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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

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dc.contributor.coauthorMenden, Michael P.
dc.contributor.coauthorWang, Dennis
dc.contributor.coauthorMason, Mike J.
dc.contributor.coauthorSzalai, Bence
dc.contributor.coauthorBulusu, Krishna C.
dc.contributor.coauthorGuan, Yuanfang
dc.contributor.coauthorYu, Thomas
dc.contributor.coauthorKang, Jaewoo
dc.contributor.coauthorJeon, Minji
dc.contributor.coauthorWolfinger, Russ
dc.contributor.coauthorNguyen, Tin
dc.contributor.coauthorZaslavskiy, Mikhail
dc.contributor.coauthorJang, In Sock
dc.contributor.coauthorGhazoui, Zara
dc.contributor.coauthorAhsen, Mehmet Eren
dc.contributor.coauthorVogel, Robert
dc.contributor.coauthorNeto, Elias Chaibub
dc.contributor.coauthorNorman, Thea
dc.contributor.coauthorTang, Eric K. Y.
dc.contributor.coauthorGarnett, Mathew J.
dc.contributor.coauthorDi Veroli, Giovanni Y.
dc.contributor.coauthorFawell, Stephen
dc.contributor.coauthorStolovitzky, Gustavo
dc.contributor.coauthorGuinney, Justin
dc.contributor.coauthorDry, Jonathan R.
dc.contributor.coauthorSaez-Rodriguez, Julio
dc.contributor.coauthorAbante, Jordi
dc.contributor.coauthorAbecassis, Barbara Schmitz
dc.contributor.coauthorAben, Nanne
dc.contributor.coauthorAghamirzaie, Delasa
dc.contributor.coauthorAittokallio, Tero
dc.contributor.coauthorAkhtari, Farida S.
dc.contributor.coauthorAl-lazikani, Bissan
dc.contributor.coauthorAlam, Tanvir
dc.contributor.coauthorAllam, Amin
dc.contributor.coauthorAllen, Chad
dc.contributor.coauthorde Almeida, Mariana Pelicano
dc.contributor.coauthorAltarawy, Doaa
dc.contributor.coauthorAlves, Vinicius
dc.contributor.coauthorAmadoz, Alicia
dc.contributor.coauthorAnchang, Benedict
dc.contributor.coauthorAntolin, Albert A.
dc.contributor.coauthorAsh, Jeremy R.
dc.contributor.coauthorRomeo Aznar, Victoria
dc.contributor.coauthorBa-alawi, Wail
dc.contributor.coauthorBagheri, Moeen
dc.contributor.coauthorBajic, Vladimir
dc.contributor.coauthorBall, Gordon
dc.contributor.coauthorBallester, Pedro J.
dc.contributor.coauthorBaptista, Delora
dc.contributor.coauthorBare, Christopher
dc.contributor.coauthorBateson, Mathilde
dc.contributor.coauthorBender, Andreas
dc.contributor.coauthorBertrand, Denis
dc.contributor.coauthorWijayawardena, Bhagya
dc.contributor.coauthorBoroevich, Keith A.
dc.contributor.coauthorBosdriesz, Evert
dc.contributor.coauthorBougouffa, Salim
dc.contributor.coauthorBounova, Gergana
dc.contributor.coauthorBrouwer, Thomas
dc.contributor.coauthorBryant, Barbara
dc.contributor.coauthorCalaza, Manuel
dc.contributor.coauthorCalderone, Alberto
dc.contributor.coauthorCalza, Stefano
dc.contributor.coauthorCapuzzi, Stephen
dc.contributor.coauthorCarbonell-Caballero, Jose
dc.contributor.coauthorCarlin, Daniel
dc.contributor.coauthorCarter, Hannah
dc.contributor.coauthorCastagnoli, Luisa
dc.contributor.coauthorCelebi, Remzi
dc.contributor.coauthorCesareni, Gianni
dc.contributor.coauthorChang, Hyeokyoon
dc.contributor.coauthorChen, Guocai
dc.contributor.coauthorChen, Haoran
dc.contributor.coauthorChen, Huiyuan
dc.contributor.coauthorCheng, Lijun
dc.contributor.coauthorChernomoretz, Ariel
dc.contributor.coauthorChicco, Davide
dc.contributor.coauthorCho, Kwang-Hyun
dc.contributor.coauthorCho, Sunghwan
dc.contributor.coauthorChoi, Daeseon
dc.contributor.coauthorChoi, Jaejoon
dc.contributor.coauthorChoi, Kwanghun
dc.contributor.coauthorChoi, Minsoo
dc.contributor.coauthorDe Cock, Martine
dc.contributor.coauthorCoker, Elizabeth
dc.contributor.coauthorCortes-Ciriano, Isidro
dc.contributor.coauthorCserzo, Miklos
dc.contributor.coauthorCubuk, Cankut
dc.contributor.coauthorCurtis, Christina
dc.contributor.coauthorVan Daele, Dries
dc.contributor.coauthorDang, Cuong C.
