Current CV for David Tyrpak

1. .
David Tyrpak
NIH Pre-Doctoral Fellow
Bioinformatician
PhD in Pharmacology and Pharmaceutical Sciences
School of Pharmacy, University of Southern California
Address Alhambra, CA, 91803
Phone 213-257-5540
E-mail tyrpak@usc.edu
LinkedIn http://www.linkedin.com/in/david-tyrpak
Github Profile https://github.com/d-tear
Google Scholar
https://scholar.google.com/citations?user=MlM8UqEA
Biomedical scientist with significant bioinformatics, image analysis, and data analysis experience. I like to code in R,
Python, and Java. Currently a PhD and NIH pre-doctoral fellow at the USC School of Pharmacy, defending this July
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
2019-09 -
Present
Bioinformatician
USC Keck School of Medicine, Los Angeles, CA
Department of Translational Genomics, Dr Brooke E. Hjelm’s Lab
• 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.
• As part of a team, I helped develop a Shiny website to track projects for the International
Parkinson's Disease Genomics Consortium (IPDGC). This project was part of the 2020 IPDGC
hackathon and code can be found here: https://github.com/ipdgc/PD-Project-Tracker

2. .
2014-08 -
2020-07
PhD Candidate and NIH Pre-Doctoral Fellow
USC School of Pharmacy, Los Angeles, CA
Department of Pharmacology and Pharmaceutical Sciences, Dr J. 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.
Code for this pipeline can be found here: https://zenodo.org/badge/latestdoi/140611525
Publications which have used this pipeline:
Tyrpak, DR., Wang, Y.. et al. ACS Biomaterials Science & Engineering 2020 6 (1), 198-204
DOI:10.1021/acsbiomaterials.9b01331
Fu, R., Guo, H. et al. Sci Rep 10, 1455 (2020) DOI:10.1038/s41598-020-58337-4
• Developed an ImageJ/FIJI plugin for reproducible image analysis: https://github.com/d-
tear/SIAL
• Obtained a highly competitive NIH F31 fellowship to fund my PhD thesis.
Education
2020-07 PhD: Pharmaceutical and Pharmacological Sciences
University of Southern California School of Pharma - Los Angeles, CA
2013-05 Bachelor of Science: Biological Sciences and Minor in Physics
Clemson University - Clemson, SC
Skills
•R/Bioconductor, Python, and Java
•SQL
•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
•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, GLMs, frequentist vs.
Bayesian) and machine learning.
•Strong of understanding of molecular biology and scientific writing

3. .
Honors and Fellowships
• 2020 The Order of Arête, University of Southern California
• 2018 NIH Ruth L. Kirschstein National Research Service Award, National Institute of Diabetes
and Digestive and Kidney Diseases
• 2014 USC Provost Fellowship, University of Southern California
• 2013 1st place winner in the undergraduate division, Bryson L. James Student Competition of the
Southern Nursery Association Research Conference
Publications
1. Caveolin Elastin-Like Polypeptide Fusions Mediate Temperature-Dependent Assembly of
Caveolar Microdomains. D Tyrpak, Y Wang. et al. 2019. ACS Biomaterials Science &
Engineering. 2020 6 (1), 198-204 DOI:10.1021/acsbiomaterials.9b01331
2. Tunable Assembly of Protein‐Microdomains in Living Vertebrate Embryos.*Z Li, *DR
Tyrpak, et al. 2018. Advanced Biosystems 2 (10), 1800112 DOI:10.1002/adbi.201800112 [*
authors contributed equally to this work]
3. A new temperature-dependent strategy to modulate the epidermal growth factor receptor. Z
Li, DR Tyrpak et al. 2018. Biomaterials183, 319-330
DOI: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]
4. 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 et al.2017. Theranostics 7 (16), 3856 DOI:10.7150/thno.19981 [I performed statistical
analyses and power calculations for the project]

4. .
References
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
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
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, 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