BioXGEM: 藥物設計與系統生物實驗室

I (Jinn-Moon Yang) am a full professor of Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Taiwan. Togglenavigation BioXGEM 首頁 教授 成員 研究 工具及資料庫 常用連結 人才招募 × Somethingerror!! 目前網站仍在建置中，尚未開放此功能 Close 最新消息LatestNews 亮點成就HighlightAchievement [學術發表][2022/04/15]本實驗室AI相關研究成果DiscoveryofmoietypreferencebyShapleyvalueinproteinkinasefamilyusingrandomforestmodels發表於BMCBioinformatics [2022/03]恭喜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 [學術發表][2022/01/07]本實驗室與京都大學合作AIGCN相關研究成果Anovelgraphconvolutionalneuralnetworkforpredictinginteractionsitesonproteinkinaseinhibitorsinphosphorylation，發表於ScientificReports [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-blood3-geneSignatureasaDecisionAidforRifapentine-basedTBPreventiveTherapy，發表於ClinicalInfectiousDiseases [2021/10/27]恭喜實驗室以「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」 [學術發表][2021/10/19]本實驗室AI相關研究成果Convolutionalneuralnetworkforhumancancertypespredictionbyintegratingproteininteractionnetworksandomicsdata發表於ScientificReports [科技部計畫]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」[相關新聞連結] [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(2019InternationalCollaborativeResearchProgramofICR,KyotoUniversity)，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[相關新聞連結] [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) 學術研究AcademicResearch 產學合作Industry-AcademiaCooperation 國際交流InternationalExchange 人才培育TalentEducation [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AnIntegratedGenomicStrategytoIdentifyCHRNB4asaDiagnostic/PrognosticBiomarkerforTargetedTherapyinHeadandNeckCancer，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-basedInvestigationofDiet-inducedObesitySynergizedwithHBx,Src,andp53MutationAcceleratingHepatocarcinogenesisinZebrafishModel，發表於Cancers [學術發表][2019/07/16]本實驗室研究成果Membraneprotein-regulatednetworksacrosshumancancers(癌症膜蛋白調節網路)，榮登國際頂級期刊[NatureCommunications] [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Molecularinteractionfamilyforsystemsbiologyanddrugdesign [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Molecularinteractionfamilyforsystemsbiologyanddrugdesign [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」[相關新聞連結] [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 [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，2019AI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[相關連結][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2018AIslanders'ShowAI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[相關新聞連結] [USPatent](US20160096848A1)Selectiveinhibitorsforproteinkinasesandpharmaceuticalcompositionandusethereof [USPatent](US20160068495A1)Compoundforpromotingapoptosisofcancercellsandapharmaceuticalcompositioncontainingthesameandusesthereof [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 [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，進一步促進與京大之間的交流合作 [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(2019InternationalCollaborativeResearchProgramofICR,KyotoUniversity)，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 [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TatsuyaAkutsu演講，講題為TwoApproachesforIntegratingOmicsDataforAnalysisofBiologicalData [演講專題][2018/11/02]邀請JSPSPost-DoctoralResearchFellow/GuestResearchAssociate(JSPS外国人特別研究員)林峻宇博士演講，講題為LifeasaresearcherinJapan-JSPSInternationalFellowshipsforResearchinJapan [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 [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JSPSPost-DoctoralResearchFellow/GuestResearchAssociate(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 教授 楊進木(Jinn-MoonYang) Dean CollegeofBiologicalScienceandTechnology Professor DrugDesignandSystemsBiologyLaboratory DepartmentofBiologicalScienceandTechnology InstituteofBioinformatics&SystemsBiology,NationalYangMingChiaoTungUniversity Address:75Po-AiStreet,Hsinchu,Taiwan,30068 Office&Lab:415-1and404(Lab)inJanQiBiomedicalEngineeringBuilding Tel:886-3-5712121ext.56942;Fax:886-3-5729288 E-mail:[email protected] ResearchOverview:     I(Jinn-MoonYang)amafullprofessorofInstituteofBioinformatics andSystemsBiology,NationalChiaoTungUniversity,Taiwan. Ourprimarygoalistostudyinhibitor-protein-pathway-diseaserelationshipsinacell. Themajorresearchareasincludedrugdiscovery,structuralbioinformatics,andsystemsbiology. Ipublishedover90SCIpapersonsomejournals,suchasGenomeBiology,NucleicAcidsResearch, PLOSComputationalBiology,ScientificReports,andBioinformatics.Myh-indexis30and22 basedonGooglescholarandISIWebofKnowledge,respectively. BasedonISIandGooglescholardatabases,totalnumbersofcitationsareover1,300and3,100, respectively.Ourteamhasdevelopedamoleculardocking(GEMDOCK)andsite-moietymap(SiMMap) formolecularinteraction(e.g.,protein-ligandandprotein-protein)mechanismanalysis. Myteamachievedsuccessfulresultsonafastproteinstructuresearchtool(3D-BLAST) whichisasfastasBLASTandhasthefeaturesofBLAST. Wearethefirstteamtointroduceprotein-proteininteractingfamilyandprotein-ligandfamily whichissimilartotheconceptoftheproteinorgenefamily. IalsojoinedtheeditorialboardsofScientificReportsandPLoSONE. SelectedPapers 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) Membraneprotein-regulatednetworksacrosshumancancers, NatureCommunications,10(1):3131. Lin,C.Y.,Lee,T.L.,Chiu,Y.Y.,Lin,Y.W.,Lo,Y.S.,Lin,C.T.,andYang,J.M.*(2015) Moduleorganizationandvarianceinprotein-proteininteractionnetworks, ScientificReports,5:9386. Chiu,Y.Y.,Lin,C.T.,Huang,J.W.,Hsu,K.C.,Tseng,J.H.,You,S.R.,andYang,J.M.*(2013) KIDFamMap:adatabaseofkinase-inhibitor-diseasefamilymapsforkinaseinhibitorselectivityandbindingmechanisms, NucleicAcidsResearch,41(Databaseissue):D430-40. Hsu,K.C.,Cheng,W.C.,Chen,Y.F.,Wang,W.C.,andYang,J.M.*(2013) Pathway-basedscreeningstrategyformultitargetinhibitorsofdiverseproteinsinmetabolicpathways, PLOSComputationalBiology,9(7):e1003127. Lin,C.Y.,Lin,Y.W.,Yu,S.W.,Lo,Y.S.,andYang,J.M.*(2012) MoNetFamily:awebservertoinferhomologousmodulesandmodule-moduleinteractionnetworksinvertebrates, NucleicAcidsResearch,40(WebServerissue):W263-70. 