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Tree inference for single-cell data
Katharina Jahn, Jack Kuipers, Niko Beerenwinkel
Genome Biology · 2016
Abstract
Electronic supplementary material. The online version of this article (doi:10.1186/s13059-016-0936-x) contains supplementary material, which is available to authorized users.
References 41
- 1.
Nowell PC. The clonal evolution of tumor cell populations. Science. 1976;194:23-8.
Not in our library10.1126/science.959840
- 2.
Merlo LM, Pepper JW, Reid BJ, Maley CC. Cancer as an evolutionary and ecological process. Nat Rev Cancer. 2006;6:924-35.
Not in our library10.1038/nrc2013
- 3.
Pepper JW, Scott Findlay C, Kassen R, Spencer SL, Maley CC. Synthesis: cancer research meets evolutionary biology. Evol Appl. 2009;2:62-70.
Not in our library10.1111/j.1752-4571.2008.00063.x
- 4.
- 5.
Yates LR, Campbell PJ. Evolution of the cancer genome. Nat Rev Genet. 2012;13:795-806.
Not in our library10.1038/nrg3317
- 6.
Greaves M, Maley CC. Clonal evolution in cancer. Nature. 2012;481:306-13.
Not in our library10.1038/nature10762
- 7.
Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012;481:506-10.
Not in our library10.1038/nature10738
- 8.
Gillies RJ, Verduzco D, Gatenby RA. Evolutionary dynamics of carcinogenesis and why targeted therapy does not work. Nat Rev Cancer. 2012;12:487-93.
Not in our library10.1038/nrc3298
- 9.
Ortmann CA, Kent DG, Nangalia J, Silber Y, Wedge DC, Grinfeld J, Baxter EJ, Massie CE, Papaemmanuil E, Menon S, et al. Effect of mutation order on myeloproliferative neoplasms. N Engl J Med. 2015;372:601-12.
Not in our library10.1056/nejmoa1412098
- 10.
Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458:719-24.
Not in our library10.1038/nature07943
- 11.
Swanton C. Intratumor heterogeneity: evolution through space and time. Cancer Res. 2012;72:4875-82.
Not in our library10.1158/0008-5472.can-12-2217
- 12.
Gusfield D. Algorithms on strings, trees and sequences: computer science and computational biology. 1997.
Not in our library
- 13.
- 14.
Gerstung M, Beisel C, Rechsteiner M, Wild P, Schraml P, Moch H, Beerenwinkel N. Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nat Commun. 2012;3:811.
Not in our library10.1038/ncomms1814
- 15.
Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486:395-9.
Not in our library10.1038/nature10933
- 16.
Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, Ha G, Aparicio S, Bouchard-Côté A, Shah SP. Pyclone: statistical inference of clonal population structure in cancer. Nat Methods. 2014;11:396-8.
Not in our library10.1038/nmeth.2883
- 17.
- 18.
- 19.
Zare H, Wang J, Hu A, Weber K, Smith J, Nickerson D, Song C, Witten D, Blau CA, Noble WS. Inferring clonal composition from multiple sections of a breast cancer. PLoS Comput Biol. 2014;10:003703.
Not in our library10.1371/journal.pcbi.1003703
- 20.
Strino F, Parisi F, Micsinai M, Kluger Y. Trap: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res. 2013;41:165-5.
Not in our library10.1093/nar/gkt641
- 21.
Hajirasouliha I, Mahmoody A, Raphael BJ. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinformatics. 2014;30:78-86.
Not in our library10.1093/bioinformatics/btu284
- 22.
El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics. 2015;31:62-70.
Not in our library10.1093/bioinformatics/btv261
- 23.
Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT. Subcloneseeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol. 2014;15:443.
Not in our library10.1186/s13059-014-0443-x
- 24.
- 25.
- 26.
Malikic S, McPherson AW, Donmez N, Sahinalp CS. Clonality inference in multiple tumor samples using phylogeny. Bioinformatics. 2015;31:1349-56.
Not in our library10.1093/bioinformatics/btv003
- 27.
- 28.
Schuh A, Becq J, Humphray S, Alexa A, Burns A, Clifford R, Feller SM, Grocock R, Henderson S, Khrebtukova I, et al. Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood. 2012;120:4191-6.
Not in our library10.1182/blood-2012-05-433540
- 29.
Van Loo P, Voet T. Single cell analysis of cancer genomes. Curr Opinion Genet Dev. 2014;24:82-91.
Not in our library10.1016/j.gde.2013.12.004
- 30.
Hou Y, Song L, Zhu P, Zhang B, Tao Y, Xu X, Li F, Wu K, Liang J, Shao D, et al. Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell. 2012;148:873-85.
Not in our library10.1016/j.cell.2012.02.028
- 31.
Chen D, Eulenstein O, Fernandez-Baca D, Sanderson M. Minimum-flip supertrees: complexity and algorithms. IEEE/ACM Trans Comput Biol Bioinform. 2006;3:165-73.
Not in our library10.1109/tcbb.2006.26
- 32.
Gusfield D, Frid Y, Brown D. Integer programming formulations and computations solving phylogenetic and population genetic problems with missing or genotypic data. Computing and combinatorics. 2007.
Not in our library
- 33.
Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N. BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biol. 2015;16:36.
Not in our library10.1186/s13059-015-0592-6
- 34.
Kim KI, Simon R. Using single cell sequencing data to model the evolutionary history of a tumor. BMC Bioinform. 2014;15:27.
Not in our library10.1186/1471-2105-15-27
- 35.
Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, et al. Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell. 2012;148:886-95.
Not in our library10.1016/j.cell.2012.02.025
- 36.
Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014;512:155-60.
Not in our library10.1038/nature13600
- 37.
Kuipers J, Moffa G. Uniform random generation of large acyclic digraphs. Stat Comput. 2015;25:227-42.
Not in our library10.1007/s11222-013-9428-y
- 38.
Friedman N, Koller D. Being Bayesian about network structure. A Bayesian approach to structure discovery in Bayesian networks. Mach Learn. 2003;50:95-125.
Not in our library10.1023/a:1020249912095
- 39.
Kuipers J, Moffa G. Partition MCMC for inference on acyclic digraphs. J Am Stat Assoc. 2016. doi:http://dx.doi.org/10.1080/01621459.2015.1133426.
Not in our library
- 40.
Markowetz F, Kostka D, Troyanskaya OG, Spang R. Nested effects models for high-dimensional phenotyping screens. Bioinformatics. 2007;23:305-12.
Not in our library10.1093/bioinformatics/btm178
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