Carlo C. Maley, PhD

Carlo C. Maley, PhD

Director, Center for Evolution and Cancer, UCSF; Adjunct Associate Professor, Surgery, UCSF; Associate Professor, School of Life Sciences, Arizona State University

Phone: (480) 965-8089

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Cancer Center Membership

Program Member » Developmental Therapeutics» Cancer Genetics

Research Summary

I specialize in the evolutionary analysis of neoplasms, both for understanding progression to malignancy and the response to therapy. Most of my work has been in Barrett’s Esophagus and acute myeloid leukemia (AML), though I am interested in all cancers. We have shown that measures of intra-tumor genetic heterogeneity predict progression to malignancy in Barrett’s esophagus. We predict that the degree of heterogeneity should also correlate with the presence of a resistant clone, and so predict time until relapse after therapy. We are developing phylogenetic methods to measure the dynamics in tumors including mutation rates, clonal expansions, stem cell population sizes and time since initiation. We are interested in whole genome sequencing and epigenetic profiling of pre-malignant and malignant neoplasms, particularly in cases where they can be tracked over time. We are currently usinging the techniques to study the impact of non-steroidal anti-inflammatory drugs (NSAIDs) on clonal evolution in Barrett’s Esophagus.


Oberlin College, Oberlin, OH B.A., 1991, Computer Science/Psychology
Oxford University, Oxford, UK, M.S., 1993, Zoology
MIT, Cambridge, MA, Ph.D., 1998, Computer Science
Harvard University, Cambridge, MA, Postdoc, 1998, Evolutionary Biology
University of New Mexico, Albuquerque, NM Postdoc, 1998-2000, Computational Biology

Professional Experience

  • 2000-2005
    Staff scientist and member of the Program in GI Oncology, working with Brian Reid, Fred Hutchinson Cancer Research Center, Seattle, WA
  • 2005-2010
    Assistant Professor, The Wistar Institute
  • 2005-2010
    Genomics and Computational Biology Graduate Program, University of Pennsylvania
  • 2007-2010
    Cell and Molecular Biology Graduate Program, University of Pennsylvania
  • 2010-present
    Adjunct Associate Professor, Dept. of Surgery, University of California San Francisco
  • 2011-present
    Director, Center for Evolution and Cancer, University of California San Francisco
  • 2015-present
    Associate Professor, School of Life Sciences, Arizona State University

Honors & Awards

  • 1990
    Award for best GPA in social sciences, Oberlin College
  • 1990
    Inducted into Phi Beta Kappa, Junior year
  • 1991
    Inducted into Sigma Xi
  • 1991
    Graduated Oberlin College, Summa Cum Laude
  • 1991
    Summer Student Fellowship at Woods Hole Oceanographic Institute
  • 1991-1993
    Marshall Scholarship
  • 1995-1998
    National Defense Science and Engineering Graduate Fellowship
  • 2000-2002
    Alfred P. Sloan/Department of Energy Postdoctoral Fellowship in Computational Molecular Biology
  • 2001
    NIGMS Fellowship in Quantitative Biology, declined.
  • 2001-2006
    NCI Howard Temin Award (K01 Research Career Award)
  • 2003
    AACR Rodger C. Haggitt Award
  • 2008
    First winner of the Landon AACR Innovator Award for Cancer Prevention Research
  • 2013-2014
    Fellow of the Berlin Institute for Advanced Study (Wissenschaftskolleg)