dc.contributor.coauthorDijkstra, Tjeerd
dc.contributor.coauthorDopazo, Joaquin
dc.contributor.coauthorDraghici, Sorin
dc.contributor.coauthorDrosou, Anastasios
dc.contributor.coauthorDumontier, Michel
dc.contributor.coauthorEhrhart, Friederike
dc.contributor.coauthorEid, Fatma-Elzahraa
dc.contributor.coauthorElHefnawi, Mahmoud
dc.contributor.coauthorElmarakeby, Haitham
dc.contributor.coauthorvan Engelen, Bo
dc.contributor.coauthorEngin, Hatice Billur
dc.contributor.coauthorde Esch, Iwan
dc.contributor.coauthorEvelo, Chris
dc.contributor.coauthorFalcao, Andre O.
dc.contributor.coauthorFarag, Sherif
dc.contributor.coauthorFernandez-Lozano, Carlos
dc.contributor.coauthorFisch, Kathleen
dc.contributor.coauthorFlobak, Asmund
dc.contributor.coauthorFornari, Chiara
dc.contributor.coauthorForoushani, Amir B. K.
dc.contributor.coauthorFotso, Donatien Chedom
dc.contributor.coauthorFourches, Denis
dc.contributor.coauthorFriend, Stephen
dc.contributor.coauthorFrigessi, Arnoldo
dc.contributor.coauthorGao, Feng
dc.contributor.coauthorGao, Xiaoting
dc.contributor.coauthorGerold, Jeffrey M.
dc.contributor.coauthorGestraud, Pierre
dc.contributor.coauthorGhosh, Samik
dc.contributor.coauthorGillberg, Jussi
dc.contributor.coauthorGodoy-Lorite, Antonia
dc.contributor.coauthorGodynyuk, Lizzy
dc.contributor.coauthorGodzik, Adam
dc.contributor.coauthorGoldenberg, Anna
dc.contributor.coauthorGomez-Cabrero, David
dc.contributor.coauthorde Graaf, Chris
dc.contributor.coauthorGray, Harry
dc.contributor.coauthorGrechkin, Maxim
dc.contributor.coauthorGuimera, Roger
dc.contributor.coauthorGuney, Emre
dc.contributor.coauthorHaibe-Kains, Benjamin
dc.contributor.coauthorHan, Younghyun
dc.contributor.coauthorHase, Takeshi
dc.contributor.coauthorHe, Di
dc.contributor.coauthorHe, Liye
dc.contributor.coauthorHeath, Lenwood S.
dc.contributor.coauthorHellton, Kristoffer H.
dc.contributor.coauthorHelmer-Citterich, Manuela
dc.contributor.coauthorHidalgo, Marta R.
dc.contributor.coauthorHidru, Daniel
dc.contributor.coauthorHill, Steven M.
dc.contributor.coauthorHochreiter, Sepp
dc.contributor.coauthorHong, Seungpyo
dc.contributor.coauthorHovig, Eivind
dc.contributor.coauthorHsueh, Ya-Chih
dc.contributor.coauthorHu, Zhiyuan
dc.contributor.coauthorHuang, Justin K.
dc.contributor.coauthorHuang, R. Stephanie
dc.contributor.coauthorHunyady, Laszlo
dc.contributor.coauthorHwang, Jinseub
dc.contributor.coauthorHwang, Tae Hyun
dc.contributor.coauthorHwang, Woochang
dc.contributor.coauthorHwang, Yongdeuk
dc.contributor.coauthorIsayev, Olexandr
dc.contributor.coauthorWalk, Oliver Bear Don't
dc.contributor.coauthorJack, John
dc.contributor.coauthorJahandideh, Samad
dc.contributor.coauthorJi, Jiadong
dc.contributor.coauthorJo, Yousang
dc.contributor.coauthorKamola, Piotr J.
dc.contributor.coauthorKanev, Georgi K.
