David Tyrpak is a PhD candidate in pharmaceutical sciences at the University of Southern California expected to graduate in May 2020. He has significant experience in bioinformatics, image analysis, and data analysis. His research focuses on analyzing large datasets from next-generation sequencing and microscopy images to glean biological insights. He has authored or co-authored several peer-reviewed publications and developed open source image analysis pipelines.

1. David Tyrpak
PhD candidate in Pharmaceutical Sciences
(emphasis in image analysis and bioinformatics)
NIH Pre-Doctoral Fellow
University of Southern California School of Pharmacy
Linkedin: http://www.linkedin.com/in/david-tyrpak
Google Scholar Profile: David Tyrpak Google Scholar Page
Github Profile: https://github.com/d-tear (David Tyrpak)
tyrpak@usc.edu
213-257-5540
Biomedical scientist with significant bioinformatics, image analysis, and data analysis experience. I like to code
in R, Python, and Java. Currently a Ph.D. candidate and NIH pre-doctoral fellow at the USC School of Pharmacy,
graduating this June 2020. I also perform bioinformatics research at the Translational Genomics Department of
the Keck School of Medicine. I’m passionate about working in a team environment to glean actionable insight
from large, messy datasets.
Experience
Bioinformatician 09/2019 - Present
Translational Genomics Department at the Keck School of Medicine USC
• Helped validate a novel bioinformatic method for detecting large deletions in the mitochondrial genome.
• With collaborators at the NIH, I analyze NGS data to determine how variations in mitochondrial DNA
accumulate with human aging and how these variations may contribute to Parkinson’s disease.
• Write statistical analysis reports and prepare presentations for collaborating labs at the NIH and other
funding agencies.
• Develop bioinformatic pipelines and best practices for data analysis.
• First author on an in-preparation manuscript describing this work.
PhD Candidate and NIH Pre-Doctoral fellow 08/14 – Present
School of Pharmacy of the University of Southern California (Andrew MacKay’ Lab)
• Published one first author paper, one co-first author paper, and two co-authorships
• Developed an open source image processing pipeline which has been used in two different publications
to quantify and catalogue thousands of microscope images.
Publications which have used this pipeline:
1) Caveolin Elastin-Like Polypeptide Fusions Mediate Temperature-Dependent Assembly of
Caveolar Microdomains. Tyrpak, DR., Wang, Y., Avila, H. et al. ACS Biomaterials Science
& Engineering 2020 6 (1), 198-204 DOI: 10.1021/acsbiomaterials.9b01331
2) Cathepsin S activation contributes to elevated CX3CL1 (fractalkine) levels in tears of a
Sjögren’s syndrome murine model. Fu, R., Guo, H., Janga, S. et al. Sci Rep 10, 1455
(2020). https://doi.org/10.1038/s41598-020-58337-4
Code for this pipeline can be found here: https://zenodo.org/badge/latestdoi/140611525
An in-progress ImageJ plugin version can be found here: https://github.com/d-tear/SIAL
• Obtained a highly competitive NIH F31 fellowship to fund my PhD thesis.
Skillset
• R/Bioconductor, Python, and Java
• SQL
• Experience with version control using Git and Maven
• Unix, bash scripting, and high-performance computing systems to perform bioinformatics analyses
• Experience with commonly used bioinformatic tools (e.g. BWA, STAR, TOPHAT, CUFFLINKS,
SAMTOOLS, BEDTOOLS, GATK, IPA) to analyze NGS data

2. • Experience with GEO and TCGA
• Track record of developing computational pipelines to quickly and reproducibly analyze high volumes
of imaging and bioinformatics data.
• Solid understanding of statistics (experimental designs, linear models, and GLMs) and machine
learning.
• Strong of understanding of molecular biology and scientific writing
Education
University of Southern California School of Pharmacy, Los Angeles CA:
Ph.D. in Pharmaceutical and Pharmacological Sciences, May 2020 graduation
Clemson University, Clemson, SC:
B.S. in Biological Sciences and minor in Physics, 2013
Honors and Fellowships
2018 NIH Ruth L. Kirschstein National Research Service Award
2014 USC Provost Fellowship
2013 1st
place winner in the undergraduate division, Bryson L. James Student Competition of the Southern Nursery
Association Research Conference
Publications
Caveolin Elastin-Like Polypeptide Fusions Mediate Temperature-Dependent Assembly of Caveolar
Microdomains
D Tyrpak, Y Wang, H Avila, Hao Guo, R Fu, AT Truong, M Park, CT Okamoto, SF Hamm-Alvarez, JA
MacKay
2019. ACS Biomaterials Science & Engineering. 2020 6 (1), 198-204 DOI:
https://doi.org/10.1021/acsbiomaterials.9b01331
Tunable Assembly of Protein‐Microdomains in Living Vertebrate Embryos
*Z Li, *DR Tyrpak, CL Lien, JA MacKay
2018. Advanced Biosystems 2 (10), 1800112
https://doi.org/10.1002/adbi.201800112
[* authors contributed equally to this work]
A new temperature-dependent strategy to modulate the epidermal growth factor receptor
Z Li, DR Tyrpak, M Park, CT Okamoto, JA MacKay
2018. Biomaterials183, 319-330
https://doi.org/10.1016/j.biomaterials.2018.07.063
[I co-developed the live cell imaging technique which was used to determine the intracellular assembly temperature of our
temperature sensitive Epidermal Growth Factor Receptor fusion protein]
Berunda polypeptides: multi-headed fusion proteins promote subcutaneous administration of rapamycin to
breast cancer in vivo
JP Dhandhukia, Z Li, S Peddi, S Kakan, A Mehta, D Tyrpak, J Despanie, JA MacKay
2017. Theranostics 7 (16), 3856
[I performed statistical analyses and power calculations for the project]
10.7150/thno.19981

3. References
J. Andrew MacKay, PhD
Gavin S. Herbert Associate Professor of Pharmaceutical Sciences
School of Pharmacy, Dept. Pharmacology and Pharmaceutical Sciences
Viterbi School of Engineering, Dept. Biomedical Engineering
Keck School of Medicine, Dept. Ophthalmology
University of Southern California
Los Angeles, CA 90033
Email: jamackay@usc.edu
Brooke E. Hjelm, PhD
Assistant Professor of Clinical Translational Genomics
Department of Translational Genomics
University of Southern California
Harlyne J. Norris Cancer Research Tower
1450 Biggy St. NRT 2502
Los Angeles, CA 90033-9601
Office: 323.442.7799
Email: bhjelm@usc.edu
Ivo Violich, M.S.
Senior Bioinformatician
Department of Translational Genomics
University of Southern California
Harlyne J. Norris Cancer Research Tower
1450 Biggy St. NRT 2517D
Los Angeles, CA 90033-9601
Email: violich@usc.edu
Sarah Hamm-Alvarez, PhD
Professor and Vice Chair, Basic Research
Department of Ophthalmology
USC Roski Eye Institute
Associate Dean, Basic and Translational Research
USC Keck School of Medicine
Director, Research Development
SC-CTSI
323-442-1445 O
323-442-6412 F
Office Location: McKibben Annex 346A
MCA 349
1333 San Pablo Street
Los Angeles CA 90033
Email: sarah.hamm-alvarez@med.usc.edu
Curtis T. Okamoto
Associate Professor of Pharmacology and Pharmaceutical Sciences
School of Pharmacy, Dept. Pharmacology and Pharmaceutical Sciences
University of Southern California
Los Angeles, CA 90033
Email: cokamoto@usc.edu