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.,andWang,A.H.(2014) CrowningProteins:ModulatingtheProteinSurfacePropertiesusingCrownEthers, AngewandteChemieInternationalEdition,53(48):13054-8. 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.*,andWang,W.C.*(2014) KDM4Basatargetforprostatecancer:structuralanalysisandselectiveinhibitionbyanovelinhibitor, JournalofMedicinalChemistry,57(14):5975-85. Tung,C.H.,Huang,J.W.,andYang,J.M.*(2007) Kappa-alphaplotderivedstructuralalphabetandBLOSUM-likesubstitutionmatrixforrapidsearchofproteinstructuredatabase, GenomeBiology,8(3):R31. Chen,Y.C.,Lo,Y.S.,Hsu,W.C.,andYang,J.M.*(2007) 3D-partner:awebservertoinferinteractingpartnersandbindingmodels, NucleicAcidsResearch,35(WebServerissue):W561-7. Chen,C.C.,Hwang,J.K.,andYang,J.M.*(2006) (PS)(2):proteinstructurepredictionserver, NucleicAcidsResearch,34(WebServerissue):W152–7. Yang,J.M.*,Chen,Y.F.,Shen,T.W.,Kristal,B.S.,andHsu,D.F.(2005) Consensusscoringcriteriaforimprovingenrichmentinvirtualscreening, JournalofChemicalInformationandModeling,45(4):1134-46. Yang,J.M.*,andChen,C.C.(2004) GEMDOCK:Agenericevolutionarymethodformoleculardocking, Proteins-StructureFunctionandBioinformatics,55(2):288-304. CompleteJournalPapers Huang,Y.W.,Hsu,Y.C.,Chuang,Y.H.,Chen,Y.T.,Lin,X.Y.,Fan,Y.W.,Pathak,N.andYang,J.M.(2022) DiscoveryofmoietypreferencebyShapleyvalueinproteinkinasefamilyusingrandomforestmodels, BMCBioinformatics,23(4):130. Wang,F.,Chen,Y.T.,Yang,J.M.andAkutsu,T.(2022) Anovelgraphconvolutionalneuralnetworkforpredictinginteractionsitesonproteinkinaseinhibitorsinphosphorylation, ScientificReports,12:229. 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.andChong,I.W.(2022) Whole-blood3-geneSignatureasaDecisionAidforRifapentine-basedTBPreventiveTherapy, ClinicalInfectiousDiseases. Chuang,Y.H.,Huang,S.H.,Hung,T.M.,Lin,X.Y.,Lee,J.Y.,Lai,W.S.andYang,J.M.*(2021) Convolutionalneuralnetworkforhumancancertypespredictionbyintegratingproteininteractionnetworksandomicsdata, ScientificReports,11:20691. Chiou,W.C.,Hsu,M.S.,Chen,Y.T.,Yang,J.M.,Tsay,Y.G.,Huang,H.C.,andHuang,C.(2021) Repurposingexistingdrugs:identificationofSARS-CoV-23C-likeproteaseinhibitors, JournalofEnzymeInhibitionandMedicinalChemistry,36(1),147-153. Chiou,W.C.,Chen,J.C.,Chen,Y.T.,Yang,J.M.,Hwang,L.H.,Lyu,Y.S.,Yang,H.Y.andHuang,C.(2021) TheinhibitoryeffectsofPGGandEGCGagainsttheSARS-CoV-23C-likeprotease, Biochemicalandbiophysicalresearchcommunications. 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.andYang,J.M.*(2020) UncoveringFlexibleActiveSiteConformationsofSARS-CoV-23CLProteasesthroughProteasePharmacophoreClustersandCOVID-19DrugRepurposing, ACSnano. 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.andYang,J.M.*(2020) Asite-moietymapandvirtualscreeningapproachfordiscoveryofnovel5-LOXinhibitors, Scientificreports,10(1),1-12. 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) AnIntegratedGenomicStrategytoIdentifyCHRNB4asaDiagnostic/PrognosticBiomarkerforTargetedTherapyinHeadandNeckCancer, Cancers,12(5),1324. Hengphasatporn,K.,Plaimas,K.,Suratanee,A.,Wongsriphisant,P.,Yang,J.M.,Shigeta,Y.,Chavasiri,W.,Boonyasuppayakorn,S.,Rungrotmongkol,T.(2020) TargetIdentificationUsingHomopharmaandNetwork-BasedMethodsforPredictingCompoundsAgainstDengueVirus-InfectedCells, Molecules,25(8),1883. Yang,W.Y.,Rao,P.S.,Luo,Y.C.,Lin,H.K.,Huang,S.H.,Yang,J.M.*,Yuh,C.H.*(2019) Omics-basedInvestigationofDiet-inducedObesitySynergizedwithHBx,Src,andp53MutationAcceleratingHepatocarcinogenesisinZebrafishModel, Cancers,11(12),1899. Simak,M.,Lu,H.H.S.,Yang,J.M.(2019) Booleanfunctionnetworkanalysisoftimecourselivertranscriptomedatatorevealnovelcircadiantranscriptionalregulatorsinmammals, JournaloftheChineseMedicalAssociation,82(11),872-880. 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) Membraneprotein-regulatednetworksacrosshumancancers, NatureCommunications,10(1):3131. 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) IdentificationofthePCA29genesignatureasapredictorinprostatecancer, JournalofBioinformaticsandComputationalBiology,17(3):1940006. Lin,C.Y.,Ruan,P.Y.,Li,R.M.,Yang,J.M.,See,S.,Song,J.N.,Akutsu,T.(2019) Deeplearningwithevolutionaryandgenomicprofilesforidentifyingcancersubtypes, JournalofBioinformaticsandComputationalBiology,17(3):1940005. 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) Alternativesplicinginhumancancercellsismodulatedbytheamiloridederivative3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxide, MolecularOncology,13(8):1744-1762. 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/Cas9GenomeEditingofEpidermalGrowthFactorReceptorSufficientlyAbolishedOncogenicityinAnaplasticThyroidCancer, DiseaseMarkers,3835783. Huang,S.H.,Lo,Y.S.,Luo,Y.C.,Tseng,Y.Y.,Yang,J.M.*(2017) Ahomologousmappingmethodforthree-dimensionalreconstructionofproteinnetworksrevealsdisease-associatedmutations, BMCSystemsBiology,12(2):13. Pathak,N.,Lai,M.L.,Chen,W.Y.,Hsieh,B.W.,Yu,G.Y.,Yang,J.M.*(2017) PharmacophoreanchormodelsofflaviviralNS3proteasesleadtodrugrepurposingforDENVinfection, BMCBioinformatics,18(16):548. 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) Clinicalassessmentofdiodelaser-assistedendoscopicintrasphenoidalvidianneurectomyinthetreatmentofrefractoryrhinitis, LasersinMedicalScience,32(9):2097-104. 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) NicotinicAcetylcholineReceptorSubtypeAlpha-9MediatesTriple-NegativeBreastCancersBasedonaSpontaneousPulmonaryMetastasisMouseModel, FrontiersinCellularNeuroscience,11:336. 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) IdentificationofneuraminidaseinhibitorsagainstdualH274Y/I222Rmutantstrains, ScientificReports,7(1):12336. 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) Vascularanatomyisadeterminingfactorofsuccessfulsubmentalflapraising:aretrospectivestudyof70clinicalcases, PeerJ,5:e3606. Hsu,H.H.,Hsu,Y.C.,Chang,L.J.,Yang,J.M.*(2017) AnintegratedapproachwithnewstrategiesforQSARmodelsandleadoptimization, BMCGenomics,18(Suppl2):104. 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) NovelClassIIa-SelectiveHistoneDeacetylaseInhibitorsDiscoveredUsinganinSilicoVirtualScreeningApproach, ScientificReports,7(1):3228. 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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。

