, Journal of Lightwave Technology, 19(4):559-70.
  111. Yang, J. M.*, and Kao, C. Y. (2001) A robust evolutionary algorithm for training neural networks, Neural Computing & Applications, 10(3):214-30.
  112. Yang, J. M.*, Horng, J. T., Lin, C. J., and Kao, C. Y. (2001) Optical coating designs using the family competition evolutionary algorithm, Evolutionary Computation, 9(4):421-43.
  113. Yang, J. M.*, and Kao, C. Y. (2000) Integrating adaptive mutations and family competition into genetic algorithms as function optimizer, Soft Computing, 4(2):89-102.
  114. Yang, J. M.*, and Kao, C. Y. (2000) A family competition evolutionary algorithm for automated docking of flexible ligands to proteins, IEEE Transactions on Information Technology in Biomedicine, 4(3):225-37.
  115. Yang, J. M.*, and Kao, C. Y. (2000) Flexible ligand docking using a robust evolutionary algorithm, Journal of Computational Chemistry, 21(11):988-998.
  116. Yang, J. M.*, Horng, J. T., and Kao, C. Y. (2000) A genetic algorithm with adaptive mutations and family competition for training neural networks, International Journal of Neural Systems, 10(5):333-52.

Patents

  1. Yang, J. M., Hsu, K. C., Sung T. Y., Lin S. R., Wang Y. M., Hsu, K. M., Lin, H. P., and Liu, W. C., Selective inhibitors for protein kinases and pharmaceutical composition and use thereof. US20160096848A1, 2016/04/07
  2. Chao, J. I., Wang, S. P., Chen, C. P., Yin, K. H., Yang, J. M., and Wu, Y. H., Compound for promoting apoptosis of cancer cells and a pharmaceutical composition containing the same and uses thereof. US20160068495A1, 2016/03/10
  3. Wang, W. C., Cheng, W. C., and Yang, J. M., Method of inhibiting the growth of Helicobacter pylori. US8175860B2, 2012/05/08
  4. 楊進木、林峻宇、邱一原、李容羽、何元順、李嘉華。安非他酮和醫藥組合物在製備治療癌症之藥物的用途及抑制腫瘤細胞遷移的方法。中華民國專利:發明第 I713875號,2020/12/21。
  5. 楊進木、許凱程、宋姿瑩、林伸融、王雲銘、許光美、林欣平、劉婉婷。蛋白質激酶之選擇性抑制劑、其醫藥組成物及其用途。中華民國專利:發明第 I538914 號,2016/06/21。
  6. 楊進木、許凱程、黃兆祺、陳文亮、趙瑞益、黃文傑。一種專一性表皮生長因子接受器之選擇性抑制劑、其醫藥組成物及其用途。中華民國專利:發明第 I536987 號,2016/06/11。
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博士班畢業生 (共19名)

姓名___________________________ 畢業學年度_____________________ 目前任職_______________________
劉宛欣 (共同指導) 2021 北一女中教師
Nikhil Pathak 2020 普睿思股份有限公司
史蔓莉 (共同指導) 2018 --
黃星翰 2017 圖策科技
陳世勳 2013 國立臺灣大學
林志達 2013 癌症顧問公司
邱一原 2013 台積電
林峻宇 2013 國立陽明交通大學
劉怡馨 2012 --
羅宇書 2011 台達電子
許凱程 2010 臺北醫學大學
丹尼爾 (共同指導) 2010 --
黃章維 2010 奎克生技光電股份有限公司
陳志杰 (共同指導) 2009 國立中山大學
陳彥甫 2009 中環股份有限公司
董其樺 2008 輔仁大學
陳俊辰 2008 --
張耀霖 (共同指導) 2008 --
朱彥煒 (共同指導) 2005 國立中興大學

MD. Ph.D.畢業生 (共2名)

姓名___________________________ 畢業學年度_____________________ 目前任職_______________________
賴文森 2017 國軍臺中 803 總醫院
李日清 2015 國防醫學院 三軍總醫院

碩士班畢業生 (共60名)

姓名___________________________ 畢業學年度_____________________ 目前任職_______________________
楊欣儒 2021 科林研發
陳宜群 2021 --
黃宇薇 2020 聯發科技
林庠豫 2020 圖策科技
范祐瑋 2020 --
吳承軒 2019 慧邦科技
林楚芸 2019 尚禾亞
李可愉 2019 --
蔡宜君 2018 Lydia.ai
劉威廷 2018 盟基生技
趙千嫣 2018 聯發科技
李力渝 2018 國立台灣大學醫學院醫學系內科
郭超望 2018 chimes AI
洪慈懋 2018 台智基因體股份有限公司
陳筠媞 (共同指導) 2018 --
林思妤 2016 --
巫思穎 2016 台積電
李容羽 2016 --
李哲勳 2016 --
楊方琪 2015 --
許元綸 2015 台灣國際商業機器股份有限公司
顏佳儀 2015 合一生技
沈培鈞 2014 台灣活性脂質股份有限公司
林傳東 2014 --
陳怡君 2014 台積電
莊佾軒 2014 --
曾仁琥 2014 美創資通
林昱葦 2014 趨勢科技
劉冠秀 2013 Supermicro
林伸融 2013 --
李采凌 2012 --
徐瑋澤 2012 --
游尚文 2011 --
李淩婷 2011 正文科技
尤宣人 2011 趨勢科技
許彥超 2011 --
黃御哲 2010 --
林怡瑋 2010 行動基因生技股份有限公司
林韋帆 2010 --
張力仁 2009 --
林峻宇 2009 國立陽明交通大學
陳彥修 2008 --
劉康平 2008 --
陳祐德 2007 --
羅宇書 2007 台達電子
許凱程 2006 臺北醫學大學
陳右儒 2006 聯發科技
陳永強 2005 新竹馬偕醫院
楊登凱 2005 --
葛振寧 2005 --
黃章維 2005 奎克生技光電股份有限公司
陳宏助 2004 --
張立人 2004 --
林柏村 2004 --
邱一原 2004 台積電
董其樺 2004 輔仁大學
林建宏 2003 --
沈再威 2003 --
陳彥甫 2003 中環股份有限公司
張育祥 2002 --

