{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T17:36:31Z","timestamp":1765042591943,"version":"3.46.0"},"reference-count":75,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T00:00:00Z","timestamp":1600992000000},"content-version":"vor","delay-in-days":24,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009729","name":"Ludwig Institute for Cancer Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009729","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012449","name":"Southern University of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012449","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.embopress.org"],"crossmark-restriction":false},"short-container-title":["Molecular Systems Biology"],"published-print":{"date-parts":[[2020,9]]},"DOI":"10.15252\/msb.20209506","type":"journal-article","created":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T04:29:04Z","timestamp":1601008144000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Integrated regulatory models for inference of subtype\u2010specific susceptibilities in glioblastoma"],"prefix":"10.1038","volume":"16","author":[{"given":"Yunpeng","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Biology Massachusetts Institute of Technology Cambridge MA USA"},{"name":"MIT Koch Institute for Integrative Cancer Research Cambridge MA USA"},{"name":"Broad Institute of MIT and Harvard Cambridge MA USA"}]},{"given":"Ning","family":"Shi","sequence":"additional","affiliation":[{"name":"School of Computer Science University of Birmingham Birmingham UK"}]},{"given":"Aviv","family":"Regev","sequence":"additional","affiliation":[{"name":"Department of Biology Massachusetts Institute of Technology Cambridge MA USA"},{"name":"MIT Koch Institute for Integrative Cancer Research Cambridge MA USA"},{"name":"Broad Institute of MIT and Harvard Cambridge MA USA"}]},{"given":"Shan","family":"He","sequence":"additional","affiliation":[{"name":"School of Computer Science University of Birmingham Birmingham UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6776-2163","authenticated-orcid":false,"given":"Michael T","family":"Hemann","sequence":"additional","affiliation":[{"name":"Department of Biology Massachusetts Institute of Technology Cambridge MA USA"},{"name":"MIT Koch Institute for Integrative Cancer Research Cambridge MA USA"},{"name":"Broad Institute of MIT and Harvard Cambridge MA USA"}]}],"member":"297","published-online":{"date-parts":[[2020,9,25]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.1001\/jamaoncol.2017.0184","article-title":"HER2\u2010specific chimeric antigen receptor\u2013modified virus\u2010specific T cells for progressive glioblastoma A phase 1 dose\u2010escalation trial","volume":"3","author":"Ahmed N","year":"2020","journal-title":"JAMA Oncol"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4463"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3593"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/0959-437X(94)90098-1"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11003"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2005.02.007"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41568-019-0196-7"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature08712"},{"key":"e_1_2_8_10_1","doi-asserted-by":"crossref","first-page":"e7035","DOI":"10.1371\/journal.pone.0007035","article-title":"Overexpression of transcription factor Sp1 leads to gene expression perturbations and cell cycle inhibition","volume":"4","author":"Chalard R","year":"2009","journal-title":"PLoS ONE"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1204"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2017.10.030"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx1081"},{"key":"e_1_2_8_14_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2018\/7148023","article-title":"EGF\u2010mediated overexpression of Myc attenuates miR\u201026b by recruiting HDAC3 to induce epithelial\u2010mesenchymal transition of lens epithelial cells","volume":"2018","author":"Dong N","year":"2018","journal-title":"Biomed Res Int"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20112746"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1145\/358669.358692"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/gbb.12106"},{"key":"e_1_2_8_19_1","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature11245","article-title":"Architecture of the human regulatory network derived from ENCODE data","volume":"488","author":"Gerstein MB","year":"2012","journal-title":"Nature"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.cellbio.16.1.653"},{"key":"e_1_2_8_21_1","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1002\/ijc.26049","article-title":"Sp1 is upregulated in human glioma, promotes MMP\u20102\u2010mediated cell invasion and predicts poor clinical outcome","volume":"601","author":"Guan H","year":"2012","journal-title":"Int J Cancer"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature09267"},{"key":"e_1_2_8_23_1","first-page":"3","article-title":"Glioblastoma multiforme: a review of its epidemiology and pathogenesis through clinical presentation and treatment","volume":"18","author":"Hanif F","year":"2017","journal-title":"Asian Pac J Cancer Prev"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0012776"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1155\/2011\/732413"},{"key":"e_1_2_8_26_1","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1007\/s11060-011-0738-7","article-title":"Improved survival time trends for glioblastoma using the SEER 17 population\u2010based registries Matthew","volume":"107","author":"Koshy M","year":"2014","journal-title":"J