B.S. - Biology and Chemistry double major. Portland State University (PSU), Portland, OR. (2002 – 2006)
M.S. - Biochemistry and Molecular Biology. Oregon Health and Science University (OHSU), Div. Environmental and Biomolecular Systems, Portland, OR. “A six-compartment Physiologically Based Pharmacokinetic (PBPK) Markov-chain Monte Carlo Model to simulate and quantify nicotine metabolism in human populations.” (2006 – 2008).
Ph.D. - Bioinformatics and Computational Biology, OHSU, Department of Medical Informatics and Clinical Epidemiology (DMICE), Division of Bioinformatics and Computational Biology (BCB), Portland, OR. “Robust and reproducible classification of rare cellular subsets/signatures (RCS) in single-cell technologies within a transfer learning framework.” (doi:10.6083/NX9EZJ). Committee members: Shannon K. McWeeney Ph.D., David M. Lewinsohn MD./Ph.D., Michael Mooney Ph.D., Christina Zheng Ph.D., and Evan Lind Ph.D. (2013 – 2018).
I am computational biologist focused and interested on solving problems related to immunology in the context of infectious disease and oncology. I have recieved my Ph.D. in Bioinformatics and Computational Biology (BCB) from Oregon Health and Science Unitversity (OHSU) in June 2018. I am profoundly fascinated by the immune system and the mechanisms of immunity to develop treatments and prophylactics, specifically within a precision-medicine framework.
My prior training was in Biology and Chemistry (BS 2006) and Biochemistry and Molecular Biology (MS 2008). From 2008 to 2012 I was a group member in Dr. Louis Picker’s Lab, where I focused on immunological studies relating to HIV Vaccines. Our work culminated in a critical examination of vaccine-mediated correlates of protection in Rhesus Macaques (Nature Medicine 2012). This experience seeded the interest and desire to contribute to multi-disciplinary translational biomedical research which propelled me to apply and be accepted as a PhD student in the Division of BCB, in the Department of Medical Informatics and Clinical Epidemiology (DMICE).
As a PhD candidate, I worked under the guidance and mentorship of Drs. David M. Lewinsohn, Marielle C. Gold and Shannon K. McWeeney. I contributed to projects and grants studying a population of tuberculosis (TB)-recognizing T-cells known as mucosal associated invariant T (MAIT) cells. A key idea of these studies was that MAIT cells may be harnessed as unconventional TB vaccine targets.
For my Ph.D. thesis (robust and reproducible classification of rare cellular subsets/signatures (RCS) in single-cell technologies within a transfer learning framework), I focused on strategies for computational phenotyping using single-cell technologies (i.e., flow cytometry, CyTOF, and RNA-Seq). Specifically, I developed a machine learning framework (the RTL framework, available on Github) to classify rare cellular subsets in single-cell data because classification of rare events from high-dimensional data is a difficult and highly variable task for humans and machines. Such robust and reproducible methods are a major pillar for accurate predictions of treatment/prophylactic effectiveness and prognostics within a precision-medicine framework. For the near future, I am interesting in continuing to develop robust computational methods to integrate and processes biomedical data as well as addressing clinical hypotheses. Long term, I am interested integrating the mechanisms of immunity and related data to better stratify patients and predicting adverse/positive outcomes.
2005 - 2007 Research Associate, Research Associate, Clinical Research Investigative Studies Program (CRISP) and Critical Care Academics Associates Program (CCAAP), OHSU. Contribution: Acquisition of clinical data from patient charts for ongoing studies and enrolment of patients into qualifying research in the emergency department and the intensive care units.
2008 - 2012 Sr. Research Associate, Louis Picker M.D., Vaccine & Gene Therapy Institute (VGTI), OHSU. Contribution: Performed experiments, analyzed flow cytometric data, performed statistical tests, and developed reports and presentation martials.
2013 - 2018 Doctoral Student, DMICE-BCB, OHSU. Research Involvement: Genome-based Bioinformatics, Assessment of bioinformatics pipelines identifying genomic structural variants across several sequenced Gibbons. Lucia Carbone Ph.D. Computational phenotyping in cancer cell lines, CyTOF-based computational analysis of phenotypic heterogeneity in breast cancer-derived cell in the context of combinatory anti-cancer drug treatments to identify sensitive phenotypic subtypes within several breast cancer cell lines. Paul T. Spellman Ph.D. Computational immunophenotyping, CyTOF-based computational immunophenotypic analysis of a unique population of tuberculosis (TB)-recognizing T-cells known as mucosal associated invariant T (MAIT) cells. David M. Lewinsohn M.D./Ph.D.