Selected Publications

  1. Paguirigan AL, Smith J, Meshinchi S, Carroll M, Maley C, Radich JP. Single-cell genotyping demonstrates complex clonal diversity in acute myeloid leukemia. Sci Transl Med. 2015 Apr 1; 7(281):281re2.
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  2. Alcock J, Maley CC, Aktipis CA. Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. Bioessays. 2014 Oct; 36(10):940-9.
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  3. Li X, Galipeau PC, Paulson TG, Sanchez CA, Arnaudo J, Liu K, Sather CL, Kostadinov RL, Odze RD, Kuhner MK, Maley CC, Self SG, Vaughan TL, Blount PL, Reid BJ. Temporal and spatial evolution of somatic chromosomal alterations: a case-cohort study of Barrett's esophagus. Cancer Prev Res (Phila). 2014 Jan; 7(1):114-27.
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  4. Aktipis CA, Boddy AM, Gatenby RA, Brown JS, Maley CC. Life history trade-offs in cancer evolution. Nat Rev Cancer. 2013 Dec; 13(12):883-92.
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  5. Kostadinov RL, Kuhner MK, Li X, Sanchez CA, Galipeau PC, Paulson TG, Sather CL, Srivastava A, Odze RD, Blount PL, Vaughan TL, Reid BJ, Maley CC. NSAIDs modulate clonal evolution in Barrett's esophagus. PLoS Genet. 2013 Jun; 9(6):e1003553.
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  6. S Datta R, Gutteridge A, Swanton C, Maley CC, Graham TA. Modelling the evolution of genetic instability during tumour progression. Evol Appl. 2013 Jan; 6(1):20-33.
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  7. Sprouffske K, Athena Aktipis C, Radich JP, Carroll M, Nedelcu AM, Maley CC. An evolutionary explanation for the presence of cancer nonstem cells in neoplasms. Evol Appl. 2013 Jan; 6(1):92-101.
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  8. Sprouffske K, Merlo LM, Gerrish PJ, Maley CC, Sniegowski PD. Cancer in light of experimental evolution. Curr Biol. 2012 Sep 11; 22(17):R762-71.
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  9. Roche B, Hochberg ME, Caulin AF, Maley CC, Gatenby RA, Misse D, Thomas F. Natural resistance to cancers: a Darwinian hypothesis to explain Peto's paradox. BMC Cancer. 2012; 12:387.
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  10. Kosoff RE, Gardiner KL, Merlo LM, Pavlov K, Rustgi AK, Maley CC. Development and characterization of an organotypic model of Barrett's esophagus. J Cell Physiol. 2012 Jun; 227(6):2654-9.
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  11. Greaves M, Maley CC. Clonal evolution in cancer. Nature. 2012 Jan 19; 481(7381):306-13.
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  12. Aktipis CA, Kwan VS, Johnson KA, Neuberg SL, Maley CC. Overlooking evolution: a systematic analysis of cancer relapse and therapeutic resistance research. PLoS One. 2011; 6(11):e26100.
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  13. Merlo LM, Kosoff RE, Gardiner KL, Maley CC. An in vitro co-culture model of esophageal cells identifies ascorbic acid as a modulator of cell competition. BMC Cancer. 2011; 11:461.
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  14. Aktipis CA, Maley CC, Pepper JW. Dispersal evolution in neoplasms: the role of disregulated metabolism in the evolution of cell motility. Cancer Prev Res (Phila). 2012 Feb; 5(2):266-75.
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  15. Chen J, Sprouffske K, Huang Q, Maley CC. Solving the puzzle of metastasis: the evolution of cell migration in neoplasms. PLoS One. 2011; 6(4):e17933.
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  16. Reid BJ, Kostadinov R, Maley CC. New strategies in Barrett's esophagus: integrating clonal evolutionary theory with clinical management. Clin Cancer Res. 2011 Jun 1; 17(11):3512-9.
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  17. Sprouffske K, Pepper JW, Maley CC. Accurate reconstruction of the temporal order of mutations in neoplastic progression. Cancer Prev Res (Phila). 2011 Jul; 4(7):1135-44.
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  18. Caulin AF, Maley CC. Peto's Paradox: evolution's prescription for cancer prevention. Trends Ecol Evol. 2011 Apr; 26(4):175-82.
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  19. Merlo LM, Shah NA, Li X, Blount PL, Vaughan TL, Reid BJ, Maley CC. A comprehensive survey of clonal diversity measures in Barrett's esophagus as biomarkers of progression to esophageal adenocarcinoma. Cancer Prev Res (Phila). 2010 Nov; 3(11):1388-97.
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  20. Lai LA, Kostadinov R, Barrett MT, Peiffer DA, Pokholok D, Odze R, Sanchez CA, Maley CC, Reid BJ, Gunderson KL, Rabinovitch PS. Deletion at fragile sites is a common and early event in Barrett's esophagus. Mol Cancer Res. 2010 Aug; 8(8):1084-94.
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