Neurooncol"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1158\/2326-6066.CIR-16-0376"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.092759.109"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw216"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003908"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.18632\/oncotarget.7961"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF01589116"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0086693"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.nicl.2018.10.014"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0560-6"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1099"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3799"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-7-S1-S7"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1176"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3984"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/cddis.2017.244"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41418-018-0248-7"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.06.024"},{"key":"e_1_2_8_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2012.04.040"},{"key":"e_1_2_8_45_1","doi-asserted-by":"crossref","first-page":"D601","DOI":"10.1093\/nar\/gkx1138","article-title":"FunCoup 4: new species, data, and visualization","volume":"46","author":"Ogris C","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"e_1_2_8_46_1","first-page":"D601","article-title":"The BioGRID interaction database: 2019 update","volume":"46","author":"Oughtred R","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"e_1_2_8_47_1","unstructured":"PageL BrinS MotwaniR WinogradT(1998)The PageRank citation ranking: bringing order to the web.Technical Report.Stanford InfoLab"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1254257"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2019.01.002"},{"key":"e_1_2_8_50_1","first-page":"2825","article-title":"Scikit\u2010learn: machine learning in python","volume":"12","author":"Pedregosa F","year":"2011","journal-title":"J Mach Learn Res"},{"key":"e_1_2_8_51_1","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-1-54"},{"key":"e_1_2_8_52_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2016.06.006"},{"volume-title":"R: a language and environment for statistical computing","year":"2013","author":"R Core Team","key":"e_1_2_8_53_1"},{"key":"e_1_2_8_54_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.91.2.752"},{"key":"e_1_2_8_55_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007"},{"key":"e_1_2_8_56_1","doi-asserted-by":"crossref","first-page":"eaaa0984","DOI":"10.1126\/scitranslmed.aaa0984","article-title":"A single dose of peripherally infused EGFRvIII\u2010directed CAR T cells mediates antigen loss and induces adaptive resistance in patients with recurrent glioblastoma","volume":"9","author":"Rourke DMO","year":"2017","journal-title":"Sci Transl Med"},{"volume-title":"RStudio: Integrated Development for R","year":"2020","author":"RStudio Team","key":"e_1_2_8_57_1"},{"key":"e_1_2_8_58_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh012"},{"key":"e_1_2_8_59_1","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1093\/nar\/gkt984","article-title":"FunCoup 3.0: database of genome\u2010wide functional coupling networks","volume":"42","author":"Schmitt T","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"e_1_2_8_60_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11060-012-0981-6"},{"key":"e_1_2_8_61_1","doi-asserted-by":"publisher","DOI":"10.1038\/msb.2012.37"},{"key":"e_1_2_8_62_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"},{"key":"e_1_2_8_63_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2798"},{"key":"e_1_2_8_64_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1219747110"},{"key":"e_1_2_8_65_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1087447"},{"key":"e_1_2_8_66_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1003"},{"key":"e_1_2_8_67_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1131"},{"key":"e_1_2_8_68_1","doi-asserted-by":"crossref","unstructured":"TraagVA NesterovYE Van DoorenP(2010)Exponential ranking: taking into account negative links. InSocial Informatics.SocInfo 2010. Lecture Notes in Computer Science Vol.6430: pp192\u2013202.Berlin:Springer","DOI":"10.1007\/978-3-642-16567-2_14"},{"key":"e_1_2_8_69_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.06.010"},{"key":"e_1_2_8_70_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks901"},{"key":"e_1_2_8_71_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccr.2009.12.020"},{"key":"e_1_2_8_72_1","doi-asserted-by":"publisher","DOI":"10.1093\/neuonc\/nou130"},{"key":"e_1_2_8_73_1","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.ccell.2017.06.003","article-title":"Tumor evolution of glioma\u2010intrinsic gene expression subtypes associates with immunological changes in the microenvironment","volume":"33","author":"Wang Q","year":"2017","journal-title":"Cancer Cell"},{"key":"e_1_2_8_74_1","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1056\/NEJMoa043330","article-title":"Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma","volume":"352","author":"Weller M","year":"2005","journal-title":"N Engl J Med"},{"key":"e_1_2_8_75_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-017-0670-3"},{"key":"e_1_2_8_76_1","article-title":"Chinese Glioma Genome Atlas (CGGA): A Comprehensive Resource with Functional Genomic Data for Chinese Glioma Patients","author":"Zhao Z","year":"2020","journal-title":"bioRxiv"}],"container-title":["Molecular Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.15252\/msb.20209506","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.15252\/msb.20209506","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.embopress.org\/doi\/pdf\/10.15252\/msb.20209506","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T17:33:49Z","timestamp":1765042429000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.15252\/msb.20209506"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9]]},"references-count":75,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2020,9]]}},"alternative-id":["10.15252\/msb.20209506"],"URL":"https:\/\/doi.org\/10.15252\/msb.20209506","archive":["Portico"],"relation":{},"ISSN":["1744-4292","1744-4292"],"issn-type":[{"type":"print","value":"1744-4292"},{"type":"electronic","value":"1744-4292"}],"subject":[],"published":{"date-parts":[[2020,9]]},"assertion":[{"value":"2020-02-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-08-27","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2020-09-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e9506"}}