{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T21:59:49Z","timestamp":1743112789588,"version":"3.40.3"},"publisher-location":"Cham","reference-count":44,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030352097"},{"type":"electronic","value":"9783030352103"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1007\/978-3-030-35210-3_1","type":"book-chapter","created":{"date-parts":[[2019,11,14]],"date-time":"2019-11-14T06:03:08Z","timestamp":1573711388000},"page":"3-28","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases"],"prefix":"10.1007","author":[{"given":"Yifeng","family":"Tao","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haoyun","family":"Lei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrian V.","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Ma","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,11,12]]},"reference":[{"issue":"456","key":"1_CR1","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1198\/016214501753381814","volume":"96","author":"D Amaratunga","year":"2001","unstructured":"Amaratunga, D., et al.: Analysis of data from viral DNA microchips. J. Am. Stat. Assoc. 96(456), 1161\u20131170 (2001)","journal-title":"J. Am. Stat. Assoc."},{"key":"1_CR2","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1146\/annurev-pathol-052016-100127","volume":"12","author":"JC Aster","year":"2017","unstructured":"Aster, J.C., et al.: The varied roles of Notch in cancer. Ann. Rev. Pathol. 12, 245\u2013275 (2017)","journal-title":"Ann. Rev. Pathol."},{"key":"1_CR3","doi-asserted-by":"crossref","unstructured":"Bell, R.M., et al.: Scalable collaborative filtering with jointly derived neighborhood interpolation weights. In: Seventh IEEE International Conference on Data Mining (ICDM 2007), pp. 43\u201352 (2007)","DOI":"10.1109\/ICDM.2007.90"},{"issue":"11","key":"1_CR4","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1158\/2159-8290.CD-15-0369","volume":"5","author":"PK Brastianos","year":"2015","unstructured":"Brastianos, P.K., et al.: Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. Cancer Discov. 5(11), 1164\u20131177 (2015)","journal-title":"Cancer Discov."},{"issue":"6206","key":"1_CR5","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1126\/science.1253462","volume":"346","author":"EC Bruin de","year":"2014","unstructured":"de Bruin, E.C., et al.: Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science (New York N.Y.) 346(6206), 251\u2013256 (2014)","journal-title":"Science (New York N.Y.)"},{"issue":"6024","key":"1_CR6","doi-asserted-by":"publisher","first-page":"1559","DOI":"10.1126\/science.1203543","volume":"331","author":"CL Chaffer","year":"2011","unstructured":"Chaffer, C.L., et al.: A perspective on cancer cell metastasis. Science 331(6024), 1559\u20131564 (2011)","journal-title":"Science"},{"issue":"8","key":"1_CR7","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1038\/nrc865","volume":"2","author":"AF Chambers","year":"2002","unstructured":"Chambers, A.F., et al.: Dissemination and growth of cancer cells in metastatic sites. Nat. Rev. Cancer 2(8), 563\u2013572 (2002)","journal-title":"Nat. Rev. Cancer"},{"issue":"16","key":"1_CR8","doi-asserted-by":"publisher","first-page":"5158","DOI":"10.1158\/1078-0432.CCR-07-4756","volume":"14","author":"C Desmedt","year":"2008","unstructured":"Desmedt, C., et al.: Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin. Cancer Res. 14(16), 5158\u20135165 (2008)","journal-title":"Clin. Cancer Res."},{"issue":"4","key":"1_CR9","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1016\/j.jtbi.2004.02.021","volume":"228","author":"R Desper","year":"2004","unstructured":"Desper, R., et al.: Tumor classification using phylogenetic methods on expression data. J. Theor. Biol. 228(4), 477\u2013496 (2004)","journal-title":"J. Theor. Biol."},{"issue":"2","key":"1_CR10","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1016\/j.canlet.2012.12.028","volume":"340","author":"L Ding","year":"2013","unstructured":"Ding, L., et al.: Advances for studying clonal evolution in cancer. Cancer Lett. 340(2), 212\u2013219 (2013)","journal-title":"Cancer Lett."},{"issue":"6","key":"1_CR11","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1145\/367766.368166","volume":"5","author":"RW Floyd","year":"1962","unstructured":"Floyd, R.W.: Algorithm 97: shortest path. Commun. ACM 5(6), 344\u2013348 (1962)","journal-title":"Commun. ACM"},{"key":"1_CR12","unstructured":"Funk, S.: Netflix update: try this at home (2006)"},{"issue":"7381","key":"1_CR13","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1038\/nature10762","volume":"481","author":"M Greaves","year":"2012","unstructured":"Greaves, M., et al.: Clonal evolution in cancer. Nature 481(7381), 306\u2013313 (2012)","journal-title":"Nature"},{"issue":"5","key":"1_CR14","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1016\/j.apsb.2015.07.005","volume":"5","author":"X Guan","year":"2015","unstructured":"Guan, X.: Cancer metastases: challenges and opportunities. Acta Pharm. Sinica B 5(5), 402\u2013418 (2015)","journal-title":"Acta Pharm. Sinica B"},{"issue":"4","key":"1_CR15","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1177\/1758834010366430","volume":"2","author":"S Gupta","year":"2010","unstructured":"Gupta, S., et al.: Targeting the Hedgehog pathway in cancer. Ther. Adv. Med. Oncol. 