Bio

Bio


Timothy is an MD/PhD student studying cancer biology and biomedical informatics at the Stanford University School of Medicine. He is a joint member of Kara Davis's laboratory in the Department of Pediatrics and Garry Nolan's Laboratory in the Department of Pathology.

As a biomedical data scientist, Timothy's research focuses on the application of machine learning to single-cell data analysis in the context of pediatric leukemia. Through the use of emerging, high-throughout single-cell technologies such as mass cytometry and sequence-based cytometry, Timothy's research is designed to build predictive models of patient outcomes - such as relapse or minimal residual disease (MRD) - at the point of diagnosis. To do so, he uses a variety of computational tools including generalized linear models, clustering, and deep learning. In addition, his work prioritizes constructing easy-to-use, highly-reproducible data analysis pipelines that can be shared as open-source tools for the scientific community.

Outside of science, Timothy has a longstanding interest in human rights and social justice work among members of the lesbian, gay, bisexual, transgender, and queer (LGBTQ+) community. He currently serves as the resident data scientist for the Medical Student Pride Alliance (MSPA), a 501(c)(3) non-profit organization that advocates for diversity, equity, and inclusion for LGBTQ+ medicals students in medical schools across the United States. As a data scientist at MSPA, Timothy analyzes and visualizes data to guide MSPA's strategic decision-making as well as for academic publication. He also advises and mentors other student members of MSPA performing data analysis in Python and R.

In recognition of his accomplishments, Timothy has received several institutional and national award for both research and advocacy. These include a National Research Service Award (NRSA) from the National Cancer Institute, a Junior Leadership Award from the Building the Next Generation of Academic Physicians (BNGAP) LGBT Workforce, Stanford Medicine’s Integrated Strategic Plan Star Award, and a Point Foundation Scholarship.

Honors & Awards


  • Point Foundation Graduate Student Scholarship, Point Foundation (2020)
  • Ruth L. Kirschstein Pre-doctoral National Research Service Award, National Institutes of Health (National Cancer Institute) (2019)
  • Community Impact Award, Stanford University (2019)
  • Integrated Strategic Plan Star Award, Stanford Medicine (2019)
  • Junior Leadership Award, Building the Next Generation of Academic Physicians (BNGAP) LGBT Workforce (2019)
  • Award for Excellence in Promotion of Diversity and Societal Citizenship, Stanford University School of Medicine (2018)

Membership Organizations


  • LGBT-Meds, Financial Officer (former)
  • SUMMA: Stanford University Minority Medical Alliance, Chair (former)
  • Medical Student Pride Alliance (MSPA), Assistant Director for Data Analytics

Education & Certifications


  • B.A., Princeton University, Psychology and Neuroscience (2014)

Publications

All Publications


  • Progressive B Cell Loss in Revertant X-SCID. Journal of clinical immunology Lin, C. H., Kuehn, H. S., Thauland, T. J., Lee, C. M., De Ravin, S. S., Malech, H. L., Keyes, T. J., Jager, A., Davis, K. L., Garcia-Lloret, M. I., Rosenzweig, S. D., Butte, M. J. 2020

    Abstract

    We report the case of a patient with X-linked severe combined immunodeficiency (X-SCID) who survived for over 20years without hematopoietic stem cell transplantation (HSCT) because of a somatic reversionmutation. An important feature of this rare case included the strategy to validate the pathogenicity of a variant of the IL2RG gene when the T and B cell lineages comprised only revertant cells. We studied the X-inactivation of sorted T cells from the mother to show that the pathogenic variant was indeed the cause of his SCID. One interesting feature was a progressive loss of B cells over 20years. CyTOF (cytometry time of flight) analysis of bone marrow offered a potential explanation of the B cell failure, with expansions of progenitor populations that suggest a developmental block. Another interesting feature was that the patient bore extensive granulomatous disease and skin cancers that contained T cells, despite severe T cell lymphopenia in the blood. Finally, the patient had a few hundred T cells on presentation but his TCRs comprised a very limited repertoire, supporting the important conclusion that repertoire size trumps numbers of T cells.

