Asya Stepansky

Learn More
Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be lost that would be useful for reconstructing evolutionary history. Here we show that with flow-sorted nuclei, whole(More)
Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but(More)
Cucumis melo L. (melon) genotypes differ widely in morphological and biochemical traits. Intraspecific classification of such variability has been difficult, and most taxonomists still rely on the work of Naudin (1859). A collection of 54 accessions representing diverse genotypes from 23 countries was surveyed. Morphological traits related to the vegetative(More)
Copy number variation (CNV) is increasingly recognized as an important contributor to phenotypic variation in health and disease. Most methods for determining CNV rely on admixtures of cells in which information regarding genetic heterogeneity is lost. Here we present a protocol that allows for the genome-wide copy number analysis of single nuclei isolated(More)
How is chromatin architecture established and what role does it play in transcription? We show that the yeast regulatory locus UASg bears, in addition to binding sites for the activator Gal4, sites bound by the RSC complex. RSC positions a nucleosome, evidently partially unwound, in a structure that facilitates Gal4 binding to its sites. The complex(More)
Timely characterization of a cancer's evolution is required to predict treatment efficacy and to detect resistance early. High content analysis of single Circulating Tumor Cells (CTCs) enables sequential characterization of genotypic, morphometric and protein expression alterations in real time over the course of cancer treatment. This concept was(More)
Sugar accumulation is a very important physiological process that determines dessert-melon fruit quality. Considerable variation in the sugar content and composition in the mature flesh of Cucumis melo L. fruits was observed among 56 genotypes which represent the wide range of morphological and horticultural types found in this species. Sucrose accumulation(More)
A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering(More)
Limited access to tumor tissue makes repeated sampling and real-time tracking of cancer progression infeasible. Circulating tumor cells (CTCs) provide the capacity for real-time genetic characterization of a disseminating tumor cell population via a simple blood draw. However, there is no straightforward method to analyze broadscale genetic rearrangements(More)
Masayuki Yamato, Satoshi Tsuneda and Teruo Okano would like to retract this protocol after concerns were raised by the community about some of the figures. Specifically, concerns were raised that the fourth graph in Figure 5a and the first graph in Figure 5b look very similar, and some of the error bars look unevenly positioned. Masayuki Yamato, Satoshi(More)
  • 1