{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,4]],"date-time":"2024-09-04T15:06:39Z","timestamp":1725462399117},"publisher-location":"Berlin, Heidelberg","reference-count":32,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642371943"},{"type":"electronic","value":"9783642371950"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013]]},"DOI":"10.1007\/978-3-642-37195-0_21","type":"book-chapter","created":{"date-parts":[[2013,3,6]],"date-time":"2013-03-06T11:40:54Z","timestamp":1362570054000},"page":"249-263","source":"Crossref","is-referenced-by-count":2,"title":["Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery"],"prefix":"10.1007","author":[{"given":"Raheleh","family":"Salari","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Syed Shayon","family":"Saleh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dorna","family":"Kashef-Haghighi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Khavari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel E.","family":"Newburger","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert B.","family":"West","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arend","family":"Sidow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Serafim","family":"Batzoglou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"21_CR1","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1101\/gr.100040.109","volume":"20","author":"V. Bansal","year":"2010","unstructured":"Bansal, V., et al.: Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res.\u00a020, 537\u2013545 (2010)","journal-title":"Genome Res."},{"key":"21_CR2","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1038\/nature08822","volume":"463","author":"R. Beroukhim","year":"2010","unstructured":"Beroukhim, R., et al.: The land-scape of somatic copy-number alteration across human cancers. Nature\u00a0463, 899\u2013905 (2010)","journal-title":"Nature"},{"key":"21_CR3","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1038\/nature08768","volume":"463","author":"G.R. Bignell","year":"2010","unstructured":"Bignell, G.R., et al.: Signatures of mutation and selection in the cancer genome. Nature\u00a0463, 893\u2013898 (2010)","journal-title":"Nature"},{"issue":"35","key":"21_CR4","doi-asserted-by":"publisher","first-page":"13081","DOI":"10.1073\/pnas.0801523105","volume":"105","author":"P.J. Campbell","year":"2008","unstructured":"Campbell, P.J., et al.: Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing. Proc. Natl. Acad. Sci. U S A\u00a0105(35), 13081\u201313086 (2008)","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"21_CR5","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1038\/nature09837","volume":"471","author":"M.A. Chapman","year":"2011","unstructured":"Chapman, M.A., et al.: Initial genome sequencing and analysis of multiple myeloma. Nature\u00a0471, 467\u2013472 (2011)","journal-title":"Nature"},{"key":"21_CR6","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"M. DePristo","year":"2011","unstructured":"DePristo, M., et al.: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet.\u00a043, 491\u2013498 (2011)","journal-title":"Nature Genet."},{"issue":"2","key":"21_CR7","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1093\/bioinformatics\/btr629","volume":"28","author":"J. Ding","year":"2012","unstructured":"Ding, J., et al.: Feature based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics\u00a028(2), 167\u2013175 (2012)","journal-title":"Bioinformatics"},{"key":"21_CR8","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1056\/NEJMoa1113205","volume":"366","author":"M. Gerlinger","year":"2012","unstructured":"Gerlinger, M., et al.: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med.\u00a0366, 883\u2013892 (2012)","journal-title":"N. Engl. J. Med."},{"key":"21_CR9","doi-asserted-by":"crossref","unstructured":"Gerstung, M., et al.: Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nature Communications 3 (2011)","DOI":"10.1038\/ncomms1814"},{"key":"21_CR10","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/nature05610","volume":"446","author":"C. Greenman","year":"2007","unstructured":"Greenman, C., et al.: Patterns of somatic mutation in human cancer genomes. Nature\u00a0446, 153\u2013158 (2007)","journal-title":"Nature"},{"key":"21_CR11","doi-asserted-by":"crossref","unstructured":"Gusfield, D., Eddhu, S., Langley, C.: Efficient Reconstruction of Phylogenetic. Networks with Constrained Recombination. In: Proc. IEEE CSB (2003)","DOI":"10.1142\/S0219720004000521"},{"key":"21_CR12","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1002\/net.3230210104","volume":"21","author":"D. Gusfield","year":"1991","unstructured":"Gusfield, D.: Efficient algorithms for inferring evolutionary trees. Networks\u00a021, 19\u201328 (1991)","journal-title":"Networks"},{"issue":"3","key":"21_CR13","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1093\/bioinformatics\/btr665","volume":"28","author":"D.E. Larson","year":"2012","unstructured":"Larson, D.E., et al.: SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data. Bioinformatics\u00a028(3), 311\u2013317 (2012)","journal-title":"Bioinformatics"},{"key":"21_CR14","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1038\/nature07485","volume":"456","author":"T.J. Ley","year":"2008","unstructured":"Ley, T.J., et al.: DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature\u00a0456, 66\u201372 (2008)","journal-title":"Nature"},{"key":"21_CR15","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H. Li","year":"2009","unstructured":"Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics\u00a025, 1754\u20131760 (2009)","journal-title":"Bioinformatics"},{"key":"21_CR16","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A. McKenna","year":"2010","unstructured":"McKenna, A., et al.: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res.