Professional Education

  • B.S., University of California, Santa Cruz, Bioengineering (2012)
  • Ph.D., Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy (2021)

Stanford Advisors

  • Mark Kay, Postdoctoral Faculty Sponsor

All Publications

  • Improving Molecular Therapy in the Kidney. Molecular diagnosis & therapy Rubin, J. D., Barry, M. A. 2020; 24 (4): 375-396


    Mutations in approximately 80 genes have been implicated as the cause of various genetic kidney diseases. However, gene delivery to kidney cells from the blood is inefficient because of the natural filtering functions of the glomerulus, and research into and development of gene therapy directed toward kidney disease has lagged behind as compared with hepatic, neuromuscular, and ocular gene therapy. This lack of progress is in spite of numerous genetic mouse models of human disease available to the research community and many vectors in existence that can theoretically deliver genes to kidney cells with high efficiency. In the past decade, several groups have begun to develop novel injection techniques in mice, such as retrograde ureter, renal vein, and direct subcapsular injections to help resolve the issue of gene delivery to the kidney through the blood. In addition, the ability to retarget vectors specifically toward kidney cells has been underutilized but shows promise. This review discusses how recent advances in gene delivery to the kidney and the field of gene therapy can leverage the wealth of knowledge of kidney genetics to work toward developing gene therapy products for patients with kidney disease.

    View details for DOI 10.1007/s40291-020-00467-6

    View details for PubMedID 32323260

    View details for PubMedCentralID PMC7367759

  • Retargeting adenoviruses for therapeutic applications and vaccines. FEBS letters Barry, M. A., Rubin, J. D., Lu, S. C. 2020; 594 (12): 1918-1946


    Adenoviruses (Ads) are robust vectors for therapeutic applications and vaccines, but their use can be limited by differences in their in vitro and in vivo pharmacologies. This review emphasizes that there is not just one Ad, but a whole virome of diverse viruses that can be used as therapeutics. It discusses that true vector targeting involves not only retargeting viruses, but importantly also detargeting the viruses from off-target cells.

    View details for DOI 10.1002/1873-3468.13731

    View details for PubMedID 31944286

    View details for PubMedCentralID PMC7311308

  • Comparison of Gene Delivery to the Kidney by Adenovirus, Adeno-Associated Virus, and Lentiviral Vectors After Intravenous and Direct Kidney Injections. Human gene therapy Rubin, J. D., Nguyen, T. V., Allen, K. L., Ayasoufi, K., Barry, M. A. 2019; 30 (12): 1559-1571


    There are many kidney diseases that might be addressed by gene therapy. However, gene delivery to kidney cells is inefficient. This is due, in part, to the fact that the kidney excludes molecules above 50 kDa and that most gene delivery vectors are megaDaltons in mass. We compared the ability of adeno-associated virus (AAV), adenovirus (Ad), and lentiviral (LV) vectors to deliver genes to renal cells. When vectors were delivered by the intravenous (IV) route in mice, weak luciferase activity was observed in the kidney with substantially more in the liver. When gene delivery was observed in the kidney, expression was primarily in the glomerulus. To avoid these limitations, vectors were injected directly into the kidney by retrograde ureteral (RU) and subcapsular (SC) injections in mice. Small AAV vectors transduced the kidney, but also leaked from the organ and mediated higher levels of transduction in off-target tissues. Comparison of AAV2, 6.2, 8, and rh10 vectors by direct kidney injection demonstrated highest delivery by AAV6.2 and 8. Larger Ad and LV vectors transduced kidney cells and mediated less off-target tissue transduction. These data demonstrate the utility of direct kidney injections to circumvent the kidney size exclusion barrier. They also identify the effects of vector size on on-target and off-target transduction. This lays the foundation for the use of different vector platforms for gene therapy of diverse kidney diseases.

