Publications
Select publications
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Schiffman JD, Schmitt DL, Maley CC. TP53 Gene and Cancer Resistance in Elephants--Reply. JAMA. 2016 Apr 26;315(16):1790-1. doi: 10.1001/jama.2016.0457. No abstract available.
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Kostadinov R, Maley CC, Kuhner MK. Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content. PLoS Comput Biol. 2016 Apr 22;12(4):e1004413. doi: 10.1371/journal.pcbi.1004413. eCollection 2016 Apr.
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Chowell D, Boddy AM, Mallo D, Tollis M, Maley CC.When (distant) relatives stay too long: implications for cancer medicine. Genome Biol. 2016 Feb 24;17:34. doi: 10.1186/s13059-016-0906-3.
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Andor, N., Graham, T.A., Jansen, M., Xia1, L.C., Aktipis, C.A., Petritsch, C., Ji*, H.P., Maley*, C.C.: Pan-cancer analysis of the extent and consequences of intra-tumor heterogeneity. Nature Medicine, 22:105-13, 2015. *co-senior authors.
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Abegglen, L.M., Caulin, A.F., Chan, A., Lee, K., Robinson, R., Campbell, M.S., Kiso, W.K., Schmitt, D.L., Waddell, P.J., Bhaskara, S., Jensen, S.T., Maley*, C.C., Schiffman*, J. D.: Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans. JAMA, 314:1850-1860, 2015. *co-senior authors.
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Maley, C.C., Koelble, K., Natrajan, R., Aktipis, A., Yuan, Y.: An ecological measure of immune-cancer colocalization as a prognostic factor for breast cancer. Breast Cancer Research, 17:131, 2015.
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Kostadinov, R., Maley, C.C., Kuhner, M.K.: Bulk genotyping of biopsies can create spurious evidence for hetereogeneity in mutation content. PLoS Computational Biology, in press.
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Li, X., Paulson, T.P., Galipeau, P.C., Sanchez, C.A., Liu, K., Kuhner, M.K., Maley, C.C., Self, S.G., Vaughan, T.L., Reid, B.J., Blount, P.L.,: Assessment of esophageal adenocarcinoma risk using somatic chromosome alterations in longitudinal samples in Barrett's esophagus. Cancer Prevention Research, 8:845-56, 2015.
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Timmer*, M.R., Martinez*,P., Lau, C.T., Westra, W.M., Silvia Calpe1, Rygiel, A.M., Rosmolen, W.D., Meijer, S.L., ten Kate, F.J.W., Dijkgraaf, M.G.W., Mallant-Hent, R.C., Naber, A.H.J., van Oijen, A.H.A.M., Baak, L.C., Scholten, P., Böhmer, C.J.M., Fockens, P., Maley, C.C., Graham, T.A., Bergman, J.J.G.H.M., Krishnadath, K.K.: Derivation of Genetic Biomarkers for Cancer Risk Stratification in Barrett's Oesophagus: A Prospective Cohort Study. Gut, epub 2015. doi: 10.1136/gutjnl-2015-309642. * co-first authors.
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Nunney, L., Maley, C.C., Breen, M., Hochberg, M.E., Schiffman, J.D.: Peto’s paradox and the promise of comparative oncology. Philosophical Transactions of the Royal Society of London B, 370 (1673):20140177.
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Aktipis, C.A., Boddy, A.M., Jansen, G., Hibner, U., Hochberg, M.E., Maley, C.C., Wilkinson, G.S.: Cancer across the tree of life: Cooperation and cheating in multicellularity. Philosophical Transactions of the Royal Society of London B, 370 (1673):20140219.
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Caulin, A.F., Maley, C.C.: Solutions to Peto’s Paradox Revealed by Mathematical Modeling and Cross-Species Cancer Gene Analysis. Philosophical Transactions of the Royal Society of London B, 370 (1673):20140222.
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Paguirigan, A.L., Smith, J., Meshinchi, S., Carroll, M., Maley, C.C., Radich, J.P.: Single-cell genotyping demonstrates complex clonal diversity in acute myeloid leukemia. Science Translational Medicine, 7:281re2, 2015. doi:10.1126/scitranslmed.aaa0763
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Walther, V., Hiley, C.T., Shibata, D., Swanton, C., Turner, P.E., and Maley C.C.: Can oncology recapitulate paleontology? Lessons from species extinctions. Nature Reviews Clinical Oncology, Published online: 17 February 2015 | doi:10.1038/nrclinonc.2015.12
2014
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Alcock, J., Maley, C.C., Aktipis, C.A.: Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. Bioessays, 36:940-949, 2014 doi: 10.1002/bies.201400071.
