Cancer Evolution: Mathematical Models and Computational Inference
Tóm tắt
Từ khóa
Tài liệu tham khảo
Adams, 2010, Tree-structured stick breaking processes for hierarchical data, Adv. Neural Inf. Process. Syst. (NIPS)., 23, 19
Adey, 2013, The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line, Nature, 500, 207, 10.1038/nature12064
Adzhubei, 2010, A method and server for predicting damaging missense mutations, Nat. Methods, 7, 248, 10.1038/nmeth0410-248
Aktipis, 2011, Overlooking evolution: a systematic analysis of cancer relapse and therapeutic resistance research, PLoS ONE, 6, e26100, 10.1371/journal.pone.0026100
Alarcón, 2005, A multiple scale model for tumor growth, Multiscale Model. Simul., 3, 440, 10.1137/040603760
Albini, 2007, The tumour microenvironment as a target for chemoprevention, Nat. Rev. Cancer, 7, 139, 10.1038/nrc2067
Almendro, 2014, Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity, Cell Rep., 6, 514, 10.1016/j.celrep.2013.12.041
Almendro, 2013, Cellular heterogeneity and molecular evolution in cancer, Annu. Rev. Pathol., 8, 277, 10.1146/annurev-pathol-020712-163923
Amir, 2013, viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia, Nat. Biotechnol., 31, 545, 10.1038/nbt.2594
Aparicio, 2013, The implications of clonal genome evolution for cancer medicine, N. Engl. J. Med., 368, 842, 10.1056/NEJMra1204892
Armitage, 1954, The age distribution of cancer and a multi-stage theory of carcinogenesis, Br. J. Cancer, 8, 1, 10.1038/bjc.1954.1
Armitage, 1957, A two-stage theory of carcinogenesis in relation to the age distribution of human cancer, Br. J. Cancer, 11, 161, 10.1038/bjc.1957.22
Attolini, 2010, A mathematical framework to determine the temporal sequence of somatic genetic events in cancer, Proc. Natl. Acad. Sci. USA, 107, 17604, 10.1073/pnas.1009117107
Axelrod, 2006, Evolution of cooperation among tumor cells, Proc. Natl. Acad. Sci. USA, 103, 13474, 10.1073/pnas.0606053103
Baca, 2013, Punctuated evolution of prostate cancer genomes, Cell, 153, 666, 10.1016/j.cell.2013.03.021
Barcellos-Hoff, 2013, The evolution of the cancer niche during multistage carcinogenesis, Nat. Rev. Cancer, 13, 511, 10.1038/nrc3536
Basanta, 2012, Investigating prostate cancer tumour-stroma interactions: Clinical and biological insights from an evolutionary game, Br. J. Cancer, 106, 174, 10.1038/bjc.2011.517
Basik, 2013, Biopsies: Next-generation biospecimens for tailoring therapy, Nat. Rev. Clin. Oncol., 10, 437, 10.1038/nrclinonc.2013.101
Beerenwinkel, 2007, Genetic progression and the waiting time to cancer, PLoS Comput. Biol., 3, e225, 10.1371/journal.pcbi.0030225
Beerenwinkel, 2006, Evolution on distributive lattices, J. Theor. Biol., 242, 409, 10.1016/j.jtbi.2006.03.013
Beerenwinkel, 2005, Learning multiple evolutionary pathways from cross-sectional data, J. Comput. Biol., 12, 584, 10.1089/cmb.2005.12.584
Beerenwinkel, 2005, Mtreemix: a software package for learning and using mixture models of mutagenetic trees, Bioinformatics, 21, 2106, 10.1093/bioinformatics/bti274
Beerenwinkel, 2009, Markov models for accumulating mutations, Biometrika, 96, 645, 10.1093/biomet/asp023
Bissell, 2011, Why don't we get more cancer? A proposed role of the microenvironment in restraining cancer progression, Nat. Med., 17, 320, 10.1038/nm.2328
Bowtell, 2010, The genesis and evolution of high-grade serous ovarian cancer, Nat. Rev. Cancer, 10, 803, 10.1038/nrc2946
Bozic, 2012, Dynamics of targeted cancer therapy, Trends Mol. Med., 18, 311, 10.1016/j.molmed.2012.04.006
Bozic, 2010, Accumulation of driver and passenger mutations during tumor progression, Proc. Natl. Acad. Sci. USA, 107, 18545, 10.1073/pnas.1010978107
Bozic, 2013, Evolutionary dynamics of cancer in response to targeted combination therapy, Elife, 2, e00747, 10.7554/eLife.00747
