Stanford Advisors

Lab Affiliations

All Publications

  • Single-cell measurement of higher-order 3D genome organization with scSPRITE NATURE BIOTECHNOLOGY Arrastia, M., Jachowicz, J. W., Ollikainen, N., Curtis, M. S., Lai, C., Quinodoz, S. A., Selck, D. A., Ismagilov, R. F., Guttman, M. 2022; 40 (1): 64-+


    Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.

    View details for DOI 10.1038/s41587-021-00998-1

    View details for Web of Science ID 000687498000001

    View details for PubMedID 34426703

  • How Can Chemometrics Improve Microfluidic Research? ANALYTICAL CHEMISTRY Jalali-Heravi, M., Arrastia, M., Gomez, F. A. 2015; 87 (7): 3544-3555


    Chemometrics has the potential to embolden microfluidics to become that enabling technology for so long sought after. In this Feature article, we describe a historical perspective on microfluidics and its current challenges, a perspective on chemometric methods including response surface methodology (RSM), and how a combination of artificial neural network with experimental design (ANN-ED) have demonstrated promise in addressing basic microfluidic problems.

    View details for DOI 10.1021/ac504863y

    View details for Web of Science ID 000352659500002

    View details for PubMedID 25651407

  • Development of a microfluidic-based assay on a novel nitrocellulose platform ELECTROPHORESIS Arrastia, M., Avoundjian, A., Ehrlich, P., Eropkin, M., Levine, L., Gomez, F. A. 2015; 36 (6): 884-888


    A novel microfluidic paper-based analytical device (μPAD) utilizing a nitrocellulose (NC) membrane to detect IgG antibodies through a colorimetric analysis is described. The μPAD was constructed using layered polyethylene terephthalate (PET) and pressure-sensitive adhesives (PSA). The biotin labeled Goat Anti-Mouse IgG antibody was spotted and dried on the NC channel prior to subjecting it to a series of wash solutions (Tris-tween), increasing concentrations of alkaline phosphatase conjugated to streptavidin (Strep-ALP), and para-nitrophenyl phosphate (p-NPP) realizing a vibrant yellow color. The reaction proceeds for 10 min before applying the p-NPP stop solution. The device was then dried, scanned, and analyzed yielding a linear range of inverse yellow color intensities versus Strep-ALP concentrations. The development of this simple μPAD should further facilitate the use of NC in colorimetric assays to detect and quantitate antibodies.

    View details for DOI 10.1002/elps.201400421

    View details for Web of Science ID 000351549900005

    View details for PubMedID 25545783