EDUCATION AND TRAINING

Johns Hopkins University, Baltimore, MD PhD Candidate in the Labs of Dr. Elana J Fertig and Dr. Genevieve L Stein-O’Brien | Graduation expected 2025

University of British Columbia, Vancouver, B.C. BSc in Computer Science, Minor in Microbiology and Immunology | Graduated May 2020 Honors and awards: NSERC SURE Research Award (2019), Faculty of Science International Student Scholarship (2016, 2019), Accenture Leadership Award (2019), Dean’s Honor List (2018-2019), Outstanding International Student Award (2015)

RESEARCH EXPERIENCE

Johns Hopkins University Department of Oncology | PhD Candidate Jun 2021-present Thesis work: Building agent-based math models of early-stage pancreatic cancer, finding ways to automatically translate cell data into mathematical models. Developed a python package for performing non-negative matrix factorization on omics data. Faculty advisors: Dr. Elana J. Fertig and Dr. Genevieve Stein-O’Brien

Johns Hopkins University Department of Rheumatology | PhD Rotation Student Mar-Jun 2021 Faculty advisor: Dr. Erika Darrah

Johns Hopkins University Department of Plastic and Reconstructive Surgery | PhD Rotation Student Jan-Mar 2021 Faculty advisor: Dr. Georgio Raimondi

Johns Hopkins University Department of Pathology | PhD Rotation Student Sep-Dec 2020 FR3AK-seq protocol to investigate primer crossover issues performed TCR CD3 sequencing after peptide stimulation using the FR3AK-seq isolation and sequencing protocol Faculty advisor: Dr. Ben Larman

University of British Columbia | Undergraduate Researcher May-Dec 2019 Working extensively with CITE-seq and CyTOF data from murine tumor biopsy samples to investigate changes in the behavior of blood monocytes in the context of colorectal cancer Introduced Monocle 3 and Seurat 3 into our data analysis pipeline for dimensionality reduction, clustering, and differential expression; wrote scripts to apply these tools to our results in a consistent and reproducible fashion Faculty advisor: Dr. Kenneth Harder

University of British Columbia | Undergraduate Researcher Jan-Mar 2019 Combined C provenance library and PostgreSQL backend with top-level Python to consume articles and render NetworkX graphs detailing their connection to other articles, authors, publications, and quoted phrases Extracted and analyzed article text to determine the correlation between provenance (data lineage) and natural language classification (objective vs. non-objective) Faculty advisor: Dr. Margo Seltzer

PROFESSIONAL EXPERIENCE

Cisco Systems/OpenDNS | Software Engineering Co-op Sep. 2017 - Sep. 2018 Worked as a software engineering intern on the Surface Intelligence Feature Team, which oversees a Java-based API server for network security data, the Umbrella reporting microapp, and multiple scalable infrastructure components Migrated API Server deployments to the EU for GDPR Compliance, performed future deployment automations Redesigned and rewrote a customer-facing automated security email system in Java with three teammates over a period of 6 months Designed and implemented a new threat intelligence report for Umbrella, Cisco’s cloud security product, using JavaScript, HTML, and CSS UBC Department of Computer Science | Academic Assistant Sep. 2018 - May 2019 Responsible for updating and curating the UBC Computer Science Job Posting Boards Organized a weekly email highlighting events, opportunities, and resources for Computer Science students University of British Columbia Department of Microbiology & Immunology | Lab Assistant Jan-Sep 2017 Worked to uphold a sterile environment in a lab that worked with norovirus and parasites alongside tissue culture Sterilized lab equipment including glassware and surgical tools Faculty advisor: Dr. Lisa Osborne