PI

楊進木 (Jinn-Moon Yang)
  • Computer-aided drug design
  • Systems Biology
  • Structural Bioinformatics
  • Machine Learning
  • Editorial Boards of PLoS ONE and Frontiers in Bioinformatics and Computational Biology
  • Member of Bioinformatics and Systems Biology Society Taiwan
  • Professor, Institute of Systems Biology Bioinformatics, National Chiao-Tung University
  • Win the 2007 National Innovation Award, iGEMDOCK: A graphical-automatic drug system for docking, screening and post-analysis
  • Win outstanding Research Award at the National Chiao-Tung University (2006, 2009-2014)
  • The total number of citations over 2,200 and my H-index is 26 based on Google scholar index

Postdoctoral Researchers

李容羽 (Jung-Yu Lee)
Major Fields in BS: Animal Science
Molecular interaction networks for tumorigenesis and metastasis
E-mail: leejungyu1012@gmail.com

Assistants

齊婉葶 (Wan-Ting Chi)
Administrative Assistant
E-mail: momochi1230@gmail.com

Ph.D. Students

許彥超 (Yen-Chao Hsu; Jerry)
Major Fields in BS: Computer Science
Protein-Ligand Family
E-mail: yenchaohsu@gmail.com
許農育 (Nung-Yu Hsu; Vincent)
Major Fields in BS: Computer Science
E-mail: jack8264@gmail.com
陳筠媞 (Yun-Ti Chen)
Major Fields in BS: Applied materials and optoelectronic engineering
E-mail: ytchen.bi07g@nctu.edu.tw

Master Students

王任琮 (Ren-Cong Wang)
Major Fields in BS: Applied Biotechnology and Animal Science
藍靖涵 (Ching-Han Lan)
Major Fields in BS: Applied Bioscience Technology
周治瑗 (Chi-hyuan Chou)
Major Fields in BS: Applied Life science
林韋霖 (Wei-Lin Lin)
Major Fields in BS: Biotechnology
林佳諦 (Jia-Di Lin)
Major Fields in BS: General Biology
張偉誠 (Wei-Cheng Chang)
Major Fields in BS: Psychology
楊子萱 (Tzu-Hsuan Yang)
Major Fields in BS: Animal Science
童政瑜 (Zheng-Yu Tong)
Major Fields in BS: Biotechnology
陳澤昕 (Tze-Shin Chen)
Major Fields in BS: Life Science
魏雅各 (Ya-Ko Wei)
Major Fields in BS: Mathematics
徐子淳 (Zi-Chun Hsu)
Major Fields in BS: Life Science
葉昱庭 (Yu-Ting Yeh)
Major Fields in BS: Biological Science and Technology        
王之炫 (Chih-Hsuan Wang)
Major Fields in BS: Computer Science        
李威成 (Wei-Cheng Lee)
Major Fields in BS: Biological Science and Technology        
李春香 (Chun-Xiang Li)
Major Fields in BS: Biological Science and Technology        
陳爰媛 (Yuan-Yuan Chen)
Major Fields in BS: Public Health        
侯亦珊 (Yi-Shan Hou)
Major Fields in BS: Bioscience Technology        

Undergraduate Students

吳又欣 (You-Hsin Wu)
Major Fields in BS: Biological Science and Technology        
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Alumni

Ph.D.

Name Major Fields in BS Memo (Research Groups, Research Directions, Publications)
Nikhil Pathak Pharmacy July 2020, Ph.D.
Drug Design for Pathogenic and infectious Diseases - Dengue
黃星翰
(Sing-Han Huang)
Biochemical Science and Technology October 2017, Ph.D.
Human Brain Aging and Neurodegeneration Disease
Journal paper: 2 papers
林峻宇
(Chun-Yu Lin)
Biological Technology July 2014, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 11 papers
林志達
(Chih-Ta Lin)
Biological Technology July 2014, Ph.D.
Anticancer drug: Kinase-specific inhibitors & networks
Journal paper: 5 papers
邱一原
(Yi-Yuan Chiu)
Computer Science July 2014, Ph.D.
Computer-aided drug design
Journal paper: 4 papers
陳世勳
(Shih-Hsun Chen)
Biochemical Engineering December 2013, Ph.D.
Computer-aided drug design
Journal paper: 3 papers
劉怡馨
(I-Hsin Liu)
Life Science July 2013, Ph.D.
Systems Biology: Protein-MHC-TCR interaction
Journal paper: 3 papers
羅宇書
(Yu-Shu Lo)
Life Science July 2012, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 10 papers
許凱程
(Kai-Cheng Hsu)
Biological Technology July 2011, Ph.D.
Computer-aided drug design
Journal paper: 16 papers
陳彥甫
(Yen-Fu Chen)
Applied Chemistry July 2010, Ph.D.
Computer-aided drug design
Journal paper: 6 papers
(Win the 2007 National Innovation Award)
黃章維
(Jhang-Wei Huang)
Biological Technology September 2010, Ph.D.
Influenza Virus: Antigenic Drift Analysis, Antigen-Antibody interaction
Journal paper: 4 papers
陳俊辰
(Chun-Chen Chen)
Biological Technology June 2009, Ph.D.
Systems Biology: Protein-protein interaction
Journal paper: 3 papers
董其樺
(Chi-Hua Tung)
Biological Science June 2009, Ph.D.
Structural Bioinformatics: 3D-BLAST, Antigen-Antibody interaction
Journal paper: 3 papers
張耀霖
(Yao-Lin Chang)
Computer Science June 2008, Ph.D.
Title: A 3D-regulog approach to predict protein-DNA binding partners and binding model
(Co-advised student with Cheng-Yan Kao in NTU)
朱彥煒
(Yen-Wei Chu)
Computer Science June 2006, Ph.D.
Title: Finding Protein Secondary Structure Regularity and Related Applications
(Co-advised student with Chuen-Tsai Sun in NCTU)
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MD. Ph.D.