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。

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。

成員 楊進木(Jinn-MoonYang) PostdoctoralResearchers: NikhilPathak Assistants: 齊婉葶(Wan-TingChi) 羅永淳(Yong-ChunLuo) 陳宜群(Yi-CyunChen) Ph.D.Students: 莊佾軒(Yi-ShenChung) 李容羽(Jung-YuLee) 許彥超(Yen-ChaoHsu;Jerry) 陳筠媞(Yun-TiChen) 許農育(Nung-YuHsu;Vincent) MasterStudents: 楊欣儒(Hsin-JuYang) 周治瑗(Chih-YuanChou) 王任琮(Ren-CongWang) 林韋霖(Wei-LinLin) 藍靖涵(Ching-HanLan) 林佳諦(Jia-DiLin) UndergraduateStudents: 李柏毅(Po-YiLi) 葉昱庭(Yu-TingYeh) 邱顯鈞(Hsien-ChunChiu) 莊辰雅(Chen-YaChuang) PI 楊進木(Jinn-MoonYang) Computer-aideddrugdesign SystemsBiology StructuralBioinformatics MachineLearning EditorialBoardsofPLoSONEandFrontiersinBioinformaticsandComputationalBiology MemberofBioinformaticsandSystemsBiologySocietyTaiwan Professor,InstituteofSystemsBiologyBioinformatics,NationalChiao-TungUniversity Winthe2007NationalInnovationAward,iGEMDOCK:Agraphical-automaticdrugsystemfordocking,screeningandpost-analysis WinoutstandingResearchAwardattheNationalChiao-TungUniversity(2006,2009-2014) Thetotalnumberofcitationsover2,200andmyH-indexis26basedonGooglescholarindex PostdoctoralResearchers NikhilPathak MajorFieldsinBS:Pharmacy DrugDesignforPathogenicandinfectiousDiseases-Dengue E-mail:[email protected] Assistants 齊婉葶(Wan-TingChi) AdministrativeAssistant E-mail:[email protected] 羅永淳(Yong-ChunLuo) ResearchAssistant MajorFieldsinBS:BiologicalTechnology         Diabetes E-mail:[email protected] 陳宜群(Yi-CyunChen) ResearchAssistant MajorFieldsinBS:AnimalScience E-mail:[email protected] Ph.D.Students 莊佾軒(Yi-ShenChung) MajorFieldsinBS:ComputerScience Molecularinteractionnetworksfortumorigenesisandmetastasisvirus E-mail:[email protected] 許彥超(Yen-ChaoHsu;Jerry) MajorFieldsinBS:ComputerScience Protein-LigandFamily E-mail:[email protected] 許農育(Nung-YuHsu;Vincent) MajorFieldsinBS:ComputerScience E-mail:[email protected] 李容羽(Jung-YuLee) MajorFieldsinBS:AnimalScience Molecularinteractionnetworksfortumorigenesisandmetastasis E-mail:[email protected] 陳筠媞(Yun-TiChen) MajorFieldsinBS:Appliedmaterialsandoptoelectronicengineering E-mail:[email protected] MasterStudents 楊欣儒(Hsin-JuYang) MajorFieldsinBS:MedicalBiotechnologyandLaboratoryScience E-mail:[email protected] 王任琮(Ren-CongWang) MajorFieldsinBS:AppliedBiotechnologyandAnimalScience E-mail: 藍靖涵(Ching-HanLan) MajorFieldsinBS:AppliedBioscienceTechnology E-mail: 周治瑗(Chi-hyuanChou) MajorFieldsinBS:AppliedLifescience E-mail: 林韋霖(Wei-LinLin) MajorFieldsinBS:Biotechnology E-mail: 林佳諦(Jia-DiLin) MajorFieldsinBS: E-mail: UndergraduateStudents 李柏毅(Po-YiLi) MajorFieldsinBS:BiologicalScience&Technology         E-mail:[email protected] 邱顯鈞(Hsien-ChunChiu) MajorFieldsinBS:BiologicalScience&Technology         E-mail: 莊辰雅(Chen-YaChuang) MajorFieldsinBS:BiologicalScience&Technology         E-mail: 葉昱庭(Yu-TingYeh) MajorFieldsinBS:BiologicalScienceandTechnology         E-mail: Backtotop Alumni Ph.D.(Total:13) Name MajorFieldsinBS Memo(ResearchGroups,ResearchDirections,Publications) 黃星翰(Sing-HanHuang) BiochemicalScienceandTechnology October2017,Ph.D.HumanBrainAgingandNeurodegenerationDiseaseJournalpaper:2papers 林峻宇(Chun-YuLin) BiologicalTechnology July2014,Ph.D.SystemsBiology:Protein-proteininteractionJournalpaper:11papersCurrentPosition:JSPSPost-DoctoralResearchFellowinKyotoUniversity 林志達(Chih-TaLin) BiologicalTechnology July2014,Ph.D.Anticancerdrug:Kinase-specificinhibitors&networksJournalpaper:5papers 邱一原(Yi-YuanChiu) ComputerScience July2014,Ph.D.Computer-aideddrugdesignJournalpaper:4papersCurrentPosition:TSMC(台積電) 陳世勳(Shih-HsunChen) BiochemicalEngineering December2013,Ph.D.Computer-aideddrugdesignJournalpaper:3papers 劉怡馨(I-HsinLiu) LifeScience July2013,Ph.D.SystemsBiology:Protein-MHC-TCRinteractionJournalpaper:3papers 羅宇書(Yu-ShuLo) LifeScience July2012,Ph.D.SystemsBiology:Protein-proteininteractionJournalpaper:10papersCurrentPosition:Meribank(宣捷生技) 許凱程(Kai-ChengHsu) BiologicalTechnology July2011,Ph.D.Computer-aideddrugdesignJournalpaper:16papersCurrentPosition:TaipeiMedicalUniversity(臺北醫學大學) 陳彥甫(Yen-FuChen) AppliedChemistry July2010,Ph.D.Computer-aideddrugdesignJournalpaper:6papers(Winthe2007NationalInnovationAward)CurrentPosition:CMC(中環科技) 黃章維(Jhang-WeiHuang) BiologicalTechnology September2010,Ph.D.InfluenzaVirus:AntigenicDriftAnalysis,Antigen-AntibodyinteractionJournalpaper:4papersCurrentPosition:CrackerBio(奎克生技光電) 陳俊辰(Chun-ChenChen) BiologicalTechnology June2009,Ph.D.SystemsBiology:Protein-proteininteractionJournalpaper:3papersCurrentPosition:康健雜誌 董其樺(Chi-HuaTung) BiologicalScience June2009,Ph.D.StructuralBioinformatics:3D-BLAST,Antigen-AntibodyinteractionJournalpaper:3papersCurrentPosition:AssistantProfessor,DepartmentofBioinformatics,ChungHuaUniversity(中華大學) 張耀霖(Yao-LinChang) ComputerScience June2008,Ph.D.Title:A3D-regulogapproachtopredictprotein-DNAbindingpartnersandbindingmodel(Co-advisedstudentwithCheng-YanKaoinNTU)通過高考三級資訊處理職系資訊處理類科 朱彥煒(Yen-WeiChu) ComputerScience June2006,Ph.D.Title:FindingProteinSecondaryStructureRegularityandRelatedApplications(Co-advisedstudentwithChuen-TsaiSuninNCTU)CurrentPosition:AssociateProfessor,InstituteofBioinformatics,NationalChungHsingUniversity(中興大學) Backtotop MD.Ph.D. Name MajorFieldsinBS Memo(ResearchGroups,ResearchDirections,Publications)                賴文森(Wen-SenLai) DepartmentofOtolaryngology,TaichungArmedforcesGeneralHospital June2018,MD.Ph.D.Journalpaper:22papers 李日清(Jih-ChinLee) InstituteofMedicalSciences,TheNationalDefenseMedicalCenter July2016,MD.Ph.D.Journalpaper:41papers Master Name MajorFieldsinBS Memo(ResearchGroups,ResearchDirections,Publications) 劉威廷(Wei-TingLiu) Foodsciences March2019,MasterSystemsBiology 郭超望(Chao-WangKuo) MedicalTechnology March2019,MasterSystemsBiology 李力渝(Li-YuLi) FoodScience March2019,MasterComputer-aideddrugdesign 趙千嫣(Chien-YenChao) ComputerScienceandInformationEngineering