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Li, X., Galipeau, P.C., Sanchez, C.A., Paulson, T.P., Arnaudo, J., Liu, K., Sather, C.L., Kostadinov, R.L., Odze, R.D., Kuhner, M.K., Maley, C.C., Self, S.G., Vaughan, T.L., Blount, P.L., Reid, B.J.: Temporal and Spatial Evolution of Somatic Chromosomal Alterations: A Case-Cohort Study of Barrett's Esophagus. Cancer Prevention Research, 7:114-127, 2014.
2013
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Aktipis, C.A., Boddy, A.M., Gatenby, R.A., Brown, J.S., Maley, C.C.: Life history tradeoffs in cancer evolution. Nature Reviews Cancer, 13:883-892, 2013.
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Kostadinov, R.L., Kuhner, M.K., Li, X., Sanchez, C.A., Galipeau, P.C., Paulson, T.G., Sather, C.L., Srivastava, A., Odze, R.D., Blount, P.L., Vaughan, T.L., Reid, B.J., Maley, C.C.: NSAIDs modulate clonal evolution in Barrett’s esophagus. PLOS Genetics, 9:e1003553, 2013. PMCID: PMC3681672
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Datta, R.S., Gutteridge, A., Swanton, C., Maley, C.C., Graham, T.A.: Modeling the evolution of genetic instability during tumour progression. Evolutionary Applications 6: 20- 33, 2013. PMCID: PMC3567468
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Sprouffske, K., Aktipis, C.A., Radich, J.P., Carroll, M., Nedelcu, A.M., Maley, C.C.: An evolutionary explanation for the presence of cancer non-stem cells in neoplasms. Evolutionary Applications, 6: 92-101, 2013. PMCID: PMC3567474
2012
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Roche, B., Hochberg, M.E., Caulin, A.F., Maley, C.C., Gatenby, R.A., Missé, D., Thomas, F.: Natural resistance to cancers: a Darwinian hypothesis to explain Peto's paradox. BMC Cancer. 12:387, 2012. PMCID: PMC3488527
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Sprouffske, K., Merlo, L.M.F., Gerrish, P.J., Maley, C.C., Sniegowski, P.D.: Cancer in light of experimental evolution. Current Biology, 22:R762-71, 2012. PMCID: PMC3457634
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Greaves, M. & Maley, C.C.: Clonal evolution in cancer. Nature. 481:306-313, 2012. PMCID: PMC3367003
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Kosoff, R.E., Gardiner, K.L., Merlo, L.M.F., Pavlov, K., Rustgi, A.K., Maley, C.C.: Development and Characterization of an Organotypic Model of Barrett’s Esophagus. Journal of Cellular Physiology. 2012. 227(6): p. 2654-2659. PMCID: PMC3352665
2011
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Merlo, L.M.F., Kosoff, R.E., Gardiner, K.L., Maley, C.C.: An in vitro co-culture model of esophageal cells identifies ascorbic acid as a modulator of cell competition. BMC Cancer, 11:461, 2011. PMCID: PMC3213018
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Martens, E.A., Kostadinov, R., Maley, C.C., Hallatschek, O.: Spatial Structure Increases the Waiting Time for Cancer. New Journal of Physics, Focus Issue "Physics of Cancer"
13:115014, 2011. PMCID: PMC3375912 -
Aktipis, C.A., Kwan, V.S.Y., Johnson, K.A., Neuberg, S.L., Maley, C.C.: Overlooking evolution: A systematic analysis of cancer relapse and therapeutic resistance research. PLoS ONE, 6(11):e26100, 2011.
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Sprouffske, K., Pepper, J. W. & Maley, C. C.: Accurate reconstruction of the temporal order of mutations in neoplastic progression. Cancer Prevention Research 4:1135-1144, 2011. PMCID: 3131446
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Aktipis, C.A., Maley, C.C., Pepper, J.W.: Dispersal evolution in neoplasms: The role of disregulated metabolism in the evolution of cell motility. Cancer Prevention Research 5, 266-275 2011. PMCID: PMC3273626
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Chen, J., Sprouffske, K., Huang, Q., Maley C.C.: Solving the puzzle of metastasis: The evolution of cell migration in neoplasms. PLoS ONE, 6:e17933, 2011. PMCID: PMC3083389
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Caulin, A.F. and Maley, C.C.: Peto's Paradox: Evolution's Prescription for Cancer Prevention. Trends in Evolution and Ecology, 26:175-82, 2011. PMCID: PMC3060950
2010
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Lai, L.A., Kostadinov, R., Barrett, M.T., Peiffer, D.A., Pokholok, D., Odze, R.D., Sanchez, C.A., Maley, C.C., Reid, B.J., Gunderson, K., Rabinovitch, P.S.: Deletion at Fragile Sites is a Common and Early Event in Barrett's Esophagus. Mol Cancer Res. 8:1084-94, 2010. PMCID: PMC3100793
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Merlo, L.M.F., Shah, N.A., Li, X., Blount, P., Vaughan, T.L., Reid, B.J., Maley, C.C.: A comprehensive survey of clonal diversity measures in Barrett’s esophagus as biomarkers of progression to esophageal adenocarcinoma. Cancer Prevention Research 3:1388-1397, 2010. PMCID: PMC3004782
2009
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Pepper, J.W., Findlay, C.S., Kassen, R., Spencer, S.L., and Maley, C.C.: Cancer research meets evolutionary biology. Evolutionary Applications 2:62-70, 2009.