Brumer, 2006, Genetic instability and the quasispecies model, J. Theor. Biol., 241, 216, 10.1016/j.jtbi.2005.11.018
Burrell, 2013, The causes and consequences of genetic heterogeneity in cancer evolution, Nature, 501, 338, 10.1038/nature12625
Cairns, 1975, Mutation selection and the natural history of cancer, Nature, 255, 197, 10.1038/255197a0
Calabrese, 2004, Pretumor progression: Clonal evolution of human stem cell populations, Am. J. Pathol., 164, 1337, 10.1016/S0002-9440(10)63220-8
Caldas, 2012, Cancer sequencing unravels clonal evolution, Nat. Biotechnol., 30, 408, 10.1038/nbt.2213
Campbell, 2010, The patterns and dynamics of genomic instability in metastatic pancreatic cancer, Nature, 467, 1109, 10.1038/nature09460
Carlson, 2012, Decoding cell lineage from acquired mutations using arbitrary deep sequencing, Nat. Methods., 9, 78, 10.1038/nmeth.1781
Carter, 2012, Absolute quantification of somatic DNA alterations in human cancer, Nat. Biotechnol., 30, 413, 10.1038/nbt.2203
Cheng, 2012, A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis, PLoS Comput. Biol., 8, e1002337, 10.1371/journal.pcbi.1002337
Chmielecki, 2011, Optimization of dosing for EGFR-mutant non-small cell lung cancer with evolutionary cancer modeling, Sci. Transl. Med., 3, 90ra59, 10.1126/scitranslmed.3002356
Chowdhury, 2013, Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations, Bioinformatics, 29, i189, 10.1093/bioinformatics/btt205
Cibulskis, 2013, Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples, Nat. Biotechnol., 31, 213, 10.1038/nbt.2514
Cooke, 2011, Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer, Br. J. Cancer, 104, 361, 10.1038/sj.bjc.6605971
Cortes, 2004, Rational Kernels: Theory and Algorithms, J. Mach. Lern. Res., 1, 1
Curtis, 2012, The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups, Nature, 486, 346, 10.1038/nature10983
Danesh, 2012, A branching process model of ovarian cancer, J. Theor. Biol., 314, 10, 10.1016/j.jtbi.2012.08.025
Datta, 2013, Modelling the evolution of genetic instability during tumour progression, Evol. Appl., 6, 20, 10.1111/eva.12024
Dawson, 2013, Analysis of circulating tumor DNA to monitor metastatic breast cancer, N. Engl. J. Med., 368, 1199, 10.1056/NEJMoa1213261
de Bruin, 2013, Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications, Genome Med., 5, 101, 10.1186/gm505
Desper, 1999, Inferring tree models for oncogenesis from comparative genome hybridization data, J. Comput. Biol., 6, 37, 10.1089/cmb.1999.6.37
Desper, 2000, Distance-based reconstruction of tree models for oncogenesis, J. Comput. Biol., 7, 789, 10.1089/10665270050514936
Deutsch, 2002, Cellular automaton models of tumor development: A critical review, Ad. Complex Syst., 05, 247, 10.1142/S0219525902000572
Dewanji, 2011, Number and size distribution of colorectal adenomas under the multistage clonal expansion model of cancer, PLoS Comput. Biol., 7, e1002213, 10.1371/journal.pcbi.1002213
Dexter, 1978, Heterogeneity of tumor cells from a single mouse mammary tumor, Cancer Res., 38, 3174
Diaz, 2012, The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers, Nature, 468, 973
Dingli, 2009, Cancer phenotype as the outcome of an evolutionary game between normal and malignant cells, Br. J. Cancer, 101, 1130, 10.1038/sj.bjc.6605288
Dormann, 2002, Modeling of self-organized avascular tumor growth with a hybrid cellular automaton, In Silico Biol, 2, 393
Durrett, 2010, Evolutionary dynamics of tumor progression with random fitness values, Theor. Popul. Biol., 78, 54, 10.1016/j.tpb.2010.05.001
Durrett, 2011, Intratumor heterogeneity in evolutionary models of tumor progression, Genetics., 188, 461, 10.1534/genetics.110.125724