March2019,MasterComputer-aideddrugdesign 洪慈懋(Tzu-MaoHung) Nutrition March2019,MasterComputer-aideddrugdesign 蔡宜君(Yi-ChunTsai) BiologicalTechnologyy January2019,MasterComputer-aideddrugdesign 巫思穎(Szu-YingWu) Microbiology July2017,MasterComputer-aideddrugdesign 李容羽(Jung-YuLee) AnimalScience July2017,MasterSystemsBiology:Protein-proteininteraction 許元綸(Yuan-LuenSheu) InformationManagement July2016,MasterSystemsBiology:Protein-proteininteraction 顏佳儀(Chia-YiYen) BiologicalTechnology July2016,MasterComputer-aideddrugdesign 楊方琪(Yi-JyunJhen) BiologicalTechnology July2016,MasterSystemsBiology:Protein-proteininteraction 李哲勳(Jhuan-DongLin) BiologicalTechnology July2016,MasterComputer-aideddrugdesign 莊佾軒(Yi-ShenChung) ComputerScience July2015,MasterSystemsBiology:Protein-proteininteraction 沈培鈞(Pei-JyunChen) LifeScience July2015,MasterComputer-aideddrugdesign 陳怡君(Yi-JyunJhen) InformationManagement July2015,MasterSystemsBiology:Protein-proteininteraction 林傳東(Jhuan-DongLin) EarthSciences July2015,MasterComputer-aideddrugdesign 曾仁琥(Jen-HuTseng) Pharmacy July2015,MasterComputer-aideddrugdesign 林昱葦(Yu-WeiLin) BiochemicalTechnology July2014,MasterSystemsBiology:Protein-Proteininteraction 劉冠秀(Kuan-ShiuLiu) ComputerScience July2014,MasterComputer-aideddrugdesign 李采凌(Tsai-LingLee) ComputerScience July2013,MasterSystemsBiology:Protein-proteininteractionJournalpaper:1paper 徐瑋澤(Wei-ZeSyu) LifeScience July2013,MasterComputer-aideddrugdesign 尤宣人(Syuan-RenYou) ComputerScience July2012,MasterComputer-aideddrugdesign 游宇震(Yu-Chen,Yu) ManagementInformationSystem July2012,MasterSystemsBiology:Protein-proteininteraction 李淩婷(Ling-TingLi) MedicineManagement July2012,MasterComputer-aideddrugdesignTitle:Coresite-moietymapsofhistonedemethylasefamilyformulti-targetinhibitorsandbindingmechanismsJournalpaper:3papers 林伸融(Shen-RongLin) ComputerScience July2014,MasterComputer-aideddrugdesignTitle:iGemdock2.0andSiMMap:Post-screeninganalysisforstructure-baseddrugdesignJournalpaper:4paper 黃御哲(Yu-ChiHuang) BiologicalTechnology July2011,MasterComputer-aideddrugdesignTitle:Awebserverforleadoptimizationusingsite-moietymap:AcasestudyonneuraminidaseJournalpaper:1paper 林怡瑋(Yi-WeiLin) LifeScience July2011,MasterSystemsBiology:Protein-proteininteractionTitle:Template-basedHomologousModulesthroughProtein-proteinInteractionFamiliesJournalpaper:2papers 許彥超(Yen-ChaoHsu) ComputerScience December2011,MasterComputer-aideddrugdesignTitle:Moiety-basedsite-moietymap 林韋帆(Wei-FanLin) LifeScience July2011,MasterInfluenzaVirus:AntigenicDriftAnalysisTitle:GeneticandantigenicanalysistothehemagglutininofinfluenzaAH1N1virusandcomparisonswithH3N2virusJournalpaper:1paper 張力仁(Li-JenChang) LifeScience July2010,MasterStructuralBioinformatics 林峻宇(Chun-YuLin) BiologicalTechnology May2010,MasterSystemsBiology:Protein-proteininteractionJournalpaper:2papers 陳彥修(Yen-HsiuChen) LifeScience June2009,MasterSystemsBiology:Protein-DNA/Protein-RNAinteraction 劉康平(Kang-PingLiu) ComputerScience June2009,MasterSystemsBiology:Protein-proteininteractionJournalpaper:1paper 陳祐德(Yu-TeChen) Aquaculture June2008,MasterTitle:ANewProfileMethodtoPredictProtein-ligandBindingSite 羅宇書(Yu-ShuLo) LifeScience June2008,MasterTitle:Template-BasedScoringFunctionforPredictingProtein-proteinInteractionJournalpaper:2papers 許凱程(Kai-ChengHsu) BiologicalTechnology June2007,MasterTitle:BindingAffinityAnalysisofProtein-ligandComplexes 陳右儒(Yo-RuChen) ComputerScience June2007,MasterTitle:iGEMDOCK:Agraphical-automaticdrugdesignsystemfordocking,screeningandpost-analysis(Winthe2007NationalInnovationAward)CurrentPosition:MediaTek(聯發科) 楊登凱(Teng-KaiYang) ComputerScience June2006,MasterTitle:StructuralBindingPocketClusteringandProtein-ligandInteractionAnalysisforATP-bindingProteins 陳永強(Yung-ChiangChen) LifeScience June2006,MasterTitle:InferringDomainAnnotatedProtein-ProteinInteractionsthrough3D-DomainInterologsJournalpaper:2papers 葛振寧(Chen-NengKo) BiologicalScience June2006,MasterTitle:Structure-basedCompoundScreeningforHelicobacterpylorishikimatekinase(HpSK)Journalpaper:1paper 黃章維(Jhang-WeiHuang) BiologicalTechnology June2006,MasterTitle:PredictingAntigenicVariantsofInfluenzaAH3N2VirusesbyBuildingRelationshipsbetweenGeneticEvolutionandAntigenicDriftJournalpaper:2papers 董其樺(Chi-HuaTung) BiologicalScience June2005,MasterTitle:PiSA-BLAST:ANewToolforProteinStructureAlignmentandDatabaseSearch(Wintheprizeof2005BestM.S.andPh.D.DissertationAwardhostedbyIICM(InstituteofInformation&ComputingMachinery))Website:3D-BLASTJournalpaper:3papers 邱一原(Yi-YuanChiu) ComputerScience June2005,MasterTitle:OptimizingNewEnergyFunctionsforProteinFoldingJournalpaper:1paper 林柏村(Po-TsunLin) LifeScience June2005,MasterTitle:LigSeeSVM:SupportVectorMachinesandDatafusionforLigand-basedCompoundScreeningandApplicationstoGPCRandGABAA 陳宏助(Heng-ChuChen) LifeScience June2005,MasterTitle:InferringProtein-proteinInteractionsfromStructuralDomain-domainInteractions 張立人(Li-JenChang) MedicalTechnology June2005,MasterTitle:IntegratingGEMDOCKwithGEM-PLSandGEM-kNNforQSARmodelingofhuAChEandAGHO 沈再威(Tsai-WeiShen) BiologicalScience June2004,MasterTitle:EnhancingGEMDOCKonVirtualDatabaseScreeningandApplicationtoEnvelopeProteinandD-Hydantoinase(Wintheprizeof2004BestM.S.andPh.D.DissertationAwardhostedbyIICM(InstituteofInformation&ComputingMachinery))Website:GEMDOCKJournalpaper:2papers 林建宏(Chien-HengLin) BiologicalScience June2004,MasterTitle:MuLiSA:AnalysisandIdentificationofFunctionalMotifsandResiduesinProteinsbyMultipleLigand-boundStructureAlignments 陳彥甫(Yen-FuChen) AppliedChemistry June2004,MasterTitle:ValidationandApplicationofGEMDOCKandApplicationofDataFusioninVirtualScreeningJournalpaper:2papers 張育祥(Yu-HsiangChang) LifeScience June2003,MasterTitle:ANewEnergyModelforProtein-ProteinInteractionPrediction Backtotop 研究及合作夥伴 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 Originalideas Drugdiscovery:PharmalogsandHomopharma Molecularinterfacefamilies(protein-drug,protein-protein,andprotein-DNA) Homologousstructuralsystemsbiology Structure-networkGWAS 應用領域 藥物傳輸老藥新用 天然藥新藥開發 