Name Major Fields in BS Memo (Research Groups, Research Directions, Publications)               
賴文森
(Wen-Sen Lai)
Department of Otolaryngology, Taichung Armed forces General Hospital June 2018, MD. Ph.D.
Journal paper: 22 papers
李日清
(Jih-Chin Lee)
Institute of Medical Sciences, The National Defense Medical Center July 2016, MD. Ph.D.
Journal paper: 41 papers

Master

Name Major Fields in BS Memo (Research Groups, Research Directions, Publications)
劉威廷
(Wei-Ting Liu)
Food sciences March 2019, Master
Systems Biology
郭超望
(Chao-Wang Kuo)
Medical Technology March 2019, Master
Systems Biology
李力渝
(Li-Yu Li)
Food Science March 2019, Master
Computer-aided drug design
趙千嫣
(Chien-Yen Chao)
Computer Science and Information Engineering March 2019, Master
Computer-aided drug design
洪慈懋
(Tzu-Mao Hung)
Nutrition March 2019, Master
Computer-aided drug design
蔡宜君
(Yi-Chun Tsai)
Biological Technologyy January 2019, Master
Computer-aided drug design
巫思穎
(Szu-Ying Wu)
Microbiology July 2017, Master
Computer-aided drug design
李容羽
(Jung-Yu Lee)
Animal Science July 2017, Master
Systems Biology: Protein-protein interaction
許元綸
(Yuan-Luen Sheu)
Information Management July 2016, Master
Systems Biology: Protein-protein interaction
顏佳儀
(Chia-Yi Yen)
Biological Technology July 2016, Master
Computer-aided drug design
楊方琪
(Yi-Jyun Jhen)
Biological Technology July 2016, Master
Systems Biology: Protein-protein interaction
李哲勳
(Jhuan-Dong Lin)
Biological Technology July 2016, Master
Computer-aided drug design
莊佾軒
(Yi-Shen Chung)
Computer Science July 2015, Master
Systems Biology: Protein-protein interaction
沈培鈞
(Pei-Jyun Chen)
Life Science July 2015, Master
Computer-aided drug design
陳怡君
(Yi-Jyun Jhen)
Information Management July 2015, Master
Systems Biology: Protein-protein interaction
林傳東
(Jhuan-Dong Lin)
Earth Sciences July 2015, Master
Computer-aided drug design
曾仁琥
(Jen-Hu Tseng)
Pharmacy July 2015, Master
Computer-aided drug design
林昱葦
(Yu-Wei Lin)
Biochemical Technology July 2014, Master
Systems Biology: Protein-Protein interaction
劉冠秀
(Kuan-Shiu Liu)
Computer Science July 2014, Master
Computer-aided drug design
李采凌
(Tsai-Ling Lee)
Computer Science July 2013, Master
Systems Biology: Protein-protein interaction
Journal paper: 1 paper
徐瑋澤
(Wei-Ze Syu)
Life Science July 2013, Master
Computer-aided drug design
尤宣人
(Syuan-Ren You)
Computer Science July 2012, Master
Computer-aided drug design
游宇震
(Yu-Chen, Yu)
Management Information System July 2012, Master
Systems Biology: Protein-protein interaction
李淩婷
(Ling-Ting Li)
Medicine Management July 2012, Master
Computer-aided drug design
Title: Core site-moiety maps of histone demethylase family for multi-target inhibitors and binding mechanisms
Journal paper: 3 papers
林伸融
(Shen-Rong Lin)
Computer Science July 2014, Master
Computer-aided drug design
Title: iGemdock 2.0 and SiMMap: Post-screening analysis for structure-based drug design
Journal paper: 4 paper
黃御哲
(Yu-Chi Huang)
Biological Technology July 2011, Master
Computer-aided drug design
Title: A web server for lead optimization using site-moiety map: A case study on neuraminidase
Journal paper: 1 paper
林怡瑋
(Yi-Wei Lin)
Life Science July 2011, Master
Systems Biology: Protein-protein interaction
Title: Template-based Homologous Modules through Protein-protein Interaction Families
Journal paper: 2 papers
許彥超
(Yen-Chao Hsu)
Computer Science December 2011, Master
Computer-aided drug design
Title: Moiety-based site-moiety map
林韋帆
(Wei-Fan Lin)
Life Science July 2011, Master
Influenza Virus: Antigenic Drift Analysis
Title: Genetic and antigenic analysis to the hemagglutinin of influenza A H1N1 virus and comparisons with H3N2 virusJournal paper: 1 paper
張力仁
(Li-Jen Chang)
Life Science July 2010, Master
Structural Bioinformatics
林峻宇
(Chun-Yu Lin)
Biological Technology May 2010, Master
Systems Biology: Protein-protein interaction
Journal paper: 2 papers
陳彥修
(Yen-Hsiu Chen)
Life Science June 2009, Master
Systems Biology: Protein-DNA/Protein-RNA interaction
劉康平
(Kang-Ping Liu)
Computer Science June 2009, Master