Durrett, 2010, Evolution of resistance and progression to disease during clonal expansion of cancer, Theor. Popul. Biol., 77, 42, 10.1016/j.tpb.2009.10.008
Durrett, 2009, A waiting time problem arising from the study of multi-stage carcinogenesis, Ann. Appl. Probab., 19, 676, 10.1214/08-AAP559
Ewens, 2004, Mathematical population genetics, Interdisciplinary Applied Mathematics, 2nd
Fearon, 1990, A genetic model for colorectal tumorigenesis, Cell, 61, 759, 10.1016/0092-8674(90)90186-I
Feller, 1951, Diffusion processes in genetics, Proceedings of the Second Berkeley Symposium on Mathematical Statistics and Probability, 227, 10.1525/9780520411586-018
Felsenstein, 2003, Inferring phylogenies
Fidler, 1978, Tumor heterogeneity and the biology of cancer invasion and metastasis, Cancer Res., 38, 2651
Fischer, 2014, High-definition reconstruction of clonal composition in cancer, Cell Rep., 7, 1740, 10.1016/j.celrep.2014.04.055
Forshew, 2012, Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA, Sci. Transl. Med., 4, 136ra68, 10.1126/scitranslmed.3003726
Frank, 2012, Nonheritable cellular variability accelerates the evolutionary processes of cancer, PLoS Biol., 10, e1001296, 10.1371/journal.pbio.1001296
Frumkin, 2008, Cell lineage analysis of a mouse tumor, Cancer Res., 68, 5924, 10.1158/0008-5472.CAN-07-6216
Fudenberg, 2006, Evolutionary game dynamics in finite populations with strong selection and weak mutation, Theor. Popul. Biol., 70, 352, 10.1016/j.tpb.2006.07.006
Garraway, 2012, Circumventing cancer drug resistance in the era of personalized medicine, Cancer Discov., 2, 214, 10.1158/2159-8290.CD-12-0012
Gatenby, 2003, An evolutionary model of carcinogenesis, Cancer Res., 63, 6212
Gerlinger, 2012, Intratumor heterogeneity and branched evolution revealed by multiregion sequencing, N. Engl. J. Med., 366, 883, 10.1056/NEJMoa1113205
Gerstung, 2009, Quantifying cancer progression with conjunctive Bayesian networks, Bioinformatics, 25, 2809, 10.1093/bioinformatics/btp505
Gerstung, 2010, Waiting time models of cancer progression, Math. Pop. Stud., 17, 115, 10.1080/08898480.2010.490994
Gerstung, 2012, Reliable detection of subclonal single-nucleotide variants in tumour cell populations, Nat. Commun., 3, 811, 10.1038/ncomms1814
Gerstung, 2011, The temporal order of genetic and pathway alterations in tumorigenesis, PLoS ONE, 6, e27136, 10.1371/journal.pone.0027136
Gerstung, 2011, Evolutionary games with affine fitness functions: Applications to cancer, Dynamic Games and Applications, 1, 370, 10.1007/s13235-011-0029-0
Goldie, 1979, A mathematic model for relating the drug sensitivity of tumors to their spontaneous mutation rate, Cancer Treat. Rep., 63, 1727
Gonzalez-Perez, 2013, Intogen-mutations identifies cancer drivers across tumor types, Nat. Methods, 10, 1081, 10.1038/nmeth.2642
Greenman, 2007, Patterns of somatic mutation in human cancer genomes, Nature, 446, 153, 10.1038/nature05610
Greenman, 2006, Statistical analysis of pathogenicity of somatic mutations in cancer, Genetics, 173, 2187, 10.1534/genetics.105.044677
Greenman, 2010, PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data, Biostatistics, 11, 164, 10.1093/biostatistics/kxp045
Greenman, 2012, Estimation of rearrangement phylogeny for cancer genomes, Genome. Res., 22, 346, 10.1101/gr.118414.110
Guenthoer, 2012, Assessment of palindromes as platforms for DNA amplification in breast cancer, Genome. Res., 22, 232, 10.1101/gr.117226.110
Ha, 2014, Titan: Inference of copy number architectures in clonal cell populations from tumor whole genome sequence data, Genome Res, 10.1101/gr.180281.114
Haccou, 2005, Branching processes: Variation, growth, and extinction of populations, 10.1017/CBO9780511629136