抗癌與抗感染藥物開發 腦及神經老化藥物開發 Overview     Ourresearchfocusedoncomputer-aideddrugdesign(GEMDOCKandSiMMap),structuralbioinformatics(3D-BLAST,(PS)2andfastSCOP),andsystemsbiology(PPISearchand3D-partner),especiallyinvestigatingthemolecularinterfaces(e.g.,protein-protein,protein-DNA,protein-ligandinteractions).Ourmaincontributionsandinnovationsaredescribedasfollows:I)Discovertheprotein-compoundinteractionfamilyformulti-targetdrugdesignandnewusesforolddrug[1-4].II)Thefirstteamproposedprotein-proteininteractions(interfacefamily)acrossmultiplespecies[5-8].III)Wehavedevelopedthefirsttool,called3D-BLASTwhichisasfastasBLASTandhasthefeaturesofBLAST(e.g.robuststatisticalbasis,andeffectiveandreliablesearchcapabilities),tosearchlargeproteinstructures(>30000)within3secondsintheworld[9-11]. Drugdiscovery:PharmalogsandHomopharma     Forstructure-basedprotein-ligandinteractionsanddrugdiscovery,wehavedevelopedamoleculardockingtool,namelyGEMDOCK[3,4,13,14],whichisoneofwide-usedtoolsintheworld.Wecooperatedwith10researchteamsondiversedrugtargets.Wecooperatedwithover10laboratorieswhichsuccessfullyappliedourtoolsforidentifyingleadcompoundsandproteinfunctionalsitesandproteinengineering.Forexample,GEMDOCKhasbeensuccessfullyappliedtoidentifytheleadcompoundsfordenguevirusenvelopprotein(cooperatingwithYangYLinNCTU)[2];inhibitorsofinfluenzavirusneuraminidase(cooperatingwithHsuTAinNHRI)[15];leadcompoundsofROCKkinase(cooperatingwithChaoJIinNCTU)foranti-cancerdrugs;antibioticsofshikimatekinasesofMycobacteriumtuberculosisandHelicobacterpylori(cooperatingwithWangWCinNTHU).WehavesuccessfullyappliedourtoolsfordiscoveringthesecondaryvitaminD3bindingsiteofmilkbeta-lactoglobulin(cooperatingwithMaoJIinNCTU)[16,17];thebindingmechanismbetweenc-di-GMPadcAMPReceptor-LikeProteinCLP(cooperatingwithChaoSHinNCHU)[18].Thetimedcitationsoftworelatedpapers[3,13]are58and61,respectively,from2004.Theserelatedpaperswerecitedover180times.Wegotthe2007NationalInnovationAwardduetotheachievementofiGEMDOCK.     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-Cpocket)，並成功針對此位點篩選出選擇性抑制劑(Type-Cinhibitors)，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。

Molecularinterfacefamilies(protein-drug,protein-protein,andprotein-DNA)     Inprotein-peptideinteractions,weimprovedourPPItemplate-basedscoringfunctionwithtemplatesimilarityandinteractingforcetoguaranteestatisticallysignificantinterfacesimilaritybetweenpeptidecandidatesandstructuretemplates.Ourmodel,consideringbothMHC-peptideandpeptide-TCRinterfaces,couldprovidevisualizationandbiologicalinsightsofMHC-peptide-TCRbindingmodels.Webelievethatitisveryhelpfulforthedevelopmentofpeptide-basedvaccines.Forprotein-DNAinteractions,wedevelopedanewapproach,namely3D-regulogs,toinferprotein-DNAbindingpartnersbyusingtheconceptofregulogandcrystalstructuresofprotein-DNAcomplexastemplates[12].Thisapproachalsoprovidesbindingmodels,interactingaminoacids,andDNAbasesofpredictedpartners.Forprotein-ligandinteractions,wehaveintroducedsite-moietymaps[1],whichrecognizeinteractionpreferencesbetweenproteinpocketsandcompoundmoieties.SiMMapwasdevelopedtoidentifysite-moietymapsfromqueryproteinstructuresandtheirdocked(orco-crystallized)compounds.Over1,400usershavecreatedmorethan1,500site-moietymapsfordifferentproteins.Site-moietymapisabletoprovidebiologicalinsightsandusefulfordrugdiscoveryandleadoptimization. Homologousstructuralsystemsbiology     Forsystemsbiologyandstructuralbioinformatics,wehaveproposedanovelconcept,called"3D-domaininterologs",todiscoverprotein-proteininteractions[6-8]andprotein-DNAinteractions[12]whichareconsideredasorthologousinteractionsamongdifferentspecies,inparticularaboutinferredinteractingdomainpairsandbindingmodels(e.g.hydrogen-bondinteractionsandconservedresidues).Forprotein-proteininteractions,weproposedthePPISearchserver[5]forsearchinghomologousprotein-proteininteractions(PPIs),calledPPIfamily,acrossmultiplespecies.Accordingtoourknowledge,PPISearchisthefirstpublicserverthatidentifieshomologousPPIsfromannotatedPPIdatabasesandinferstransferabilityofinteractingdomainsandfunctionsbetweenhomologousPPIsandthequery.Bytakingaccountofstructuralbioinformaticscrossspecies,weextendedPPISearchtoPCFamily[8],whichisusefulforbindingmodelvisualizationsandannotatingqueryproteinsbasedonhomologousproteincomplexes.UntilSeptember2010,over3,500usershaveusedPPISearchandPCFamilyservers.Furthermore,thenumberofaccessing3D-BLASTexceeds6,000from44countriesandrelatedpaperswerecited~50timessince2007. 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（Försterresonanceenergytransfer），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(mRNAmicroarray)、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(PPIfamily)、模組交互作用家族(Modulefamily)、蛋白質-配體交互作用家族(Protein-ligandfamily)，進而揭露大腦疾病詳細生化機制。

合作夥伴     Wehaveaccumulatedextensiveexperiencesindrugdesigntoachievethespecificaims.Ourteamconsistsofexpertsindifferentfields,includingcomputationaldrugdesign,systemsbiology,clinicaltrial,leadoptimization,biochemistry,andanimalmodels.Wehavesuccessfullydiscovered45leadcompounds(<10μM)forvariousdiseasesorpathogens.Oneoftheidentifiednaturalcompounds,rosmarinicacid,iscurrentlyapplyingfortheU.S.patentandIRBapprovalatMackayMemorialHospital(馬偕醫院)forclinicaltrials.Basedontheseresults,wehavereceivedoneU.S.patent(US8,175,860B2),andhaveappliedoneU.S.patent(13/872,456)andoneROCpatent.Inuniversity-industrycollaborations,wehavecollaboratedwithScinoPharm(台灣神隆),PhalanxBiotechGroup(華聯生技),FoodIndustryResearchandDevelopmentInstitute(食品工業研究所),andJasonLifeTechfordevelopingnewdrugs,botanicaldrugs,healthyfood,andmicroarrayplatformfordetectingdiseases.Wehavecollaboratedwithover30laboratories(e.g.,ProfessorWangHJ[王惠鈞院士]andProfessorMarkvonItzstein,inventorofthefirstanti-influenzadrug,Zanamivir),fiveteachinghospitals,and15nationalinstitutesfordrugdiscovery,systemsbiology,bindingmechanisms,andmulti-targetdrugs.Inaddition,wehaveachievedsomesignificantresultsinmolecularinteractionsandstructuralsystemsbiology:1)Wearethefirstteamproposedmolecular-interfacefamilies;2)Wehaveestablishedthestatisticalbiophysicsmethodstoinfersite-moietymaps(hotspots)ofproteinsforprotein-ligandbindingmechanismsanddrugdiscovery;3)Wehaveproposedthecomprehensivemolecularinteractionnetworksforstudyinginteractomes;4)WehavedevelopedGEMDOCK,whichisaworld-wideuseddockingprograms. References