Systems Biology: Protein-protein interaction
Journal paper: 1 paper
陳祐德
(Yu-Te Chen)
Aquaculture June 2008, Master
Title: A New Profile Method to Predict Protein-ligand Binding Site
羅宇書
(Yu-Shu Lo)
Life Science June 2008, Master
Title: Template-Based Scoring Function for Predicting Protein-protein Interaction
Journal paper: 2 papers
許凱程
(Kai-Cheng Hsu)
Biological Technology June 2007, Master
Title: Binding Affinity Analysis of Protein-ligand Complexes
陳右儒
(Yo-Ru Chen)
Computer Science June 2007, Master
Title: iGEMDOCK: A graphical-automatic drug design system for docking, screening and post-analysis
(Win the 2007 National Innovation Award)
楊登凱
(Teng-Kai Yang)
Computer Science June 2006, Master
Title: Structural Binding Pocket Clustering and Protein-ligand Interaction Analysis for ATP-binding Proteins
陳永強
(Yung-Chiang Chen)
Life Science June 2006, Master
Title: Inferring Domain Annotated Protein-Protein Interactions through 3D-Domain Interologs
Journal paper: 2 papers
葛振寧
(Chen-Neng Ko)
Biological Science June 2006, Master
Title: Structure-based Compound Screening for Helicobacter pylori shikimate kinase (HpSK)
Journal paper: 1 paper
黃章維
(Jhang-Wei Huang)
Biological Technology June 2006, Master
Title: Predicting Antigenic Variants of Influenza A H3N2 Viruses by Building Relationships between Genetic Evolution and Antigenic Drift
Journal paper: 2 papers
董其樺
(Chi-Hua Tung)
Biological Science June 2005, Master
Title: PiSA-BLAST: A New Tool for Protein Structure Alignment and Database Search
(Win the prize of 2005 Best M.S. and Ph. D. Dissertation Award hosted by IICM (Institute of Information & Computing Machinery))
Website: 3D-BLAST
Journal paper: 3 papers
邱一原
(Yi-Yuan Chiu)
Computer Science June 2005, Master
Title: Optimizing New Energy Functions for Protein Folding
Journal paper: 1 paper
林柏村
(Po-Tsun Lin)
Life Science June 2005, Master
Title: LigSeeSVM: Support Vector Machines and Data fusion for Ligand-based Compound Screening and Applications to GPCR and GABAA
陳宏助
(Heng-Chu Chen)
Life Science June 2005, Master
Title: Inferring Protein-protein Interactions from Structural Domain-domain Interactions
張立人
(Li-Jen Chang)
Medical Technology June 2005, Master
Title: Integrating GEMDOCK with GEM-PLS and GEM-kNN for QSAR modeling of huAChE and AGHO
沈再威
(Tsai-Wei Shen)
Biological Science June 2004, Master
Title: Enhancing GEMDOCK on Virtual Database Screening and Application to Envelope Protein and D-Hydantoinase
(Win the prize of 2004 Best M.S. and Ph. D. Dissertation Award hosted by IICM (Institute of Information & Computing Machinery))
Website: GEMDOCK
Journal paper: 2 papers
林建宏
(Chien-Heng Lin)
Biological Science June 2004, Master
Title: MuLiSA: Analysis and Identification of Functional Motifs and Residues in Proteins by Multiple Ligand-bound Structure Alignments
陳彥甫
(Yen-Fu Chen)
Applied Chemistry June 2004, Master
Title: Validation and Application of GEMDOCK and Application of Data Fusion in Virtual Screening
Journal paper: 2 papers
張育祥
(Yu-Hsiang Chang)
Life Science June 2003, Master
Title: A New Energy Model for Protein-Protein Interaction Prediction
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建立藥物-蛋白質-生化途徑-疾病機制的關連

建立基礎研究-轉譯醫學-產業的連結

Overview

    Our research focused on computer-aided drug design (GEMDOCK and SiMMap), structural bioinformatics (3D-BLAST, (PS)2 and fastSCOP), and systems biology (PPISearch and 3D-partner), especially investigating the molecular interfaces (e.g., protein-protein, protein-DNA, protein-ligand interactions). Our main contributions and innovations are described as follows: I) Discover the protein-compound interaction family for multi-target drug design and new uses for old drug [1-4]. II) The first team proposed protein-protein interactions (interface family) across multiple species [5-8]. III) We have developed the first tool, called 3D-BLAST which is as fast as BLAST and has the features of BLAST (e.g. robust statistical basis, and effective and reliable search capabilities), to search large protein structures (> 30000) within 3 seconds in the world [9-11].