2(4), 237\u2013250 (2010)","journal-title":"Ther. Adv. Med. Oncol."},{"issue":"5","key":"1_CR16","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1152\/physiol.00019.2007","volume":"22","author":"AM Hofer","year":"2007","unstructured":"Hofer, A.M., et al.: Extracellular calcium and cAMP: second messengers as \u201cthird messengers\u201d? Physiology 22(5), 320\u2013327 (2007)","journal-title":"Physiology"},{"issue":"10","key":"1_CR17","doi-asserted-by":"publisher","first-page":"R70","DOI":"10.1186\/gb-2003-4-10-r70","volume":"4","author":"DA Hosack","year":"2003","unstructured":"Hosack, D.A., et al.: Identifying biological themes within lists of genes with EASE. Genome Biol. 4(10), R70\u2013R70 (2003)","journal-title":"Genome Biol."},{"issue":"1","key":"1_CR18","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DW Huang","year":"2009","unstructured":"Huang, D.W., et al.: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4(1), 44\u201357 (2009)","journal-title":"Nat. Protoc."},{"issue":"1","key":"1_CR19","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","volume":"28","author":"M Kanehisa","year":"2000","unstructured":"Kanehisa, M., et al.: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1), 27\u201330 (2000)","journal-title":"Nucleic Acids Res."},{"key":"1_CR20","unstructured":"Kingma, D., et al.: Adam: a method for stochastic optimization. In: International Conference on Learning Representations, December 2014"},{"issue":"4","key":"1_CR21","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1016\/j.ccell.2019.02.007","volume":"35","author":"V K\u00f6rber","year":"2019","unstructured":"K\u00f6rber, V., et al.: Evolutionary trajectories of IDHWT glioblastomas reveal a common path of early tumorigenesis instigated years ahead of initial diagnosis. Cancer Cell 35(4), 692\u2013704 (2019)","journal-title":"Cancer Cell"},{"issue":"8","key":"1_CR22","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1109\/MC.2009.263","volume":"42","author":"Y Koren","year":"2009","unstructured":"Koren, Y., et al.: Matrix factorization techniques for recommender systems. Computer 42(8), 30\u201337 (2009)","journal-title":"Computer"},{"key":"1_CR23","unstructured":"Lee, D.D., et al.: Algorithms for non-negative matrix factorization. In: Proceedings of the 13th International Conference on Neural Information Processing Systems, NIPS 2000, pp. 535\u2013541. MIT Press, Cambridge (2000)"},{"issue":"4","key":"1_CR24","doi-asserted-by":"publisher","first-page":"3856","DOI":"10.3390\/cancers3043856","volume":"3","author":"S Lee","year":"2011","unstructured":"Lee, S., et al.: Cytokines in cancer immunotherapy. Cancers 3(4), 3856\u20133893 (2011)","journal-title":"Cancers"},{"key":"1_CR25","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1007\/978-3-030-17083-7_11","volume-title":"Research in Computational Molecular Biology","author":"H Lei","year":"2019","unstructured":"Lei, H., et al.: Tumor copy number deconvolution integrating bulk and single-cell sequencing data. In: Cowen, L.J. (ed.) RECOMB 2019. LNCS, vol. 11467, pp. 174\u2013189. Springer, Cham (2019). \nhttps:\/\/doi.org\/10.1007\/978-3-030-17083-7_11"},{"issue":"17","key":"1_CR26","doi-asserted-by":"publisher","first-page":"3608","DOI":"10.1200\/JCO.2004.01.175","volume":"22","author":"NU Lin","year":"2004","unstructured":"Lin, N.U., et al.: CNS metastases in breast cancer. J. Clin. Oncol. 22(17), 3608\u20133617 (2004)","journal-title":"J. Clin. Oncol."},{"issue":"1","key":"1_CR27","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/S0304-3975(03)00209-3","volume":"306","author":"CL Lu","year":"2003","unstructured":"Lu, C.L., et al.: The full Steiner tree problem. Theor. Comput. Sci. 306(1), 55\u201367 (2003)","journal-title":"Theor. Comput. Sci."},{"issue":"2","key":"1_CR28","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.cell.2008.07.001","volume":"134","author":"J Massagu\u00e9","year":"2008","unstructured":"Massagu\u00e9, J.: TGF$$\\beta $$ in cancer. Cell 134(2), 215\u2013230 (2008)","journal-title":"Cell"},{"issue":"4","key":"1_CR29","first-page":"406","volume":"4","author":"M Nei","year":"1987","unstructured":"Nei, M., et al.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4), 406\u2013425 (1987)","journal-title":"Mol. Biol. Evol."},{"issue":"2","key":"1_CR30","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1109\/TCBB.2008.126","volume":"6","author":"Y Park","year":"2009","unstructured":"Park, Y., et al.: Network-based inference of cancer progression from microarray data. IEEE\/ACM Trans. Comput. Biol. Bioinf. 6(2), 200\u2013212 (2009)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf."},{"issue":"5","key":"1_CR31","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1001\/jamaoncol.2016.5630","volume":"3","author":"N Priedigkeit","year":"2017","unstructured":"Priedigkeit, N., et al.: Intrinsic subtype switching and acquired ERBB2\/HER2 amplifications and mutations in breast cancer brain metastases. JAMA Oncol. 3(5), 666\u2013671 (2017)","journal-title":"JAMA Oncol."