ChenYF,HsuKC,LinSR,WangWC,HuangYC,YangJM: SiMMap:awebserverforinferringsite-moietymaptorecognizeinteractionpreferencesbetweenproteinpocketsandcompoundmoieties. NucleicAcidsResearch2010,38:W424-W430. YangJM,ChenYF,TuYY,YenKR,YangYL: Combinatorialcomputationalapproachestoidentifytetracyclinederivativesasflavivirusinhibitors. PLoSONE2007:e428. YangJM,ChenCC: GEMDOCK:agenericevolutionarymethodformoleculardocking. Proteins:Structure,Function,andBioinformatics2004,55:288-304. YangJM,ShenTW: Apharmacophore-basedevolutionaryapproachforscreeningselectiveestrogenreceptormodulators. Proteins:Structure,Function,andBioinformatics2005,59:205-220. ChenCC,LinCY,LoYS,YangJM: PPISearch:awebserverforsearchinghomologousprotein-proteininteractionsacrossmultiplespecies. NucleicAcidsResearch2009,37:W369-W375. ChenYC,LoYS,HsuWC,YangJM: 3D-partner:awebservertoinferinteractingpartnersandbindingmodels. NucleicAcidsResearch2007:W561-W567. LoYS,ChenYC,YangJM: 3D-interologs:Anevolutiondatabaseofphysicalprotein-proteininteractionsacrossmultiplegenomes. BMCGenomics2010,11,Suppl3:S7. LoYS,LinCY,YangJM: PCFamily:awebserverforsearchinghomologousproteincomplexes. NucleicAcidsResearch2010,38:W516-W522. YangJM,TungCH: Proteinstructuredatabasesearchandevolutionaryclassification. NucleicAcidsResearch2006,34:3646-3659. TungCH,HuangJW,YangJM: Kappa-alphaplotderivedstructuralalphabetandBLOSUM-likesubstitutionmatrixforrapidsearchofproteinstructuredatabase. GenomeBiology2010,2007,8:R31. TungCH,YangJM: fastSCOP:afastwebserverforrecognizingproteinstructuraldomainsandSCOPsuperfamilies. NucleicAcidsResearch2007,35:W438-W443. ChangYL,TsaiHK,KaoCY,ChenYC,HuYJ,YangJM: EvolutionaryconservationofDNA-contactresiduesinDNA-bindingdomains. BMCBioinformatics2008,9(S6):S3.1-S3.9. YangJM,ChenYF,ShenTW,KristalBS,HsuDF: Consensusscoringcriteriaforimprovingenrichmentinvirtualscreening. JournalofChemicalInformationandModeling2005,45:1134-1146. YangJM: Developmentandevaluationofagenericevolutionarymethodforprotein-liganddocking. JournalofComputationalChemistry2004,25:843-857. HungHC,TsengCP,YangJM,JuYW,TsengSN,ChenYF,ChaoYS,HsiehHP,ShihSR,HsuJT: Aurintricarboxylicacidinhibitsinfluenzavirusneuraminidase. AntiviralResearch2009,81:123-131. YangMC,GuanHH,LiuMY,LinYH,YangJM,ChenWL,ChenCJ,MaoSJT: CrystalStructureofaSecondaryVitaminD3BindingSiteofMilkß-Lactoglobulin. Proteins:Structure,Function,andBioinformatics2008:1197-1210. YangMC,GuanHH,YangJM,KoCN,LiuMY,LinYH,ChenCJ,MaoSJT: RationalDesignforcrystallizationofb-LactoglobulinandvitaminD3complex:revealofasecondarybindingsite. CrystalGrowth&Design2008:DOI:10.1021/cg800697s. ChinKH,LeeYC,TuZL,ChenCH,TsengYH,YangJM,RyanRP,McCarthyY,DowJM,WangAHetal: ThecAMPreceptor-likeproteinCLPisanovelc-di-GMPreceptorlinkingcell-cellsignalingtovirulencegeneexpressioninXanthomonascampestris. JournalofMolecularBiology2010,396:646-662. 工具及資料庫 BioXGEM所發展的生物資訊網頁工具及資料庫 GEMDOCK GEMDOCK-aGenericEvolutionaryMethodformolecularDOCKingGEMDOCKisaprogramforcomputingaligandconformationandorientationrelativetotheactivesiteoftargetprotein.ThetoolwasdevelopedbyJinn-MoonYang,aprofesoroftheInstituteofBioinformatics,NationalChiaoTungUniversity. URL:http://gemdock.life.nctu.edu.tw/ SiMMap SiMMap:Site-moietymapfordrugdiscoveryandmechanisms URL:http://simfam.life.nctu.edu.tw/ 3D-BLAST 3D-BLASTisaveryfastandaccuratemethodfordiscoveringthehomologousproteinsandevolutionaryclassificationsofanewlydeterminedproteinstructure.Our3D-BLASThastheadvantagesofBLASTtoolforfastproteinstructuredatabasescanning. URL:http://3d-blast.life.nctu.edu.tw/ Protein-ProteinInteractionSearch Inputaninteractingproteinpairasaquerytosearchitshomologousinteractionsacrossmultiplespecies URL:http://gemdock.life.nctu.edu.tw/ppisearch/ PCFamily PCFamily:ProteinComplexFamilySearch URL:http://pcfamily.life.nctu.edu.tw/ MoNetFamily MoNetFamily-Homologousmodulesandmodule-moduleinteractionnetworksinvertebrates URL:http://monetfamily.life.nctu.edu.tw/ KIDFamMap KIDFamMap:Kinase-inhibitor-diseasefamilymap URL:http://gemdock.life.nctu.edu.tw/KIDFamMap/ CaMPNets CaMPNets:Membraneprotein-regulatednetworksacrosshumancancers URL:http://campnets.life.nctu.edu.tw/ BioXGEMIntegratedDiscoveryforOmicsdata URL:http://140.113.120.248/BioXGEM-tools/ BioXGEMIntegratedDiscoveryforDrugDesign URL:http://140.113.120.248/BioXGEM-drug/ FooDisNET URL:http://140.113.120.248/FooDisNET TranditionalChineseHerb TranditionalChineseHerb URL:http://gemdock.life.nctu.edu.tw/HERBID/ BioXGEM常用DataSets SARS-CoV-2mainproteasedata(Downloadall) Sequencedata:IncludeSARS-CoV-2mainprotease(fasta),12Coronavirusmainproteases(fasta)andMSAresults Structuredata:Include57alignedSARS-CoVmainproteases(pdb)and187alignedSARS-CoV-2mainproteases(pdb) FDAapproveddrugs:Include2125approveddrugsfromDrugBank(mol) Selecteddockingposes:Include8dockingposesofdifferentPPCs Molecularrecognition 100PDBcomplexesset:100protein-ligandcomplexes CCDC/Astextestset:305protein-ligandcomplexes Virtualscreeningsets Thymidinekinaseinhibitors:10knowninhibitorsforthymidinekinase Estrogenreceptoralphaagonists:10knownagonistsforestrogenreceptoralpha Estrogenreceptoralphaantagonists:10knownantagonistsofestrogenreceptoralpha Dihydrofolatereductaseinhibitors:10knownligandsforhumandihydrofolatereductase HumancarbonicanhydraseII(HCAII):20inhibitorsofhumancarbonicanhydraseII ACD990dataset:990randomlyselectedcompoundsfromACD CMCdatabase:7375pharmaceuticalcompounds(1900-present)fromComprehensiveMedicinalChemistry(CMC) Geneexpressionsets Breastcancer Breastcancer_100genes:150samples(30N,120P)with100genesforteaching Breastcancer_allgenes:150samples(30N,120P)with20531genesforcomprehensiveanalysis Breastcancer_clinical:TCGAclinicalinformationofbreastcancerpatients Livercancer Livercancer_100genes:150samples(50N,100P)with100genesforteaching