Drug discovery: Pharmalogs and Homopharma

    For structure-based protein-ligand interactions and drug discovery, we have developed a molecular docking tool, namely GEMDOCK [3, 4, 13, 14], which is one of wide-used tools in the world. We cooperated with 10 research teams on diverse drug targets. We cooperated with over 10 laboratories which successfully applied our tools for identifying lead compounds and protein functional sites and protein engineering. For example, GEMDOCK has been successfully applied to identify the lead compounds for dengue virus envelop protein (cooperating with Yang YL in NCTU)[2]; inhibitors of influenza virus neuraminidase (cooperating with Hsu TA in NHRI) [15]; lead compounds of ROCK kinase (cooperating with Chao JI in NCTU) for anti-cancer drugs; antibiotics of shikimate kinases of Mycobacterium tuberculosis and Helicobacter pylori (cooperating with Wang WC in NTHU). We have successfully applied our tools for discovering the secondary vitamin D3 binding site of milk beta-lactoglobulin (cooperating with Mao JI in NCTU)[16, 17]; the binding mechanism between c-di-GMP ad cAMP Receptor-Like Protein CLP (cooperating with Chao SH in NCHU) [18]. The timed citations of two related papers [3, 13] are 58 and 61, respectively, from 2004. These related papers were cited over 180 times. We got the 2007 National Innovation Award due to the achievement of iGEMDOCK.
    在藥物開發部份,本實驗室透過獨立研發的全台第一個藥物嵌合軟體 GEMDOCK(榮獲 2007 國家新創獎)與超過 400 個 CPU 的計算資源,可快速的針對特定藥物標靶於虛擬藥物資料庫中(超過 30 萬筆小分子化合物)進行篩選,並利用全球首創的區域官能基地圖技術分析標靶蛋白的藥物結合機制,進而篩選出新型抑制劑。有別於其他計算實驗室缺乏自主實驗驗證,我們已建構由全波長式多功能微量分析儀暨冷螢光數位影像分析系統為主的高效藥篩平台,可對篩選出的抑制劑進行活性分析,並可針對常見癌症(肝癌、乳癌、頭頸癌)或發炎反應進行細胞實驗分析。此外,我們並與淡水馬偕醫院與三軍總醫院合作進行臨床試驗,是國內少數從計算跨足轉譯醫學的藥物設計與系統生物實驗室。在癌症與許多複雜疾病的主要藥物標靶-蛋白激酶上,我們透過上述程序,發現了特定受體酪氨酸激酶專屬的結合位點(Type-C pocket),並成功針對此位點篩選出選擇性抑制劑(Type-C inhibitors),而大規模蛋白激酶抑制活性分析結果亦顯示出高選擇性,並能克服傳統化療藥物所產生的常見抗藥性突變,順利突破此類年產值高達 185 億美金的藥物目前所面對的瓶頸--選擇性與抗藥性,為其選擇性與抗藥性設計開闢另一個方向。

Molecular interface families (protein-drug, protein-protein, and protein-DNA)

    In protein-peptide interactions, we improved our PPI template-based scoring function with template similarity and interacting force to guarantee statistically significant interface similarity between peptide candidates and structure templates. Our model, considering both MHC-peptide and peptide-TCR interfaces, could provide visualization and biological insights of MHC-peptide-TCR binding models. We believe that it is very helpful for the development of peptide-based vaccines. For protein-DNA interactions, we developed a new approach, namely 3D-regulogs, to infer protein-DNA binding partners by using the concept of regulog and crystal structures of protein-DNA complex as templates [12]. This approach also provides binding models, interacting amino acids, and DNA bases of predicted partners. For protein-ligand interactions, we have introduced site-moiety maps [1], which recognize interaction preferences between protein pockets and compound moieties. SiMMap was developed to identify site-moiety maps from query protein structures and their docked (or co-crystallized) compounds. Over 1,400 users have created more than 1,500 site-moiety maps for different proteins. Site-moiety map is able to provide biological insights and useful for drug discovery and lead optimization.

Homologous structural systems biology

    For systems biology and structural bioinformatics, we have proposed a novel concept, called "3D-domain interologs", to discover protein-protein interactions[6-8] and protein-DNA interactions [12] which are considered as orthologous interactions among different species, in particular about inferred interacting domain pairs and binding models (e.g. hydrogen-bond interactions and conserved residues). For protein-protein interactions, we proposed the PPISearch server [5] for searching homologous protein-protein interactions (PPIs), called PPI family, across multiple species. According to our knowledge, PPISearch is the first public server that identifies homologous PPIs from annotated PPI databases and infers transferability of interacting domains and functions between homologous PPIs and the query. By taking account of structural bioinformatics cross species, we extended PPISearch to PCFamily [8], which is useful for binding model visualizations and annotating query proteins based on homologous protein complexes. Until September 2010, over 3,500 users have used PPISearch and PCFamily servers. Furthermore, the number of accessing 3D-BLAST exceeds 6,000 from 44 countries and related papers were cited ~50 times since 2007.