Haeno, 2007, The evolution of two mutations during clonal expansion, Genetics, 177, 2209, 10.1534/genetics.107.078915
Hanahan, 2011, Hallmarks of cancer: the next generation, Cell., 144, 646, 10.1016/j.cell.2011.02.013
Hastings, 2009, Mechanisms of change in gene copy number, Nat. Rev. Genet., 10, 551, 10.1038/nrg2593
Hidalgo, 2014, Patient-derived xenograft models: An emerging platform for translational cancer research, Cancer Discov., 4, 998, 10.1158/2159-8290.CD-14-0001
Hjelm, 2006, New probabilistic network models and algorithms for oncogenesis, J. Comput. Biol., 13, 853, 10.1089/cmb.2006.13.853
Höglund, 2001, Multivariate analyses of genomic imbalances in solid tumors reveal distinct and converging pathways of karyotypic evolution, Genes Chromosomes Cancer, 31, 156, 10.1002/gcc.1129
Hong, 2010, Using DNA methylation patterns to infer tumor ancestry, PLoS ONE, 5, e12002, 10.1371/journal.pone.0012002
Hou, 2012, Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm, Cell, 148, 873, 10.1016/j.cell.2012.02.028
Iwasa, 2003, Evolutionary dynamics of escape from biomedical intervention, Proc. Biol. Sci., 270, 2573, 10.1098/rspb.2003.2539
Iwasa, 2004, Evolutionary dynamics of invasion and escape, J. Theor. Biol., 226, 205, 10.1016/j.jtbi.2003.08.014
Iwasa, 2006, Evolution of resistance during clonal expansion, Genetics, 172, 2557, 10.1534/genetics.105.049791
Jeon, 2008, Evaluation of screening strategies for pre-malignant lesions using a biomathematical approach, Math. Biosci., 213, 56, 10.1016/j.mbs.2008.02.006
Jiang, 2000, Construction of evolutionary tree models for renal cell carcinoma from comparative genomic hybridization data, Cancer Res., 60, 6503
Jiao, 2014, Inferring clonal evolution of tumors from single nucleotide somatic mutations, BMC Bioinformatics, 15, 35, 10.1186/1471-2105-15-35
Johnston, 2007, Mathematical modeling of cell population dynamics in the colonic crypt and in colorectal cancer, Proc. Natl. Acad. Sci. USA, 104, 4008, 10.1073/pnas.0611179104
Junttila, 2013, Influence of tumour micro-environment heterogeneity on therapeutic response, Nature, 501, 346, 10.1038/nature12626
Karp, 1971, A simple derivation of Edmonds' algorithm for optimum branching, Networks, 1, 265, 10.1002/net.3230010305
Khalique, 2009, The clonal evolution of metastases from primary serous epithelial ovarian cancers, Int. J. Cancer, 124, 1579, 10.1002/ijc.24148
Kim, 2014, Using single cell sequencing data to model the evolutionary history of a tumor, BMC Bioinformatics, 15, 27, 10.1186/1471-2105-15-27
Klein, 2013, Selection and adaptation during metastatic cancer progression, Nature, 501, 365, 10.1038/nature12628
Knudson, 1971, Mutation and cancer: statistical study of retinoblastoma, Proc. Natl. Acad. Sci. USA, 68, 820, 10.1073/pnas.68.4.820
Koboldt, 2012, Varscan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res., 22, 568, 10.1101/gr.129684.111
Kolmogorov, 1931, Über die analytischen Methoden in der Wahrscheinlichkeitsrechnung, Math. Annalen., 104, 415, 10.1007/BF01457949
Komarova, 2006, Spatial stochastic models for cancer initiation and progression, Bull. Math. Biol., 68, 1573, 10.1007/s11538-005-9046-8
Komarova, 2007, Loss- and gain-of-function mutations in cancer: mass-action, spatial and hierarchical models, J. Statist. Phys., 128, 413, 10.1007/s10955-006-9238-0
Korbel, 2013, Criteria for inference of chromothripsis in cancer genomes, Cell, 152, 1226, 10.1016/j.cell.2013.02.023
Kreso, 2014, Evolution of the cancer stem cell model, Cell Stem Cell, 14, 3, 10.1016/j.stem.2014.02.006
Kumar, 2009, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nat. Protoc., 4, 1073, 10.1038/nprot.2009.86
Kunkel, 2000, DNA replication fidelity, Annu. Rev. Biochem., 69, 497, 10.1146/annurev.biochem.69.1.497