    View details for DOI 10.1007/s10875-020-00825-3

    View details for PubMedID 32681206

  • A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. Cytometry. Part A : the journal of the International Society for Analytical Cytology Keyes, T. J., Domizi, P., Lo, Y., Nolan, G. P., Davis, K. L. 2020

    Abstract

    The application of machine learning and artificial intelligence to high-dimensional cytometry data sets has increasingly become a staple of bioinformatic data analysis over the past decade. This is especially true in the field of cancer biology, where protocols for collecting multiparameter single-cell data in a high-throughput fashion are rapidly developed. As the use of machine learning methodology in cytometry becomes increasingly common, there is a need for cancer biologists to understand the basic theory and applications of a variety of algorithmic tools for analyzing and interpreting cytometry data. We introduce the reader to several keystone machine learning-based analytic approaches with an emphasis on defining key terms and introducing a conceptual framework for making translational or clinically relevant discoveries. The target audience consists of cancer cell biologists and physician-scientists interested in applying these tools to their own data, but who may have limited training in bioinformatics. © 2020 International Society for Advancement of Cytometry.

    View details for DOI 10.1002/cyto.a.24158

    View details for PubMedID 32602650

  • Documenting Social Media Engagement as Scholarship: A New Model for Assessing Academic Accomplishment for the Health Professions. Journal of medical Internet research Acquaviva, K. D., Mugele, J. n., Abadilla, N. n., Adamson, T. n., Bernstein, S. L., Bhayani, R. K., Büchi, A. E., Burbage, D. n., Carroll, C. L., Davis, S. P., Dhawan, N. n., English, K. n., Grier, J. T., Gurney, M. K., Hahn, E. S., Haq, H. n., Huang, B. n., Jain, S. n., Jun, J. n., Kerr, W. T., Keyes, T. n., Kirby, A. R., Leary, M. n., Marr, M. n., Major, A. n., Meisel, J. V., Petersen, E. A., Raguan, B. n., Rhodes, A. n., Rupert, D. D., Sam-Agudu, N. A., Saul, N. n., Shah, J. R., Sheldon, L. K., Sinclair, C. T., Spencer, K. n., Strand, N. H., Streed, C. G., Trudell, A. M. 2020; 22 (12): e25070

    Abstract

    The traditional model of promotion and tenure in the health professions relies heavily on formal scholarship through teaching, research, and service. Institutions consider how much weight to give activities in each of these areas and determine a threshold for advancement. With the emergence of social media, scholars can engage wider audiences in creative ways and have a broader impact. Conventional metrics like the h-index do not account for social media impact. Social media engagement is poorly represented in most curricula vitae (CV) and therefore is undervalued in promotion and tenure reviews.The objective was to develop crowdsourced guidelines for documenting social media scholarship. These guidelines aimed to provide a structure for documenting a scholar's general impact on social media, as well as methods of documenting individual social media contributions exemplifying innovation, education, mentorship, advocacy, and dissemination.To create unifying guidelines, we created a crowdsourced process that capitalized on the strengths of social media and generated a case example of successful use of the medium for academic collaboration. The primary author created a draft of the guidelines and then sought input from users on Twitter via a publicly accessible Google Document. There was no limitation on who could provide input and the work was done in a democratic, collaborative fashion. Contributors edited the draft over a period of 1 week (September 12-18, 2020). The primary and secondary authors then revised the draft to make it more concise. The guidelines and manuscript were then distributed to the contributors for edits and adopted by the group. All contributors were given the opportunity to serve as coauthors on the publication and were told upfront that authorship would depend on whether they were able to document the ways in which they met the 4 International Committee of Medical Journal Editors authorship criteria.We developed 2 sets of guidelines: Guidelines for Listing All Social Media Scholarship Under Public Scholarship (in Research/Scholarship Section of CV) and Guidelines for Listing Social Media Scholarship Under Research, Teaching, and Service Sections of CV. Institutions can choose which set fits their existing CV format.With more uniformity, scholars can better represent the full scope and impact of their work. These guidelines are not intended to dictate how individual institutions should weigh social media contributions within promotion and tenure cases. Instead, by providing an initial set of guidelines, we hope to provide scholars and their institutions with a common format and language to document social media scholarship.