Livercancer_allgenes:150samples(50N,100P)with20531genesforcomprehensiveanalysis Livercancer_clinical:TCGAclinicalinformationoflivercancerpatients Headandneckcancer Headandneckcancer_100genes:120samples(40N,80P)with100genesforteaching Headandneckcancer_allgenes:120samples(40N,80P)with20531genesforcomprehensiveanalysis Headandneckcancer_clinical:TCGAclinicalinformationofheadandneckcancerpatients Diabetes Diabetes_100genes:17samples(9N,8P)with100genesforteaching Diabetes_allgenes:17samples(9N,8P)sampleswith14463genesforcomprehensiveanalysis Convolutionalneuralnetworkforhumancancertypesprediction SourcecodeofCNNmodelandexamplesamples:ThezipfilecontainedthreeprogramsandexamplesamplesforbuildingCNNmodel 常用連結 UsefulLinksforPaper(Thesis)WritingandResearchCareerAdvice HowtobeaGoodGraduateStudent/Advisor,byMariedesJardins YouandYourResearch[English.pdf][Chinese.pdf]byRichardW.Hamming UsefulThingsToKnowaboutPh.D.ThesisResearchbyH.T.Kung BetterDissertationWritinginEnglishfromProf.Yuh-DauhLyuu'shomepage HowtoOrganizeyourThesis,byJohnW.Chinneck WritingandPresentingYourThesisorDissertation,byS.JosephLevine,Ph.D. TheElementsofStyle,4thed.byWilliamStrunk,Jr.,E.B.White,andRogerAngell.The1918version(free). TheChicagoManualofStyle ResearchcareeradvicefromDavidPatternson'shomepage Protein PDB ThisresourceispoweredbytheProteinDataBankarchive-informationaboutthe3Dshapesofproteins,nucleicacids,andcomplexassembliesthathelpsstudentsandresearchersunderstandallaspectsofbiomedicineandagriculture,fromproteinsynthesistohealthanddisease. UniProt ThemissionofUniProtistoprovidethescientificcommunitywithacomprehensive,high-qualityandfreelyaccessibleresourceofproteinsequenceandfunctionalinformation. PDBsum ThePDBsumisapictorialdatabasethatprovidesanat-a-glanceoverviewofthecontentsofeach3DstructuredepositedintheProteinDataBank(PDB).Itshowsthemolecule(s)thatmakeupthestructure(ieproteinchains,DNA,ligandsandmetalions)andschematicdiagramsoftheirinteractions.ExtensiveuseismadeofthefreelyavailableRasMolmoleculargraphicsprogramtoviewthemoleculesandtheirinteractionsin3D. CATH CATHisaclassificationofproteinstructuresdownloadedfromtheProteinDataBank.Wegroupproteindomainsintosuperfamilieswhenthereissufficientevidencetheyhavedivergedfromacommonancestor. PFam ThePfamdatabaseisalargecollectionofproteinfamilies,eachrepresentedbymultiplesequencealignmentsandhiddenMarkovmodels(HMMs).Proteinsaregenerallycomposedofoneormorefunctionalregions,commonlytermeddomains.Differentcombinationsofdomainsgiverisetothediverserangeofproteinsfoundinnature.Theidentificationofdomainsthatoccurwithinproteinscanthereforeprovideinsightsintotheirfunction. DaliDatabase TheDaliDatabaseisbasedonall-against-all3DstructurecomparisonofproteinstructuresintheProteinDataBank(PDB).ThestructuralneighbourhoodsandalignmentsareautomaticallymaintainedandregularlyupdatedusingtheDalisearchengine. SWISS-MODEL SWISS-MODELisafullyautomatedproteinstructurehomology-modellingserver. (PS)2 (PS)2isanautomatichomologymodelingserver. TheConSurfServer ItprovidesevolutionaryconservationprofilesforproteinsofknownstructureinthePDB. THPA TheHumanProteinAtlasportalisapubliclyavailabledatabasewithmillionsofhigh-resolutionimagesshowingthespatialdistributionofproteinsin44differentnormalhumantissuesand20differentcancertypes,aswellas46differenthumancelllines. STRING STRINGisadatabaseofknownandpredictedproteininteractions.Theinteractionsincludedirect(physical)andindirect(functional)associations;theyarederivedfromfoursources:GenomicContext,High-throughputExperiments,(Conserved)CoexpressionandPreviousKnowledge. Brenda Thecomprehensiveenzymeinformationsystem PhosphoSitePlus PhosphoSitePlus®(PSP)isanonlinesystemsbiologyresourceprovidingcomprehensiveinformationandtoolsforthestudyofproteinpost-translationalmodifications(PTMs)includingphosphorylation,ubiquitination,acetylationandmethylation. BLAST ForblastsearchtofindsimilarDNAorProteinsequences CLUSTALOmegaandotherMSAtools ForProteinMSA T-Coffee T-Coffeeisamultiplesequencealignmentprogram.Itsmaincharacteristicisthatitwillallowyoutocombineresultsobtainedwithseveralalignmentmethods. WebLogo WebLogoisawebbasedapplicationdesignedtomakethegenerationofsequencelogosaseasyandpainlessaspossible. WebLogo3 WebLogoisawebbasedapplicationdesignedtomakethegenerationofsequencelogoseasyandpainless. Backtotop Compound PubChem PubChemisadatabaseofchemicalmoleculesandtheiractivitiesagainstbiologicalassays. ChEMBL Itisamanuallycuratedchemicaldatabaseofbioactivemoleculeswithdrug-likeproperties. DrugBank TheDrugBankdatabaseisauniquebioinformaticsandcheminformaticsresourcethatcombinesdetaileddrug. BindingDB BindingDBisapublic,web-accessibledatabaseofmeasuredbindingaffinities,focusingchieflyontheinteractionsofproteinconsideredtobedrug-targetswithsmall,drug-likemolecules. STITCH STITCHisaresourcetoexploreknownandpredictedinteractionsofchemicalsandproteins. Avogadro Moleculebuildingandeditingtooltobuildandminimizecompoundstructures TCMID ProvideinformationonallrespectsofTraditionalChineseMedicineincludingformulae,herbsandherbalingredients Dr.Duke'sPhytochemicalandEthnobotanicalDatabases Providetheinfomationaboutplantsandtheiringredients. EDB ProvidetheinfomationaboutplantsinBangladeshandtheiringredients. ZINC Afreedatabaseofcommercially-availablecompounds. MolPort MolPortisadvancedchemicalmarketplace. Selleckchem SelleckChemicalssuppliesover3,000inhibitorsusedinthestudyofcellsignalingpathways.Weactivelytracksthelatestsciencesoourcustomerscanrelyonustobetheleadingsupplierofthenewestinhibitors. ChemicalBook 查詢化合物相關資訊的網站 Backtotop Gene GeneOntology TheGeneOntology(GO)projectisamajorbioinformaticsinitiativetodevelopacomputationalrepresentationofourevolvingknowledgeofhowgenesencodebiologicalfunctionsatthemolecular,cellularandtissuesystemlevels. GeneExpressionData(L1000) Geneexpressionishighlycorrelated.Wetakeadvantageofthishighdegreeofcorrelationtoreducethenumberofmeasurementsneededtogeneratemeaningfulgeneexpressiondatafortheapproximately20,000genesinthehumangenome. DAVID DAVIDnowprovidesacomprehensivesetoffunctionalannotationtoolsforinvestigatorstounderstandbiologicalmeaningbehindlargelistofgenes. GEO(GeneExpressionOmnibus) GEOisapublicfunctionalgenomicsdatarepositorysupportingMIAME-compliantdatasubmissions.Array-andsequence-baseddataareaccepted.Toolsareprovidedtohelpusersqueryanddownloadexperimentsandcuratedgeneexpressionprofiles. Genome Thisresourceorganizesinformationongenomesincludingsequences,maps,chromosomes,assemblies,andannotations. 