Professional Education

  • Bachelor of Arts, Cornell University (2006)
  • Doctor of Philosophy, Massachusetts Institute of Technology (2012)

Stanford Advisors

All Publications

  • Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia GENOME MEDICINE Weng, Z., Spies, N., Zhu, S. X., Newburger, D. E., Kashef-Haghighi, D., Batzoglou, S., Sidow, A., West, R. B. 2015; 7
  • Concepts in solid tumor evolution TRENDS IN GENETICS Sidow, A., Spies, N. 2015; 31 (4): 208-214


    Evolutionary mechanisms in cancer progression give tumors their individuality. Cancer evolution is different from organismal evolution, however, and we discuss where concepts from evolutionary genetics are useful or limited in facilitating an understanding of cancer. Based on these concepts we construct and apply the simplest plausible model of tumor growth and progression. Simulations using this simple model illustrate the importance of stochastic events early in tumorigenesis, highlight the dominance of exponential growth over linear growth and differentiation, and explain the clonal substructure of tumors.

    View details for DOI 10.1016/j.tig.2015.02.001

    View details for Web of Science ID 000353089500006

    View details for PubMedID 25733351

  • Constraint and divergence of global gene expression in the mammalian embryo. eLife Spies, N., Smith, C. L., Rodriguez, J. M., Baker, J. C., Batzoglou, S., Sidow, A. 2015; 4


    The effects of genetic variation on gene regulation in the developing mammalian embryo remain largely unexplored. To globally quantify these effects, we crossed two divergent mouse strains and asked how genotype of the mother or of the embryo drives gene expression phenotype genomewide. Embryonic expression of 331 genes depends on the genotype of the mother. Embryonic genotype controls allele-specific expression of 1594 genes and a highly overlapping set of cis-expression quantitative trait loci (eQTL). A marked paucity of trans-eQTL suggests that the widespread expression differences do not propagate through the embryonic gene regulatory network. The cis-eQTL genes exhibit lower-than-average evolutionary conservation and are depleted for developmental regulators, consistent with purifying selection acting on expression phenotype of pattern formation genes. The widespread effect of maternal and embryonic genotype in conjunction with the purifying selection we uncovered suggests that embryogenesis is an important and understudied reservoir of phenotypic variation.

    View details for DOI 10.7554/eLife.05538

    View details for PubMedID 25871848