dc.contributor.coauthorKaracosta, Loukia
dc.contributor.coauthorKarimi, Mostafa
dc.contributor.coauthorKaski, Samuel
dc.contributor.coauthorKazanov, Marat
dc.contributor.coauthorKhamis, Abdullah M.
dc.contributor.coauthorKhan, Suleiman Ali
dc.contributor.coauthorKiani, Narsis A.
dc.contributor.coauthorKim, Allen
dc.contributor.coauthorKim, Jinhan
dc.contributor.coauthorKim, Juntae
dc.contributor.coauthorKim, Kiseong
dc.contributor.coauthorKim, Kyung
dc.contributor.coauthorKim, Sunkyu
dc.contributor.coauthorKim, Yongsoo
dc.contributor.coauthorKim, Yunseong
dc.contributor.coauthorKirk, Paul D. W.
dc.contributor.coauthorKitano, Hiroaki
dc.contributor.coauthorKlambauer, Gunter
dc.contributor.coauthorKnowles, David
dc.contributor.coauthorKo, Melissa
dc.contributor.coauthorKohn-Luque, Alvaro
dc.contributor.coauthorKooistra, Albert J.
dc.contributor.coauthorKuenemann, Melaine A.
dc.contributor.coauthorKuiper, Martin
dc.contributor.coauthorKurz, Christoph
dc.contributor.coauthorKwon, Mijin
dc.contributor.coauthorvan Laarhoven, Twan
dc.contributor.coauthorLaegreid, Astrid
dc.contributor.coauthorLederer, Simone
dc.contributor.coauthorLee, Heewon
dc.contributor.coauthorLee, Jeon
dc.contributor.coauthorLee, Yun Woo
dc.contributor.coauthorLeppaho, Eemeli
dc.contributor.coauthorLewis, Richard
dc.contributor.coauthorLi, Jing
dc.contributor.coauthorLi, Lang
dc.contributor.coauthorLiley, James
dc.contributor.coauthorLim, Weng Khong
dc.contributor.coauthorLin, Chieh
dc.contributor.coauthorLiu, Yiyi
dc.contributor.coauthorLopez, Yosvany
dc.contributor.coauthorLow, Joshua
dc.contributor.coauthorLysenko, Artem
dc.contributor.coauthorMachado, Daniel
dc.contributor.coauthorMadhukar, Neel
dc.contributor.coauthorDe Maeyer, Dries
dc.contributor.coauthorMalpartida, Ana Belen
dc.contributor.coauthorMamitsuka, Hiroshi
dc.contributor.coauthorMarabita, Francesco
dc.contributor.coauthorMarchal, Kathleen
dc.contributor.coauthorMarttinen, Pekka
dc.contributor.coauthorMason, Daniel
dc.contributor.coauthorMazaheri, Alireza
dc.contributor.coauthorMehmood, Arfa
dc.contributor.coauthorMehreen, Ali
dc.contributor.coauthorMichaut, Magali
dc.contributor.coauthorMiller, Ryan A.
dc.contributor.coauthorMitsopoulos, Costas
dc.contributor.coauthorModos, Dezso
dc.contributor.coauthorVan Moerbeke, Marijke
dc.contributor.coauthorMoo, Keagan
dc.contributor.coauthorMotsinger-Reif, Alison
dc.contributor.coauthorMovva, Rajiv
dc.contributor.coauthorMuraru, Sebastian
dc.contributor.coauthorMuratov, Eugene
dc.contributor.coauthorMushthofa, Mushthofa
dc.contributor.coauthorNagarajan, Niranjan
dc.contributor.coauthorNakken, Sigve
dc.contributor.coauthorNath, Aritro
dc.contributor.coauthorNeuvial, Pierre
dc.contributor.coauthorNewton, Richard
dc.contributor.coauthorNing, Zheng
dc.contributor.coauthorDe Niz, Carlos
dc.contributor.coauthorOliva, Baldo
dc.contributor.coauthorOlsen, Catharina
dc.contributor.coauthorPalmeri, Antonio
dc.contributor.coauthorPanesar, Bhawan
dc.contributor.coauthorPapadopoulos, Stavros
dc.contributor.coauthorPark, Jaesub
dc.contributor.coauthorPark, Seonyeong
dc.contributor.coauthorPark, Sungjoon
dc.contributor.coauthorPawitan, Yudi
dc.contributor.coauthorPeluso, Daniele
dc.contributor.coauthorPendyala, Sriram
dc.contributor.coauthorPeng, Jian
dc.contributor.coauthorPerfetto, Livia
dc.contributor.coauthorPirro, Stefano
dc.contributor.coauthorPlevritis, Sylvia
dc.contributor.coauthorPoliti, Regina
dc.contributor.coauthorPoon, Hoifung
dc.contributor.coauthorPorta, Eduard
dc.contributor.coauthorPrellner, Isak
dc.contributor.coauthorPreuer, Kristina
dc.contributor.coauthorAngel Pujana, Miguel
dc.contributor.coauthorRamnarine, Ricardo
dc.contributor.coauthorReid, John E.