\u00a020, 1297\u20131303 (2010)","journal-title":"Genome Res."},{"key":"21_CR17","doi-asserted-by":"publisher","first-page":"1182","DOI":"10.1101\/gr.4565806","volume":"16","author":"R.E. Mills","year":"2006","unstructured":"Mills, R.E., Luttig, C.T., Larkins, C.E., Beauchamp, A., Tsui, C., Pittard, W.S., Devine, S.E.: An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res.\u00a016, 1182\u20131190 (2006)","journal-title":"Genome Res."},{"key":"21_CR18","unstructured":"muTect: A Reliable and Accurate Method for Detecting Somatic Mutations in Next Generation Cancer Genome Sequencing, https:\/\/confluence.broadinstitute.org\/display\/CGATools\/MuTect"},{"key":"21_CR19","unstructured":"Newburger, D.E., et al.: Genome Evolution during Progression to Breast Cancer (submitted)"},{"key":"21_CR20","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1016\/j.cell.2012.04.024","volume":"149","author":"S. Nik-Zainal","year":"2012","unstructured":"Nik-Zainal, S., et al.: Mutational Processes Molding the Genomes of 21 Breast Cancers. Cell\u00a0149, 979\u2013993 (2012)","journal-title":"Cell"},{"key":"21_CR21","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1016\/j.cell.2012.04.023","volume":"149","author":"S. Nik-Zainal","year":"2012","unstructured":"Nik-Zainal, S., et al.: The life history of 21 breast cancers. Cell\u00a0149, 994\u20131007 (2012)","journal-title":"Cell"},{"key":"21_CR22","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1038\/nature08658","volume":"463","author":"E.D. Pleasance","year":"2010","unstructured":"Pleasance, E.D., et al.: A comprehensive catalogue of somatic mutations from a human cancer genome. Nature\u00a0463, 191\u2013196 (2010)","journal-title":"Nature"},{"issue":"7","key":"21_CR23","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1093\/bioinformatics\/bts053","volume":"28","author":"A. Roth","year":"2012","unstructured":"Roth, A., et al.: JointSNVMix: A Probabilistic Model For Accurate Detection of Somatic Mutations in Normal\/Tumour Paired Next Generation Sequencing Data. Bioinformatics\u00a028(7), 907\u2013913 (2012)","journal-title":"Bioinformatics"},{"key":"21_CR24","doi-asserted-by":"crossref","unstructured":"Rozowsky, J., et al.: Allseq: analysis of allele Specific Expression and Binding in a Network Framework. Mol. Sys. Bio. (2011)","DOI":"10.1038\/msb.2011.54"},{"key":"21_CR25","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/1471-2105-11-42","volume":"11","author":"R. Schwartz","year":"2010","unstructured":"Schwartz, R., Schackney, S.E.: Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinformatics\u00a011, 42 (2010)","journal-title":"BMC Bioinformatics"},{"issue":"7265","key":"21_CR26","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1038\/nature08489","volume":"461","author":"S. Shah","year":"2009","unstructured":"Shah, S., et al.: Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature\u00a0461(7265), 809\u2013813 (2009)","journal-title":"Nature"},{"key":"21_CR27","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1126\/science.1204040","volume":"331","author":"M.R. Stratton","year":"2011","unstructured":"Stratton, M.R.: Exploring the genomes of cancer cells: progress and promise. Science\u00a0331, 1553\u20131558 (2011)","journal-title":"Science"},{"key":"21_CR28","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1038\/nature07943","volume":"458","author":"M.R. Stratton","year":"2009","unstructured":"Stratton, M.R., Campbell, P.J., Futreal, P.A.: The cancer genome. Nature\u00a0458, 719\u2013724 (2009)","journal-title":"Nature"},{"key":"21_CR29","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"The 1000 Genomes Project Consortium","year":"2010","unstructured":"The 1000 Genomes Project Consortium, et al.: A map of human genome variation from population-scale sequencing. Nature 467, 1061\u20131073 (2010)","journal-title":"Nature"},{"key":"21_CR30","unstructured":"Whole Genome Simulation, http:\/\/sourceforge.net\/apps\/mediawiki\/dnaa\/index.php"},{"issue":"5","key":"21_CR31","first-page":"1447","volume":"25","author":"G. Zhang","year":"2011","unstructured":"Zhang, G., et al.: Development of a phylogenetic tree model to investigate the role of genetic mutations in endometrial tumors. Oncol. Rep.\u00a025(5), 1447\u20131454 (2011)","journal-title":"Oncol. Rep."},{"issue":"2","key":"21_CR32","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1158\/1535-7163.MCT-09-0508","volume":"9","author":"Y. Zhang","year":"2010","unstructured":"Zhang, Y., et al.: Molecular Evolutionary Analysis of Cancer Cell Lines. Mol. Cancer Ther.\u00a09(2), 279\u2013291 (2010)","journal-title":"Mol. Cancer Ther."}],"container-title":["Lecture Notes in Computer Science","Research in Computational Molecular Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-37195-0_21","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,2,10]],"date-time":"2022-02-10T07:05:36Z","timestamp":1644476736000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-37195-0_21"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"ISBN":["9783642371943","9783642371950"],"references-count":32,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-37195-0_21","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2013]]}}}