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Paulson, T.G., Maley, C.C., Chao, D., Li, X., Li, X., Zhang, G., Sanchez, C.A. Odze, R., Vaughan, T., Blount, P., Ayub, K., Reid, B.J.: Copy number alterations in Barrett’s esophagus and esophageal adenocarcinoma. Clinical Cancer Research 15:3305-14, 2009. PMCID: PMC2684570
2008
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Liu, Z., Venkatesh, S.S., Maley, C.C.: Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples. BMC Genomics, 9:509, 2008. PMCID: PMC2628393
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Li X., Galipeau, P.C., Sanchez, C.A., Blount, P.L., Maley, C.C., Arnaudo, J., Peiffer, D.A., Pokholok, D., Gunderson, K.L., Reid, B.J.: SNP-based Genome-wide Chromosome Copy Change, LOH, and Aneuploidy in Barrett’s Esophagus Neoplastic Progression. Cancer Prevention Research 1:413-423, 2008. PMCID: PMC2882787
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Chao. D.L., Eck, T., Brash, D., Maley, C.C., Luebeck, E.G.: Pre-neoplastic lesion growth driven by the death of adjacent normal stem cells. PNAS 105:15034-15039, 2008. PMCID: PMC2567488
2007
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Pepper, J., Sprouffske, K., Maley, C.C.: Cell Differentiation Patterns Suppress Somatic Evolution. PLoS Computational Biology, 3:e250, 2007. Highlighted in Nature Online (http://www.nature.com/news/2007/070917/full/news070917-11.html) PMCID: PMC2134960
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Lai, L.A., Paulson T.G., Li X., Sanchez C.A., Maley C., Odze R.D., Reid B.J., Rabinovitch, P.S.: Increasing genomic instability during premalignant neoplastic progression revealed through high resolution array-CGH. Genes, Chromosomes and Cancer. 46:532-542, 2007.
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Srivastava, A., Hornick, J.L., Li, X., Blount, P.L., Sanchez, C.A., Cowan, D.S., Ayub, K., Maley, C.C., Reid, B.J., and Odze R.D.: Extent of low-grade dysplasia Is a risk factor for the development of esophageal adenocarcinoma in Barrett's esophagus. Am. J. Gastro. 102:483-493, 2007.
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Galipeau, P.C., Li X., Blount, P.L., Maley, C.C., Sanchez, C.A., Odze, R.D., Ayub, K., Rabinovitch, P.S., Vaughan, T.V., Reid, B.J.: NSAIDs modulate CDKN2A, TP53, and DNA content risk for progression to esophageal adenocarcinoma. PLoS Medicine. 4(2):e67, 2007. PMCID: PMC1808095
2006
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Merlo, L., Pepper, J., Reid, B.J., Maley, C.C.: Cancer as an evolutionary and ecological process. Nature Reviews Cancer, 6:924-35, 2006.
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Chao, D.L., Maley, C.C., Wu, X., Farrow, D.C., Galipeau, P.C., Sanchez, C.A., Paulson, T.G., Rabinovitch, P.S., Reid, B.J., Spitz, M.R., and Vaughan, T.L.: Mutagen sensitivity and neoplastic progression in patients with Barrett’s esophagus: A prospective analysis. Cancer Epidemiology, Biomarkers and Prevention, 15:1935-40, 2006. PMCID: PMC2567488
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Maley, C.C., Galipeau, P.C., Finley, J.C., Wongsurawat, V.J., Li, X., Sanchez, C.A., Paulson, T.G., Blount, P.L., Risques, R., Rabinovitch, P.S. and Reid, B.J.: Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nature Genetics, 38:468-473,
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Wongsurawat, V.J., Finley, J.C., Galipeau, P.C., Sanchez, C.A., Maley, C.C., Li, X., Blount, P.L., Odze, R.D., Rabinovitch, P.S. and Reid, B.J.: Genetic mechanisms of TP53 loss of heterozygosity in Barrett’s esophagus: Implications for biomarker validation. Cancer Epidemiology, Biomarkers and Prevention, 15:509-516, 2006.