dc.contributor.coauthorReyal, Fabien
dc.contributor.coauthorRichardson, Sylvia
dc.contributor.coauthorRicketts, Camir
dc.contributor.coauthorRieswijk, Linda
dc.contributor.coauthorRocha, Miguel
dc.contributor.coauthorRodriguez-Gonzalvez, Carmen
dc.contributor.coauthorRoell, Kyle
dc.contributor.coauthorRotroff, Daniel
dc.contributor.coauthorde Ruiter, Julian R.
dc.contributor.coauthorRukawa, Ploy
dc.contributor.coauthorSadacca, Benjamin
dc.contributor.coauthorSafikhani, Zhaleh
dc.contributor.coauthorSafitri, Fita
dc.contributor.coauthorSales-Pardo, Marta
dc.contributor.coauthorSauer, Sebastian
dc.contributor.coauthorSchlichting, Moritz
dc.contributor.coauthorSeoane, Jose A.
dc.contributor.coauthorSerra, Jordi
dc.contributor.coauthorShang, Ming-Mei
dc.contributor.coauthorSharma, Alok
dc.contributor.coauthorSharma, Hari
dc.contributor.coauthorShen, Yang
dc.contributor.coauthorShiga, Motoki
dc.contributor.coauthorShin, Moonshik
dc.contributor.coauthorShkedy, Ziv
dc.contributor.coauthorShopsowitz, Kevin
dc.contributor.coauthorSinai, Sam
dc.contributor.coauthorSkola, Dylan
dc.contributor.coauthorSmirnov, Petr
dc.contributor.coauthorSoerensen, Izel Fourie
dc.contributor.coauthorSoerensen, Peter
dc.contributor.coauthorSong, Je-Hoon
dc.contributor.coauthorSong, Sang Ok
dc.contributor.coauthorSoufan, Othman
dc.contributor.coauthorSpitzmueller, Andreas
dc.contributor.coauthorSteipe, Boris
dc.contributor.coauthorSuphavilai, Chayaporn
dc.contributor.coauthorTamayo, Sergio Pulido
dc.contributor.coauthorTamborero, David
dc.contributor.coauthorTang, Jing
dc.contributor.coauthorTanoli, Zia-ur-Rehman
dc.contributor.coauthorTarres-Deulofeu, Marc
dc.contributor.coauthorTegner, Jesper
dc.contributor.coauthorThommesen, Liv
dc.contributor.coauthorTonekaboni, Seyed Ali Madani
dc.contributor.coauthorTran, Hong
dc.contributor.coauthorDe Troyer, Ewoud
dc.contributor.coauthorTruong, Amy
dc.contributor.coauthorTsunoda, Tatsuhiko
dc.contributor.coauthorTuru, Gabor
dc.contributor.coauthorTzeng, Guang-Yo
dc.contributor.coauthorVerbeke, Lieven
dc.contributor.coauthorVidela, Santiago
dc.contributor.coauthorVis, Daniel
dc.contributor.coauthorVoronkov, Andrey
dc.contributor.coauthorVotis, Konstantinos
dc.contributor.coauthorWang, Ashley
dc.contributor.coauthorWang, Hong-Qiang Horace
dc.contributor.coauthorWang, Po-Wei
dc.contributor.coauthorWang, Sheng
dc.contributor.coauthorWang, Wei
dc.contributor.coauthorWang, Xiaochen
dc.contributor.coauthorWang, Xin
dc.contributor.coauthorWennerberg, Krister
dc.contributor.coauthorWernisch, Lorenz
dc.contributor.coauthorWessels, Lodewyk
dc.contributor.coauthorvan Westen, Gerard J. P.
dc.contributor.coauthorWesterman, Bart A.