Lambert, 2011, An analogy between the evolution of drug resistance in bacterial communities and malignant tissues, Nat. Rev. Cancer, 11, 375, 10.1038/nrc3039
Landau, 2013, Evolution and impact of subclonal mutations in chronic lymphocytic leukemia, Cell, 152, 714, 10.1016/j.cell.2013.01.019
Landry, 2013, The genomic and transcriptomic landscape of a HeLa cell line, G3 (Bethesda), 3, 1213, 10.1534/g3.113.005777
Larson, 2013, Purbayes: estimating tumor cellularity and subclonality in next-generation sequencing data, Bioinformatics, 29, 1888, 10.1093/bioinformatics/btt293
Lawrence, 2014, Discovery and saturation analysis of cancer genes across 21 tumour types, Nature., 505, 495, 10.1038/nature12912
Lawrence, 2013, Mutational heterogeneity in cancer and the search for new cancer-associated genes, Nature, 499, 214, 10.1038/nature12213
Letouzé, 2010, Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis, Genome Biol., 11, R76, 10.1186/gb-2010-11-7-r76
Loeb, 2001, A mutator phenotype in cancer, Cancer Res., 61, 3230
Loeb, 2011, Human cancers express mutator phenotypes: origin, consequences and targeting, Nat. Rev. Cancer, 11, 450, 10.1038/nrc3063
Luebeck, 2013, Impact of tumor progression on cancer incidence curves, Cancer Res., 73, 1086, 10.1158/0008-5472.CAN-12-2198
Luebeck, 2002, Multistage carcinogenesis and the incidence of colorectal cancer, Proc. Natl. Acad. Sci. USA, 99, 15095, 10.1073/pnas.222118199
Luria, 1943, Mutations of bacteria from virus sensitivity to virus resistance, Genetics, 28, 491, 10.1093/genetics/28.6.491
Maley, 2006, Genetic clonal diversity predicts progression to esophageal adenocarcinoma, Nat. Genet., 38, 468, 10.1038/ng1768
Marjoram, 2003, Markov chain Monte Carlo without likelihoods, Proc. Natl. Acad. Sci. USA, 100, 15324, 10.1073/pnas.0306899100
Marusyk, 2012, Intra-tumour heterogeneity: a looking glass for cancer?, Nat. Rev. Cancer, 12, 323, 10.1038/nrc3261
McFarland, 2013, Impact of deleterious passenger mutations on cancer progression, Proc. Natl. Acad. Sci. USA, 110, 2910, 10.1073/pnas.1213968110
Meacham, 2013, Tumour heterogeneity and cancer cell plasticity, Nature, 501, 328, 10.1038/nature12624
Merlo, 2006, Cancer as an evolutionary and ecological process, Nat. Rev. Cancer, 6, 924, 10.1038/nrc2013
Meza, 2008, Age-specific incidence of cancer: Phases, transitions, and biological implications, Proc. Natl. Acad. Sci. USA, 105, 16284, 10.1073/pnas.0801151105
Michor, 2010, The origins and implications of intratumor heterogeneity, Cancer Prev. Res. (Phila), 3, 1361, 10.1158/1940-6207.CAPR-10-0234
Miller, 2014, Sciclone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution, PLoS Comput. Biol., 10, e1003665, 10.1371/journal.pcbi.1003665
Moran, 1958, Random processes in genetics, Math. Proc. Cambridge., 54, 60, 10.1017/S0305004100033193
Murtaza, 2013, Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA, Nature, 497, 108, 10.1038/nature12065
Navin, 2011, Tumour evolution inferred by single-cell sequencing, Nature, 472, 90, 10.1038/nature09807
Navin, 2010, Inferring tumor progression from genomic heterogeneity, Genome Res., 20, 68, 10.1101/gr.099622.109
Nazarian, 2010, Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation, Nature, 468, 973, 10.1038/nature09626
Neuhauser, 1997, The genealogy of samples in models with selection, Genetics, 145, 519, 10.1093/genetics/145.2.519
Nicolas, 2007, The stem cell population of the human colon crypt: analysis via methylation patterns, PLoS Comput. Biol., 3, e28, 10.1371/journal.pcbi.0030028
Nik-Zainal, 2012, Mutational processes molding the genomes of 21 breast cancers, Cell., 149, 979, 10.1016/j.cell.2012.04.024
Nolan-Stevaux, 2013, Measurement of cancer cell growth heterogeneity through lentiviral barcoding identifies clonal dominance as a characteristic of in vivo tumor engraftment, PLoS ONE, 8, e67316, 10.1371/journal.pone.0067316