1000GenomeBrowser Aglobalreferenceforhumangeneticvariation TCGA(TheCancerGenomeAtlas) TheCancerGenomeAtlas(TCGA)DataPortalprovidesaplatformforresearcherstosearch,download,andanalyzedatasetsgeneratedbyTCGA.Itcontainsclinicalinformation,genomiccharacterizationdata,andhighlevelsequenceanalysisofthetumorgenomes. cBioPortal ThecBioPortalforCancerGenomicsprovidesvisualization,analysisanddownloadoflarge-scalecancergenomicsdatasets(e.g.TCGA). CCLE(CancerCellLineEncyclopedia) TheCancerCellLineEncyclopedia(CCLE)projectisanefforttoconductadetailedgeneticcharacterizationofalargepanelofhumancancercelllines.TheCCLEprovidespublicaccessanalysisandvisualizationofDNAcopynumber,mRNAexpression,mutationdataandmore,for1000cancercelllines. GeneCards GeneCardsisasearchable,integrativedatabasethatprovidescomprehensive,user-friendlyinformationonallannotatedandpredictedhumangenes.Itautomaticallyintegratesgene-centricdatafrom~125websources,includinggenomic,transcriptomic,proteomic,genetic,clinicalandfunctionalinformation. HPRD Provideintegratedinformationofdomainarchitecture,post-translationalmodifications,interactionnetworksanddiseaseassociationforeachproteininthehumanproteome. AllenBrainAtlas Ananatomicallycomprehensiveatlasoftheadulthumanbraintranscriptome MGI Provideintegratedgenetic,genomic,andbiologicaldataformouse. SGD ProvideintegratedbiologicalinformationforthebuddingyeastSaccharomycescerevisiae. ArrayExpress ArrayExpressArchiveofFunctionalGenomicsDatastoresdatafromhigh-throughputfunctionalgenomicsexperiments,andprovidesthesedataforreusetotheresearchcommunity. Backtotop Tools Chimera ProteinVisualizationtool Cytoscape Cytoscapeisanopensourcesoftwareplatformforvisualizingcomplexnetworksandintegratingthesewithanytypeofattributedata. MeV MeVisaversatilemicroarraydataanalysistool,incorporatingsophisticatedalgorithmsforclustering,visualization,classification,statisticalanalysisandbiologicalthemediscovery. GENE-E GENE-Eisamatrixvisualizationandanalysisplatformdesignedtosupportvisualdataexploration. Backtotop Others Google學術搜尋 站在巨人的肩膀上 KEGG KEGGPATHWAYisacollectionofmanuallydrawnpathwaymapsrepresentingourknowledgeonthemolecularinteractionandreactionnetworks. EBI(TheEuropeanBioinformaticsInstitute) EMBL-EBIprovidesfreelyavailabledatafromlifescienceexperiments,performsbasicresearchincomputationalbiologyandoffersanextensiveusertrainingprogramme,supportingresearchersinacademiaandindustry. COSMIC AllcancersariseasaresultoftheacquisitionofaseriesoffixedDNAsequenceabnormalities,mutations,manyofwhichultimatelyconferagrowthadvantageuponthecellsinwhichtheyhaveoccurred.Thereisavastamountofinformationavailableinthepublishedscientificliteratureaboutthesechanges.COSMICisdesignedtostoreanddisplaysomaticmutationinformationandrelateddetailsandcontainsinformationrelatingtohumancancers. Ensembl IncludingGeneexpressiondatabase,SNPdatabaseandENCODE(EncyclopediaofDNAElements(ENCODE)Consortium)*TheEncyclopediaofDNAElements(ENCODE)ConsortiumisaninternationalcollaborationofresearchgroupsfundedbytheNationalHumanGenomeResearchInstitute(NHGRI) RefSeq:NCBIReferenceSequenceDatabase Acomprehensive,integrated,non-redundant,well-annotatedsetofreferencesequencesincludinggenomic,transcript,andprotein. ExPASy ExPASyistheSIBBioinformaticsResourcePortalwhichprovidesaccesstoscientificdatabasesandsoftwaretools(i.e.,resources)indifferentareasoflifesciencesincludingproteomics,genomics,phylogeny,systemsbiology,populationgenetics,transcriptomicsetc.OnthisportalyoufindresourcesfrommanydifferentSIBgroupsaswellasexternalinstitutions. SMART SMART(aSimpleModularArchitectureResearchTool)allowstheidentificationandannotationofgeneticallymobiledomainsandtheanalysisofdomainarchitectures.Morethan500domainfamiliesfoundinsignalling,extracellularandchromatin-associatedproteinsaredetectable.Thesedomainsareextensivelyannotatedwithrespecttophyleticdistributions,functionalclass,tertiarystructuresandfunctionallyimportantresidues.Eachdomainfoundinanon-redundantproteindatabaseaswellassearchparametersandtaxonomicinformationarestoredinarelationaldatabasesystem.Userinterfacestothisdatabaseallowsearchesforproteinscontainingspecificcombinationsofdomainsindefinedtaxa.Forallthedetails,pleaserefertothepublicationsonSMART. BioPharmaInsight BioPharmInsightisyourdefinitiveguidetothegloballifesciencescommunity,combininganonlinebusinessintelligencesystemofcomprehensivemarketanalyticsandkeyindustrycontactswithanindependentinvestigativejournalismnewsservice. GlobalData GlobalDataisthepremiersourceofactionableinsightintotheenergyandhealthcareindustries.Withthecombinedexpertiseofmorethan1,000researchers,marketanalystsandconsultants,weprovidehigh-quality,accurateandtransparentindustryinsightthathelpsourclientstoachievegrowthandincreasebusinessvalue. GEN GeneticEngineering&BiotechnologyNews(GEN)hasretaineditspositionasthepremierbiotechpublicationsinceitslaunchin1981.GENpublishesaprintedition21timesayearandhasadditionalexclusiveeditorialcontentonline,includingnewsandanalysisaswellaswebinars,videos,andpolls.GEN'suniquenewsandtechnologyfocuscoverstheentirebioproductlifecycle,includingdrugdiscovery,early-stageR&D,appliedresearch(e.g.,omics,biomarkers,anddiagnostics),bioprocessing,andcommercialization. PhysOrg:Biologynews 海峽生技醫藥品風雲 Backtotop 人才招募 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 THEWORLDOFDRUGDISCOVERY, FUNCTIONBIOINFORMATICSANDSYSTEMSBIOLOGY. 楊進木教授 03-5712121#56942(Lab:#56946) [email protected] 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(MarkvonItzstein)、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 活動花絮 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 藥物設計與系統生物實驗室©BioXGEM2015