dc.contributor.coauthorWhite, Simon Richard
dc.contributor.coauthorWillighagen, Egon
dc.contributor.coauthorWurdinger, Tom
dc.contributor.coauthorXie, Lei
dc.contributor.coauthorXie, Shuilian
dc.contributor.coauthorXu, Hua
dc.contributor.coauthorYadav, Bhagwan
dc.contributor.coauthorYau, Christopher
dc.contributor.coauthorYeerna, Huwate
dc.contributor.coauthorYin, Jia Wei
dc.contributor.coauthorYu, Michael
dc.contributor.coauthorYu, MinHwan
dc.contributor.coauthorYun, So Jeong
dc.contributor.coauthorZakharov, Alexey
dc.contributor.coauthorZamichos, Alexandros
dc.contributor.coauthorZanin, Massimiliano
dc.contributor.coauthorZeng, Li
dc.contributor.coauthorZenil, Hector
dc.contributor.coauthorZhang, Frederick
dc.contributor.coauthorZhang, Pengyue
dc.contributor.coauthorZhang, Wei
dc.contributor.coauthorZhao, Hongyu
dc.contributor.coauthorZhao, Lan
dc.contributor.coauthorZheng, Wenjin
dc.contributor.coauthorZoufir, Azedine
dc.contributor.coauthorZucknick, Manuela
dc.contributor.departmentDepartment of Industrial Engineering
dc.contributor.kuauthorGönen, Mehmet
dc.contributor.kuprofileFaculty Member
dc.contributor.otherDepartment of Industrial Engineering
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.contributor.yokid237468
dc.date.accessioned2024-11-09T13:10:15Z
dc.date.issued2019
dc.description.abstractThe effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven approaches to find optimal patient-specific treatments. Here we report AstraZeneca's large drug combination dataset, consisting of 11,576 experiments from 910 combinations across 85 molecularly characterized cancer cell lines, and results of a DREAM Challenge to evaluate computational strategies for predicting synergistic drug pairs and biomarkers. 160 teams participated to provide a comprehensive methodological development and benchmarking. Winning methods incorporate prior knowledge of drug-target interactions. Synergy is predicted with an accuracy matching biological replicates for >60% of combinations. However, 20% of drug combinations are poorly predicted by all methods. Genomic rationale for synergy predictions are identified, including ADAM17 inhibitor antagonism when combined with PIK3CB/D inhibition contrasting to synergy when combined with other PI3K-pathway inhibitors in PIK3CA mutant cells.
dc.description.fulltextYES
dc.description.indexedbyWoS
dc.description.indexedbyScopus
dc.description.openaccessYES
dc.description.publisherscopeInternational
dc.description.sponsoredbyTubitakEuEU
dc.description.sponsorshipAstraZeneca
dc.description.sponsorshipEuropean Union Horizon 2020 Research
dc.description.sponsorshipEuropean Union (European Union)
dc.description.sponsorshipHorizon 2020
dc.description.sponsorshipJoint Research Center for Computational Biomedicine
dc.description.sponsorshipNational Institute for Health Research (NIHR) Sheffield Biomedical Research Center
dc.description.sponsorshipPremium Postdoctoral Fellowship Program of the Hungarian Academy of Sciences
dc.description.sponsorshipWellcome Trust
dc.description.versionPublisher version
dc.description.volume10
dc.formatpdf
dc.identifier.doi10.1038/s41467-019-09799-2
dc.identifier.embargoNO
dc.identifier.filenameinventorynoIR01717
dc.identifier.issn2041-1723
dc.identifier.linkhttps://doi.org/10.1038/s41467-019-09799-2
dc.identifier.quartileQ1
dc.identifier.scopus2-s2.0-85067453487
dc.identifier.urihttps://hdl.handle.net/20.500.14288/2802
dc.identifier.wos471758500010
dc.keywordsAndrogen receptor
dc.keywordsBreast-cancer
dc.keywordsGene
dc.keywordsCell
dc.keywordsInhibition
dc.keywordsResistance
dc.keywordsPathway
dc.keywordsMutations
dc.keywordsLandscape
dc.keywordsResource
dc.languageEnglish
dc.publisherNature Publishing Group (NPG)
dc.relation.grantno668858 PrECISE
dc.relation.grantno102696
dc.relation.grantno206194
dc.relation.urihttp://cdm21054.contentdm.oclc.org/cdm/ref/collection/IR/id/8303
dc.sourceNature Communications
dc.subjectScience and technology
dc.titleCommunity assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.authorid0000-0002-2483-075X
local.contributor.kuauthorGönen, Mehmet
relation.isOrgUnitOfPublicationd6d00f52-d22d-4653-99e7-863efcd47b4a
relation.isOrgUnitOfPublication.latestForDiscoveryd6d00f52-d22d-4653-99e7-863efcd47b4a

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