Norquist, 2011, Secondary somatic mutations restoring BRCA1/2 predict chemotherapy resistance in hereditary ovarian carcinomas, J. Clin. Oncol., 29, 3008, 10.1200/JCO.2010.34.2980
Nowak, 2006, Five rules for the evolution of cooperation, Science, 314, 1560, 10.1126/science.1133755
Nowak, 2003, The linear process of somatic evolution, Proc. Natl. Acad. Sci. USA, 100, 14966, 10.1073/pnas.2535419100
Nowell, 1976, The clonal evolution of tumor cell populations, Science, 194, 23, 10.1126/science.959840
Oesper, 2013, Theta: Inferring intra-tumor heterogeneity from high-throughput DNA sequencing data, Genome Biol., 14, R80, 10.1186/gb-2013-14-7-r80
Orr, 2005, The probability of parallel evolution, Evolution: Int. J. Org. Evolut., 59, 216, 10.1111/j.0014-3820.2005.tb00907.x
Otto, 2001, Fixation probabilities and times
Owen, 2009, Angiogenesis and vascular remodelling in normal and cancerous tissues, J. Math. Biol., 58, 689, 10.1007/s00285-008-0213-z
Papaemmanuil, 2013, Clinical and biological implications of driver mutations in myelodysplastic syndromes, Blood, 122, 3616, 10.1182/blood-2013-08-518886
Park, 2010, The speed of evolution in large asexual populations, J. Stat. Phys., 138, 381, 10.1007/s10955-009-9915-x
Perfahl, 2011, Multiscale modelling of vascular tumour growth in 3D: the roles of domain size and boundary conditions, PLoS ONE, 6, e14790, 10.1371/journal.pone.0014790
Pharoah, 2004, Association studies for finding cancer-susceptibility genetic variants, Nat. Rev. Cancer, 4, 850, 10.1038/nrc1476
Poste, 1981, Interactions among clonal subpopulations affect stability of the metastatic phenotype in polyclonal populations of B16 melanoma cells, Proc. Natl. Acad. Sci. USA, 78, 6226, 10.1073/pnas.78.10.6226
Potter, 2013, Single-cell mutational profiling and clonal phylogeny in cancer, Genome Res., 23, 2115, 10.1101/gr.159913.113
Purdom, 2013, Methods and challenges in timing chromosomal abnormalities within cancer samples, Bioinformatics, 29, 3113, 10.1093/bioinformatics/btt546
Radmacher, 2001, Graph models of oncogenesis with an application to melanoma, J. Theor. Biol., 212, 535, 10.1006/jtbi.2001.2395
Rahnenführer, 2005, Estimating cancer survival and clinical outcome based on genetic tumor progression scores, Bioinformatics, 21, 2438, 10.1093/bioinformatics/bti312
Roose, 2007, Mathematical models of avascular tumor growth, SIAM Review, 49, 179, 10.1137/S0036144504446291
Rosenberg, 2002, Genealogical trees, coalescent theory and the analysis of genetic polymorphisms, Nat. Rev. Genet., 3, 380, 10.1038/nrg795
Roth, 2014, Pyclone: statistical inference of clonal population structure in cancer, Nature Methods, 10.1038/nmeth.2883
Saitou, 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406
Sakoparnig, 2012, Efficient sampling for Bayesian inference of conjunctive Bayesian networks, Bioinformatics, 28, 2318, 10.1093/bioinformatics/bts433
Salk, 2010, Mutational heterogeneity in human cancers: origin and consequences, Annu. Rev. Pathol., 5, 51, 10.1146/annurev-pathol-121808-102113
Schöllnberger, 2010, Cell selection as driving force in lung and colon carcinogenesis, Cancer Res., 70, 6797, 10.1158/0008-5472.CAN-09-4392
Schwarz, 2010, Evolutionary distances in the twilight zone–a rational kernel approach, PLoS ONE, 5, e15788, 10.1371/journal.pone.0015788
Schwarz, 2014, Phylogenetic quantification of intra-tumor heterogeneity predicts time to relapse in high-grade serous ovarian cancer, PLoS Medicine
Schwarz, 2014, Phylogenetic quantification of intra-tumour heterogeneity, PLoS Comput. Biol., 10, e1003535, 10.1371/journal.pcbi.1003535
Shah, 2012, The clonal and mutational evolution spectrum of primary triple-negative breast cancers, Nature, 486, 395, 10.1038/nature10933