藥物傳輸老藥新用:尼古丁乙醯膽鹼受體α9在尼古丁誘導之癌症中的調控機制

    本團隊與台北醫學大學乳癌研究團隊(何元順教授團隊及雙和醫院院長 吳志雄教授等)合作,探討尼古丁(Nicotine)誘導多種疾病(如肺癌、頭頸癌、乳癌、畸形兒等)發生之轉譯醫學研究,尼古丁乙醯膽鹼受體α9(α9-nAChR)被認為參與由尼古丁所誘發的人類正常乳腺上皮細胞的轉型,由於目前所有的PPI資料庫都缺乏α9-nAChR的交互作用蛋白質,我們透過同源映射網路及蛋白質-化合物交互作用家族概念,發現5個新的α9-nAChR之交互作用蛋白質(X1、X2、X3、X4和X5)及其相關生化途徑。透過免疫共沉澱及螢光共振能量轉移影像(Förster resonance energy transfer),發現α9-nAChR正常情況下會與生長因子受體(如X1、X2)結合,降低其活性;當尼古丁結合α9-nAChR會使其與生長因子受體分離,因而活化下游生化途徑抑制細胞凋亡及促進細胞增生。目前已將此發現透過臨床檢體進行驗證,成功發現尼古丁誘發乳癌之機制,相關成果發表撰寫中。

天然藥新藥開發

    中草藥在中華民族的生活與歷史上扮演重要角色,然而隨著西風東漸,國人因為中草藥的傳統理論基礎缺乏現今科學化的解釋而漸趨勢微,這無論對已有數千年臨床驗證的中草藥或是對人類的健康都是一大損失,所以將中草藥的療效賦予科學化的解釋是相當重要且刻不容緩的。本實驗室透過系統生物的策略,建構出跨物種的同源交互作用網絡,並成功解釋疾病的致病機制。並透過在藥物設計領域的積累,提出全球首創的同源藥理概念,可利用蛋白與藥物的共結晶結構預測出其他具有類似結合機制的標靶蛋白與藥物,有助於舊藥新用與副作用預測。而本實驗室進一步將系統生物與藥物設計結合,可透過將中草藥或整株植物的成分以同源藥理概念找出潛在作用蛋白,並標註於同源交互作用網絡,如此將可以作用標靶、作用途徑、影響疾病等科學化方式闡述中草藥的療效,目前並已成功應用於痲瘋樹、紅麴與牛樟芝的治療與保健功效預測上。

抗癌與抗感染藥物開發:頭頸癌病人傳統藥物治療偕同健康食品進行輔助療法

    本團隊與三軍總醫院頭頸癌研究團隊(病理部聶鑫主任及李日清醫師)合作,透過系統生物策略模型,發展可以用於診斷、預後及治療之頭頸癌生物標記-HNC88(88個基因),並試圖以 HNC88 從分子階層角度對病患進行分類與治療,大致可將病患分成 HPV-infected、Immune-enriched 及 Proliferation-enriched 三大類。葡萄王生技為國內保健食品製造龍頭,本團隊與葡萄王生技合作進行生技健康食品科學化及功效驗證,如:分析樟芝王關鍵成分對口腔癌病患化放療之副作用緩解分析及預後評估,探討食用前、後之各病患子類血液中基因表現與癌症生化途徑的變化。

腦及神經老化藥物開發

    人類對於大腦運作所負責的腦區已有了解但對於詳細運作機制仍然尚未釐清,因此對於大腦研究進而衍伸出幾個議題:1. 因應世界人口老齡化的趨勢因而衍生出老年神經退化性疾病,例如:阿茲海默症,根據統計在 2010 年全球有將近 2100 萬到 3500 萬名阿茲海默症患者,而歸因於阿茲海默症相關的死亡案例大約有 48.6 萬例。阿茲海默症會使患者越來越需要他人的照護,因此導致在已開發國家中阿茲海默症是相當耗費社會資源的疾病之一。世界衛生組織指出目前並沒有特定藥物有實證證明對阿茲海默症治療有效,只有少數可能可以暫時(緩解)改善症狀的方法,而健康食品及植物藥被視為是另類可能的有效途徑;2. 由於許多大腦疾病已知與性別有關,例如:男生易患自閉症、女生易患阿茲海默症,因此透過了解男女大腦先天上的差異對於釐清疾病病理機制具有莫大幫助,本團隊透過表徵型資料:腦電波圖譜(EEG)、大腦核磁共振(MRI)、動物模式,以及基因型資料:基因表達圖譜(mRNA microarray)、次世代定序(NGS)、蛋白質體圖譜(Proteomics),整合本團隊核心技術蛋白質交互作用家族(PPI family)、模組交互作用家族(Module family)、蛋白質-配體交互作用家族(Protein-ligand family),進而揭露大腦疾病詳細生化機制。

合作夥伴

    We have accumulated extensive experiences in drug design to achieve the specific aims. Our team consists of experts in different fields, including computational drug design, systems biology, clinical trial, lead optimization, biochemistry, and animal models. We have successfully discovered 45 lead compounds (<10 μM) for various diseases or pathogens. One of the identified natural compounds, rosmarinic acid, is currently applying for the U.S. patent and IRB approval at Mackay Memorial Hospital (馬偕醫院) for clinical trials. Based on these results, we have received one U.S. patent (US 8,175,860 B2), and have applied one U.S. patent (13/872,456) and one ROC patent. In university-industry collaborations, we have collaborated with ScinoPharm (台灣神隆), Phalanx Biotech Group (華聯生技), Food Industry Research and Development Institute (食品工業研究所), and Jason Life Tech for developing new drugs, botanical drugs, healthy food, and microarray platform for detecting diseases. We have collaborated with over 30 laboratories (e.g., Professor Wang HJ [王惠鈞院士] and Professor Mark von Itzstein, inventor of the first anti-influenza drug, Zanamivir), five teaching hospitals, and 15 national institutes for drug discovery, systems biology, binding mechanisms, and multi-target drugs. In addition, we have achieved some significant results in molecular interactions and structural systems biology: 1) We are the first team proposed molecular-interface families; 2) We have established the statistical biophysics methods to infer site-moiety maps (hotspots) of proteins for protein-ligand binding mechanisms and drug discovery; 3) We have proposed the comprehensive molecular interaction networks for studying interactomes; 4) We have developed GEMDOCK, which is a world-wide used docking programs.