    View details for DOI 10.2196/25070

    View details for PubMedID 33263554

  • Medical Student Pride Alliance: The first national LGBTQ+ medical student affinity organisation. Medical education Goetz, T. G., Zucker, S. n., Keyes, T. n., Gisondi, M. n. 2020; 54 (5): 471–72

    View details for DOI 10.1111/medu.14112

    View details for PubMedID 32242963

  • Student Education About Pre-exposure Prophylaxis (PrEP) Varies Between Regions of the United States. Journal of general internal medicine Bunting, S. R., Garber, S. S., Goldstein, R. H., Ritchie, T. D., Batteson, T. J., Keyes, T. J. 2020

    Abstract

    Daily, oral pre-exposure prophylaxis (PrEP) is an effective and safe prevention strategy for people at risk for HIV. However, prescription of PrEP has been limited for patients at the highest risk. Disparities in PrEP prescription are pronounced among racial and gender minority patients. A significant body of literature indicates that practicing healthcare providers have little awareness and knowledge of PrEP. Very little work has investigated the education about PrEP among health professionals in training.The objective of this study was to compare health professions students' awareness of PrEP and education about PrEP between regions of the US, and to determine if correlations between regional HIV incidence and PrEP use were present.Survey study.A cross-sectional sample of health professions students (N = 1859) representing future prescribers (MD, DO, PA), pharmacists, and nurses in the US.Overall, 83.4% of students were aware of PrEP, but only 62.2% of fourth-year students indicated they had been taught about PrEP at any time during their training. Education about PrEP was most comprehensive in the Northeastern US, the area with the highest PrEP to need ratio (4.7). In all regions, transgender patients and heterosexual men and women were least likely to be presented in education as PrEP candidates, and men who have sex with men were the most frequently presented.There are marked differences in education regarding PrEP both between academic programs and regions of the USA.

    View details for DOI 10.1007/s11606-020-05736-y

    View details for PubMedID 32080792

  • Navigating Controversy: A Critical Element of Medical Education. Academic medicine : journal of the Association of American Medical Colleges Jia, J. L., Kamceva, M. n., Keyes, T. J. 2018; 93 (12): 1750

    View details for PubMedID 30489297

  • Structural and functional features of central nervous system lymphatic vessels NATURE Louveau, A., Smirnov, I., Keyes, T. J., Eccles, J. D., Rouhani, S. J., Peske, J. D., Derecki, N. C., Castle, D., Mandell, J. W., Lee, K. S., Harris, T. H., Kipnis, J. 2015; 523 (7560): 337-?

    Abstract

    One of the characteristics of the central nervous system is the lack of a classical lymphatic drainage system. Although it is now accepted that the central nervous system undergoes constant immune surveillance that takes place within the meningeal compartment, the mechanisms governing the entrance and exit of immune cells from the central nervous system remain poorly understood. In searching for T-cell gateways into and out of the meninges, we discovered functional lymphatic vessels lining the dural sinuses. These structures express all of the molecular hallmarks of lymphatic endothelial cells, are able to carry both fluid and immune cells from the cerebrospinal fluid, and are connected to the deep cervical lymph nodes. The unique location of these vessels may have impeded their discovery to date, thereby contributing to the long-held concept of the absence of lymphatic vasculature in the central nervous system. The discovery of the central nervous system lymphatic system may call for a reassessment of basic assumptions in neuroimmunology and sheds new light on the aetiology of neuroinflammatory and neurodegenerative diseases associated with immune system dysfunction.

    View details for DOI 10.1038/nature14432

    View details for Web of Science ID 000357950900040

    View details for PubMedID 26030524

    View details for PubMedCentralID PMC4506234

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