PUBLICATIONS

Johnson J, Tsang A, Mitchell JT, Davis-Marcisak E, Sherman T, Liefeld T, Loth M, Goff LA, Zimmerman J, Kinny-Köster B, Jaffee E, Tamayo P, Mesirov JP, Reich M, Fertig EJ, Stein-O’Brien GL “Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS” bioRxiv 2022.07.09.499398; doi: https://doi.org/10.1101/2022.07.09.499398, Nature Protocols Godet I, Oza H, Joe N, Weinstein A, Johnson J, Xu R, Mbulaiteye D, Stein-O’Brien GL, Kagohara L, Santa-Maria C, Dr Fertig EJ “Hypoxia induces a ROS-resistant phenotype that is preserved upon reoxygenation and drives metastasis via MUC1-C” under review at Nature Communications Eaton WW, Rodriguez KM, Thomas MA, Johnson J, Talor MV, Dohan C, Bingham CO 3rd, Musci R, Roth K, Kelly DL, Cihakova D, Darrah E. “Immunologic profiling in schizophrenia and rheumatoid arthritis.” Psychiatry Res. 2022 Aug 28;317:114812. doi: 10.1016/j.psychres.2022.114812

PRESENTATIONS

Minisymposium talk: “Integrating Omics Data and Agent-Based Models for Comprehensive Digital Biology” Society Math Biology Annual Meeting, July 2023 The Ohio State University, Columbus, OH

Poster: “Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R, and GenePattern Notebook implementations of CoGAPS“ Systems Immunology Meeting, April 2023 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

MENTORSHIP

Ashley Tsang: Mentored 2021-2023 Undergraduate Researcher in the Fertig Lab Major topic: Biochemical Engineering Current position: Incoming PhD student at the University of Michigan Project: Ashley and I wrote the python CoGAPS interface and the cloud-based GenePattern Notebook module supporting it. This work is currently under review at Nature Protocols.

Max Booth: Mentored 2022-2023 Undergraduate Researcher in the Fertig Lab Major topic: Mathematics Current position: PhD applicant Project: Max and I worked together to do exploratory integration of a spatial 10x VISIUM dataset with PhysiCell agent-based modeling framework. Max went on to perform sensitivity analysis and to explore new ways of modeling oxygen availability within simulated tissues. This work is in preparation to be submitted Summer 2023.

David Zhou: Mentored 2022-present Undergraduate Researcher in the Stein-O’Brien Lab Major topic: Neuroscience

Participated in the UBC Computer Science Tri-mentorship program for two years first as a junior mentee and then as the senior mentee.

TECHNICAL SKILLS

Lab Techniques: PCR, flow cytometry, cell culture, western blot, murine work, sterile technique Programming Languages: Python, R, Java, C, C++, x86 Assembly Tools and Frameworks: AWS, Docker, Linux/UNIX, RStudio, Git, Illustrator, Bioconductor

TEACHING

Johns Hopkins University School of Medicine | Teaching Assistant Spring 2023 TA for Introduction to R, which teaches basics of R data analysis to students and trainees in the School of Medicine Worked with beginner coders with biomedical backgrounds during class and office hours to help them become familiar with the R and Rstudio coding environment and develop intuition for troubleshooting common coding problems prepared and taught two lessons; one on Debugging practices and the other on using the biomaRt R package Students presented a final project analyzing their own data using techniques from the class

UBC Department of Computer Science | Teaching Assistant Summer 2017, Winter 2018 TA for Introduction to Computer Systems, a 200-student second year Computer Science course at UBC Taught labs ranging from memory management and pointer manipulation to asynchronous programming Held weekly office hours to help students individually, actively answered questions remotely on Piazza Marked exams and assignments, invigilated midterms and finals

COMMUNITY BUILDING

UBC Women in Science Club | Vice President 2016 - 2019 Served as an executive for three years for a 200-member club with the mission of connecting women and gender minority STEM undergraduates to more senior, established peers in the Vancouver, BC scientific community. Mentor participation was robust and always on a volunteer basis. Organized and facilitated events e.g. research lab tours, meet-a-mentor nights, and panel discussions Leveraged email and social media to keep our members up-to-date about club events and woman scientists in the news Designed the club’s website, www.ubcwomeninscience.com

Download PDF: JeanetteJohnsonResume2022.pdf