References

  1. Chen YF, Hsu KC, Lin SR, Wang WC, Huang YC, Yang JM: SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties. Nucleic Acids Research 2010, 38:W424-W430.
  2. Yang JM, Chen YF, Tu YY, Yen KR, Yang YL: Combinatorial computational approaches to identify tetracycline derivatives as flavivirus inhibitors. PLoS ONE 2007:e428.
  3. Yang JM, Chen CC: GEMDOCK: a generic evolutionary method for molecular docking. Proteins: Structure, Function, and Bioinformatics 2004, 55:288-304.
  4. Yang JM, Shen TW: A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators. Proteins: Structure, Function, and Bioinformatics 2005, 59:205-220.
  5. Chen CC, Lin CY, Lo YS, Yang JM: PPISearch: a web server for searching homologous protein-protein interactions across multiple species. Nucleic Acids Research 2009, 37:W369-W375.
  6. Chen YC, Lo YS, Hsu WC, Yang JM: 3D-partner: a web server to infer interacting partners and binding models. Nucleic Acids Research 2007:W561-W567.
  7. Lo YS, Chen YC, Yang JM: 3D-interologs: An evolution database of physical protein-protein interactions across multiple genomes. BMC Genomics 2010, 11, Suppl 3:S7.
  8. Lo YS, Lin CY, Yang JM: PCFamily: a web server for searching homologous protein complexes. Nucleic Acids Research 2010, 38:W516-W522.
  9. Yang JM, Tung CH: Protein structure database search and evolutionary classification. Nucleic Acids Research 2006, 34:3646-3659.
  10. Tung CH, Huang JW, Yang JM: Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database. Genome Biology 2010, 2007, 8:R31.
  11. Tung CH, Yang JM: fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies. Nucleic Acids Research 2007, 35:W438-W443.
  12. Chang YL, Tsai HK, Kao CY, Chen YC, Hu YJ, Yang JM: Evolutionary conservation of DNA-contact residues in DNA-binding domains. BMC Bioinformatics 2008, 9(S6):S3.1-S3.9.
  13. Yang JM, Chen YF, Shen TW, Kristal BS, Hsu DF: Consensus scoring criteria for improving enrichment in virtual screening. Journal of Chemical Information and Modeling 2005, 45:1134-1146.
  14. Yang JM: Development and evaluation of a generic evolutionary method for protein-ligand docking. Journal of Computational Chemistry 2004, 25:843-857.
  15. Hung HC, Tseng CP, Yang JM, Ju YW, Tseng SN, Chen YF, Chao YS, Hsieh HP, Shih SR, Hsu JT: Aurintricarboxylic acid inhibits influenza virus neuraminidase. Antiviral Research 2009, 81:123-131.
  16. Yang MC, Guan HH, Liu MY, Lin YH, Yang JM, Chen WL, Chen CJ, Mao SJT: Crystal Structure of a Secondary Vitamin D3 Binding Site of Milk ß-Lactoglobulin. Proteins: Structure, Function, and Bioinformatics 2008:1197-1210.
  17. Yang MC, Guan HH, Yang JM, Ko CN, Liu MY, Lin YH, Chen CJ, Mao SJT: Rational Design for crystallization of b-Lactoglobulin and vitamin D3 complex: reveal of a secondary binding site. Crystal Growth & Design 2008:DOI: 10.1021/cg800697s.
  18. Chin KH, Lee YC, Tu ZL, Chen CH, Tseng YH, Yang JM, Ryan RP, McCarthy Y, Dow JM, Wang AH et al: The cAMP receptor-like protein CLP is a novel c-di-GMP receptor linking cell-cell signaling to virulence gene expression in Xanthomonas campestris. Journal of Molecular Biology 2010, 396:646-662.

BioXGEM 所發展的生物資訊網頁工具及資料庫

GEMDOCK

GEMDOCK - a Generic Evolutionary Method for molecular DOCKing GEMDOCK is a program for computing a ligand conformation and orientation relative to the active site of target protein. The tool was developed by Jinn-Moon Yang, a profesor of the Institute of Bioinformatics, National Chiao Tung University.
URL: http://gemdock.life.nctu.edu.tw/


SiMMap

SiMMap: Site-moiety map for drug discovery and mechanisms
URL: http://simfam.life.nctu.edu.tw/


3D-BLAST

3D-BLAST is a very fast and accurate method for discovering the homologous proteins and evolutionary classifications of a newly determined protein structure. Our 3D-BLAST has the advantages of BLAST tool for fast protein structure database scanning.
URL: http://3d-blast.life.nctu.edu.tw/


Protein-Protein Interaction Search

Input an interacting protein pair as a query to search its homologous interactions across multiple species
URL: http://gemdock.life.nctu.edu.tw/ppisearch/


PCFamily

PCFamily : Protein Complex Family Search
URL: http://pcfamily.life.nctu.edu.tw/


MoNetFamily

MoNetFamily - Homologous modules and module-module interaction networks in vertebrates
URL: http://monetfamily.life.nctu.edu.tw/


KIDFamMap

KIDFamMap: Kinase-inhibitor-disease family map
URL: http://gemdock.life.nctu.edu.tw/KIDFamMap/