},{"issue":"10","key":"1_CR32","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1038\/nbt.1991","volume":"29","author":"P Qiu","year":"2011","unstructured":"Qiu, P., et al.: Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat. Biotechnol. 29(10), 886\u2013891 (2011)","journal-title":"Nat. Biotechnol."},{"issue":"5","key":"1_CR33","doi-asserted-by":"publisher","first-page":"e1000777","DOI":"10.1371\/journal.pcbi.1000777","volume":"6","author":"M Riester","year":"2010","unstructured":"Riester, M., et al.: A differentiation-based phylogeny of cancer subtypes. PLoS Comput. Biol. 6(5), e1000777 (2010)","journal-title":"PLoS Comput. Biol."},{"key":"1_CR34","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1038\/323533a0","volume":"323","author":"DE Rumelhart","year":"1986","unstructured":"Rumelhart, D.E., et al.: Learning representations by back-propagating errors. Nature 323, 533 (1986)","journal-title":"Nature"},{"key":"1_CR35","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1038\/nrg.2016.170","volume":"18","author":"R Schwartz","year":"2017","unstructured":"Schwartz, R., et al.: The evolution of tumour phylogenetics: principles and practice. Nat. Rev. Genet. 18, 213 (2017)","journal-title":"Nat. Rev. Genet."},{"issue":"1","key":"1_CR36","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/1471-2105-11-42","volume":"11","author":"R Schwartz","year":"2010","unstructured":"Schwartz, R., et al.: Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinform. 11(1), 42 (2010)","journal-title":"BMC Bioinform."},{"key":"1_CR37","unstructured":"Tao, Y., et al.: From genome to phenome: Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer. In: Pacific Symposium on Biocomputing (2020)"},{"issue":"4","key":"1_CR38","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1093\/jnci\/djy110","volume":"111","author":"D Vareslija","year":"2018","unstructured":"Vareslija, D., et al.: Transcriptome characterization of matched primary breast and brain metastatic tumors to detect novel actionable targets. J. Natl Cancer Inst. 111(4), 388\u2013398 (2018)","journal-title":"J. Natl Cancer Inst."},{"issue":"301","key":"1_CR39","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1080\/01621459.1963.10500845","volume":"58","author":"JH Ward","year":"1963","unstructured":"Ward, J.H.: Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 58(301), 236\u2013244 (1963)","journal-title":"J. Am. Stat. Assoc."},{"issue":"1","key":"1_CR40","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1145\/321105.321107","volume":"9","author":"S Warshall","year":"1962","unstructured":"Warshall, S.: A theorem on boolean matrices. J. ACM 9(1), 11\u201312 (1962)","journal-title":"J. ACM"},{"issue":"1","key":"1_CR41","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1186\/s13058-015-0665-1","volume":"18","author":"I Witzel","year":"2016","unstructured":"Witzel, I., et al.: Breast cancer brain metastases: biology and new clinical perspectives. Breast Cancer Res. 18(1), 8 (2016)","journal-title":"Breast Cancer Res."},{"issue":"1","key":"1_CR42","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/1756-9966-30-87","volume":"30","author":"RSY Wong","year":"2011","unstructured":"Wong, R.S.Y.: Apoptosis in cancer: from pathogenesis to treatment. J. Exp. Clinical Cancer Res. 30(1), 87 (2011)","journal-title":"J. Exp. Clinical Cancer Res."},{"key":"1_CR43","doi-asserted-by":"publisher","first-page":"1461","DOI":"10.1038\/onc.2016.304","volume":"36","author":"T Zhan","year":"2016","unstructured":"Zhan, T., et al.: Wnt signaling in cancer. Oncogene 36, 1461 (2016)","journal-title":"Oncogene"},{"key":"1_CR44","doi-asserted-by":"crossref","unstructured":"Zhu, L., et al.: Metastatic breast cancers have reduced immune cell recruitment but harbor increased macrophages relative to their matched primary tumors. bioRxiv: 525071 (2019)","DOI":"10.1101\/525071"}],"container-title":["Lecture Notes in Computer Science","Mathematical and Computational Oncology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-35210-3_1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,11,14]],"date-time":"2019-11-14T17:02:01Z","timestamp":1573750921000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-35210-3_1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030352097","9783030352103"],"references-count":44,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-35210-3_1","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"12 November 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"ISMCO","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Symposium on Mathematical and Computational Oncology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Lake Tahoe, NV","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"14 October 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"15 October 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"1","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"ismco2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/ismco.net\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Double-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"30","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"7","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"23% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"1","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}