Shahrabi Farahani, 2013, Learning oncogenetic networks by reducing to MILP, PLoS ONE, 8, e65773, 10.1371/journal.pone.0065773
Shapiro, 2013, Single-cell sequencing-based technologies will revolutionize whole-organism science, Nat. Rev. Genet., 14, 618, 10.1038/nrg3542
Shen, 2013, Chromoplexy: a new category of complex rearrangements in the cancer genome, Cancer Cell, 23, 567, 10.1016/j.ccr.2013.04.025
Sottoriva, 2013, Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics, Proc. Natl. Acad. Sci. USA, 110, 4009, 10.1073/pnas.1219747110
Sottoriva, 2013, Single-molecule genomic data delineate patient-specific tumor profiles and cancer stem cell organization, Cancer Res., 73, 41, 10.1158/0008-5472.CAN-12-2273
Sprouffske, 2011, Accurate reconstruction of the temporal order of mutations in neoplastic progression, Cancer Prev. Res. (Phila), 4, 1135, 10.1158/1940-6207.CAPR-10-0374
Stadler, 1991, Dynamics of autocatalytic reaction networks. IV: Inhomogeneous replicator networks, Biosystems, 26, 1, 10.1016/0303-2647(91)90033-H
Stephens, 2011, Massive genomic rearrangement acquired in a single catastrophic event during cancer development, Cell, 144, 27, 10.1016/j.cell.2010.11.055
Strino, 2013, Trap: a tree approach for fingerprinting subclonal tumor composition, Nucleic Acids Res., 41, e165, 10.1093/nar/gkt641
Szabo, 2002, Estimating an oncogenetic tree when false negatives and positives are present, Math. Biosci., 176, 219, 10.1016/S0025-5564(02)00086-X
Taylor, 2004, Evolutionary game dynamics in finite populations, Bull. Math. Biol., 66, 1621, 10.1016/j.bulm.2004.03.004
Thalhauser, 2010, Selection in spatial stochastic models of cancer: migration as a key modulator of fitness, Biol. Direct., 5, 21, 10.1186/1745-6150-5-21
Tofigh, 2011, A global structural EM algorithm for a model of cancer progression, Advances in neural information processing systems 24, 163
Tomasetti, 2013, Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation, Proc. Natl. Acad. Sci. USA, 110, 1999, 10.1073/pnas.1221068110
Tomlinson, 1997, Game-theory models of interactions between tumour cells, Eur. J. Cancer, 33, 1495, 10.1016/S0959-8049(97)00170-6
Trinh, 2014, Goifish: a system for the quantification of single cell heterogeneity from ifish images, Genome Biol., 15, 442, 10.1186/s13059-014-0442-y
Van Loo, 2010, Allele-specific copy number analysis of tumors, Proc. Natl. Acad. Sci. USA, 107, 16910, 10.1073/pnas.1009843107
von Heydebreck, 2004, Maximum likelihood estimation of oncogenetic tree models, Biostatistics, 5, 545, 10.1093/biostatistics/kxh007
Weinreich, 2006, Darwinian evolution can follow only very few mutational paths to fitter proteins, Science, 312, 111, 10.1126/science.1123539
Werner, 2013, A deterministic model for the occurrence and dynamics of multiple mutations in hierarchically organized tissues, J. R. Soc. Interface, 10, 20130349, 10.1098/rsif.2013.0349
Wilm, 2012, Lofreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets, Nucleic Acids Res., 40, 11189, 10.1093/nar/gks918
Wright, 1945, The differential equation of the distribution of gene frequencies, Proc. Natl. Acad. Sci. USA, 31, 382, 10.1073/pnas.31.12.382
Xu, 2012, Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor, Cell, 148, 886, 10.1016/j.cell.2012.02.025
Youn, 2012, Estimating the order of mutations during tumorigenesis from tumor genome sequencing data, Bioinformatics, 28, 1555, 10.1093/bioinformatics/bts168
Yuan, 2012, Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling, Sci. Transl. Med., 4, 157ra143, 10.1126/scitranslmed.3004330
Zare, 2014, Inferring clonal composition from multiple sections of a breast cancer, PLoS Comput. Biol., 10, e1003703, 10.1371/journal.pcbi.1003703