    View details for DOI 10.1089/hum.2019.127

    View details for PubMedID 31637925

    View details for PubMedCentralID PMC6919283

  • Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife Pope, W. H., Bowman, C. A., Russell, D. A., Jacobs-Sera, D., Asai, D. J., Cresawn, S. G., Jacobs, W. R., Hendrix, R. W., Lawrence, J. G., Hatfull, G. F. 2015; 4: e06416


    The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

    View details for DOI 10.7554/eLife.06416

    View details for PubMedID 25919952

    View details for PubMedCentralID PMC4408529

  • Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PloS one Pope, W. H., Jacobs-Sera, D., Russell, D. A., Peebles, C. L., Al-Atrache, Z., Alcoser, T. A., Alexander, L. M., Alfano, M. B., Alford, S. T., Amy, N. E., Anderson, M. D., Anderson, A. G., Ang, A. A., Ares, M., Barber, A. J., Barker, L. P., Barrett, J. M., Barshop, W. D., Bauerle, C. M., Bayles, I. M., Belfield, K. L., Best, A. A., Borjon, A., Bowman, C. A., Boyer, C. A., Bradley, K. W., Bradley, V. A., Broadway, L. N., Budwal, K., Busby, K. N., Campbell, I. W., Campbell, A. M., Carey, A., Caruso, S. M., Chew, R. D., Cockburn, C. L., Cohen, L. B., Corajod, J. M., Cresawn, S. G., Davis, K. R., Deng, L., Denver, D. R., Dixon, B. R., Ekram, S., Elgin, S. C., Engelsen, A. E., English, B. E., Erb, M. L., Estrada, C., Filliger, L. Z., Findley, A. M., Forbes, L., Forsyth, M. H., Fox, T. M., Fritz, M. J., Garcia, R., George, Z. D., Georges, A. E., Gissendanner, C. R., Goff, S., Goldstein, R., Gordon, K. C., Green, R. D., Guerra, S. L., Guiney-Olsen, K. R., Guiza, B. G., Haghighat, L., Hagopian, G. V., Harmon, C. J., Harmson, J. S., Hartzog, G. A., Harvey, S. E., He, S., He, K. J., Healy, K. E., Higinbotham, E. R., Hildebrandt, E. N., Ho, J. H., Hogan, G. M., Hohenstein, V. G., Holz, N. A., Huang, V. J., Hufford, E. L., Hynes, P. M., Jackson, A. S., Jansen, E. C., Jarvik, J., Jasinto, P. G., Jordan, T. C., Kasza, T., Katelyn, M. A., Kelsey, J. S., Kerrigan, L. A., Khaw, D., Kim, J., Knutter, J. Z., Ko, C. C., Larkin, G. V., Laroche, J. R., Latif, A., Leuba, K. D., Leuba, S. I., Lewis, L. O., Loesser-Casey, K. E., Long, C. A., Lopez, A. J., Lowery, N., Lu, T. Q., Mac, V., Masters, I. R., McCloud, J. J., McDonough, M. J., Medenbach, A. J., Menon, A., Miller, R., Morgan, B. K., Ng, P. C., Nguyen, E., Nguyen, K. T., Nguyen, E. T., Nicholson, K. M., Parnell, L. A., Peirce, C. E., Perz, A. M., Peterson, L. J., Pferdehirt, R. E., Philip, S. V., Pogliano, K., Pogliano, J., Polley, T., Puopolo, E. J., Rabinowitz, H. S., Resiss, M. J., Rhyan, C. N., Robinson, Y. M., Rodriguez, L. L., Rose, A. C., Rubin, J. D., Ruby, J. A., Saha, M. S., Sandoz, J. W., Savitskaya, J., Schipper, D. J., Schnitzler, C. E., Schott, A. R., Segal, J. B., Shaffer, C. D., Sheldon, K. E., Shepard, E. M., Shepardson, J. W., Shroff, M. K., Simmons, J. M., Simms, E. F., Simpson, B. M., Sinclair, K. M., Sjoholm, R. L., Slette, I. J., Spaulding, B. C., Straub, C. L., Stukey, J., Sughrue, T., Tang, T. Y., Tatyana, L. M., Taylor, S. B., Taylor, B. J., Temple, L. M., Thompson, J. V., Tokarz, M. P., Trapani, S. E., Troum, A. P., Tsay, J., Tubbs, A. T., Walton, J. M., Wang, D. H., Wang, H., Warner, J. R., Weisser, E. G., Wendler, S. C., Weston-Hafer, K. A., Whelan, H. M., Williamson, K. E., Willis, A. N., Wirtshafter, H. S., Wong, T. W., Wu, P., Yang, Y. j., Yee, B. C., Zaidins, D. A., Zhang, B., Zúniga, M. Y., Hendrix, R. W., Hatfull, G. F. 2011; 6 (1): e16329


    Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

    View details for DOI 10.1371/journal.pone.0016329

    View details for PubMedID 21298013

    View details for PubMedCentralID PMC3029335