Katharine Chen Email & Phone Number

Seattle, WA, US

Genomic data modeling lab

Seattle, Washington, United States

Developing open-source software in JavaScript for visualizing rule-based biological models generated by NFSim.Leading an effort to create instructional resources that teach scientific researchers how to convert their traditional lab notebook setups into version controlled, reproducible, and collaborative workspaces using Git, GitHub, and Docker.

Seattle, Washington, United States

Led a study using barcoded massively parallel reporter assays (MPRAs) to probe for RNA sequences that trigger mRNA degradation by quality control factors in microbial cells. This work is published in Nucleic Acids Research and our code is publicly available at https://github.com/rasilab/chen_2023.Used FACS-based CRISPR screening to uncover novel regulators.

Seattle, Washington, United States

- Identification of transcription start sites from ultra-low pass sequencing data from patient CRPC blood samples using experimental algorithms in Dr. Gavin Ha’s group. My contributions were published in Doebley et al., Nature Communications, 2022.- Development of CRISPR screens for KRAS regulators in Dr. Alice Berger’s lab.

Managed collaborations and day to day operations. Provided technical laboratory support in the form of primary and secondary cell culture of neural stem cell lines, mouse model experimentation, and various types of cell-based and molecular assays. My experimental contributions and collaborations spanned four different labs across two institutions and have.

Received the UC Berkeley Summer Undergraduate Research Award, which funded my travels to the Mpala Research Center of Kenya, where I performed fieldwork and data collection of marine species in the Ewaso Ng’iro river.Wrote and submitted our manuscript regarding trophic interactions and resource partitioning patterns in the aquatic species we sampled using.

While performing support duties (restocking, cleaning glassware, autoclaving biohazardous waste), I learned various fundamental molecular biology techniques from different lab members and ultimately produced a senior honors thesis characterizing different fatty acid transporter proteins in different genetic mouse models. Presented the results of my honors.

Officiated intramural volleyball games before becoming a site supervisor.Managed referees and supervised operations at each site.

Doctor Of Philosophy - Phd, Molecular/Cellular Biology: Data Science

Joint Data Science PhD Degree Option with the UW eScience Institute. Used massively parallel reporter assays to characterize sequence.

Bachelor Of Arts (Ba), Molecular And Cell Biology With Honors

Department of Molecular and Cell Biology, with Honors Minor in Environmental Science, Policy, and Management - Conservation and Resource.