Publications

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  1. Schiffman JD, Schmitt DL, Maley CCTP53 Gene and Cancer Resistance in Elephants--Reply. JAMA. 2016 Apr 26;315(16):1790-1. doi: 10.1001/jama.2016.0457. No abstract available.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  1. 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.

  2. 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

  1. 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.

  2. 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

  3. 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

  4. 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

  1. 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

  2. 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

  3. Greaves, M. & Maley, C.C.: Clonal evolution in cancer. Nature. 481:306-313, 2012. PMCID: PMC3367003

  4. 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

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  1. 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

  2. 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

  1. 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.

  2. 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

  1. 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

  2. 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

  3. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  1. Merlo, L., Pepper, J., Reid, B.J., Maley, C.C.: Cancer as an evolutionary and ecological process. Nature Reviews Cancer, 6:924-35, 2006.

  2. 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

  3. 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,

  4. 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.