CaMPNets

CaMPNets: Membrane protein-regulated networks across human cancers
URL: http://campnets.life.nctu.edu.tw/


PharmaCoNets

PharmaCoNets: Drug community–regulated networks
URL: http://pharmaconets.life.nctu.edu.tw/


BioXGEM Integrated Discovery for Omics data

URL: http://140.113.120.248/BioXGEM-tools/


BioXGEM Integrated Discovery for Drug Design

URL: http://140.113.120.248/BioXGEM-drug/


FooDisNET

URL: http://140.113.120.248/FooDisNET


Tranditional Chinese Herb

Tranditional Chinese Herb
URL: http://gemdock.life.nctu.edu.tw/HERBID/


BioXGEM 常用 Data Sets

SARS-CoV-2 main protease data (Download all)

  • Sequence data: Include SARS-CoV-2 main protease(fasta), 12 Coronavirus main proteases(fasta) and MSA results
  • Structure data: Include 57 aligned SARS-CoV main proteases(pdb) and 187 aligned SARS-CoV-2 main proteases(pdb)
  • FDA approved drugs: Include 2125 approved drugs from DrugBank(mol)
  • Selected docking poses: Include 8 docking poses of different PPCs
  • Molecular recognition

  • 100 PDB complexes set: 100 protein-ligand complexes
  • CCDC/Astex test set: 305 protein-ligand complexes
  • Virtual screening sets

  • Thymidine kinase inhibitors: 10 known inhibitors for thymidine kinase
  • Estrogen receptor alpha agonists: 10 known agonists for estrogen receptor alpha
  • Estrogen receptor alpha antagonists: 10 known antagonists of estrogen receptor alpha
  • Dihydrofolate reductase inhibitors: 10 known ligands for human dihydrofolate reductase
  • Human carbonic anhydrase II (HCAII): 20 inhibitors of human carbonic anhydrase II
  • ACD 990 dataset: 990 randomly selected compounds from ACD
  • CMC database: 7375 pharmaceutical compounds (1900 - present) from Comprehensive Medicinal Chemistry (CMC)
  • Gene expression sets

    Breast cancer

  • Breast cancer_100 genes: 150 samples (30N,120P) with 100 genes for teaching
  • Breast cancer_all genes: 150 samples (30N,120P) with 20531 genes for comprehensive analysis
  • Breast cancer_clinical: TCGA clinical information of breast cancer patients
  • Liver cancer

  • Liver cancer_100 genes: 150 samples (50N,100P) with 100 genes for teaching
  • Liver cancer_all genes: 150 samples (50N,100P) with 20531 genes for comprehensive analysis
  • Liver cancer_clinical: TCGA clinical information of liver cancer patients
  • Head and neck cancer

  • Head and neck cancer_100 genes: 120 samples (40N,80P) with 100 genes for teaching
  • Head and neck cancer_all genes: 120 samples (40N,80P) with 20531 genes for comprehensive analysis
  • Head and neck cancer_clinical: TCGA clinical information of head and neck cancer patients
  • Diabetes

  • Diabetes_100 genes: 17 samples (9N,8P) with 100 genes for teaching
  • Diabetes_all genes: 17 samples (9N,8P) samples with 14463 genes for comprehensive analysis
  • Convolutional neural network for human cancer types prediction

  • Source code of CNN model and example samples: The zip file contained three programs and example samples for building CNN model
  • 歡迎有熱情 有想法的碩博生 專題生加入我們的行列
    誠徵博士後研究員 碩士級專任研究助理
    THE WORLD OF DRUG DISCOVERY,
    FUNCTION BIOINFORMATICS AND SYSTEMS BIOLOGY.





    楊進木 教授
    03-5712121 #56942 (Lab: #56946)
    moon@nycu.edu.tw
    賢齊館 415-1 室
    研究內容
    • 生物領域
      • 藥物設計、系統生物與結構生物學
      • 成功對 15 個標靶蛋白質發現 43 個前導藥物,如肺癌、前列腺癌、結核桿菌、幽門螺旋桿菌、流感病毒
      • 全球第一建立蛋白質-蛋白質交互作用家族與跨多物種模組-模組交互作用網路

    發現四環抗生素對
    登革熱病毒有效

    • 資訊領域
      • 軟體撰寫、網頁與資料庫設計
      • 開發了 9 個生物技術產業及新藥開發的網頁服務或工具
      • GEMDOCK 獲得 2007 國家新創獎
      • 3D-BLAST 為目前最快的蛋白質結構搜尋工具
    • 拓展視野
      • 與第一個抗流感藥物發明者(Mark von Itzstein)、藥華藥廠、4 個教學醫院和 12 個國家型機構合作(如中研院與國衛院)
    • 就業發展
      • 生技產業、資訊科技業、研究人員、教職

    活動照片

    運動

    時間 ► 2015年5月7日 (星期四)
    地點 ► 國立交通大學光復校區 排球場

    參加生科系運排球比賽賽後合照

    出遊

    時間 ► 2014年2月18日 (星期二)
    地點 ► 老師的農莊

    在老師的農莊摘橘子

    耶誕晚會

    時間 ► 2013年12月23日 (星期一)
    地點 ► 國立交通大學博愛校區 生科實驗館 生資中心

    耶誕晚會交換禮物

    謝師宴

    時間 ► 2013年8月7日 (星期三)
    地點 ► 新竹加賀日本料理

    在加賀日本料理舉辦謝師宴

    成員合照

    研討會集錦