Joshua Cook
Programmer & Computational Biologist
Programming Languages
Python
Data analysis & vis., AI/ML, automation, command line apps
Rust
Automation, command line apps
R
Data analysis & vis., AI/ML
Skills
Bayesian data analysis
Bespoke, tailored Bayesian statical models for data analysis and prediction (with PyMC and Stan)
Data Visualization
Presenting analysis and results with intuitive visualizations
Software development tools
Proficient with standard software development tools (e.g. Unix/Linux, git, GitHub, VSCode)
Machine Learning
Design, construction, analysis of mathematical models.
Arduino & Raspberry Pi
Home automation and robotics projects
iOS, macOS & watchOS
App development for hardware devices
Hobbies
Fishing 🎣
Backpacking ⛺️
Bread baking 🥖
Running 🏃🏻♂️
Summary
Computational biologist and bioinformatician with 6 years experience. Passionate about Bayesian modeling. Proficient in data processing and visualization, machine learning, and communicating results to diverse audiences. Good leader and follower, adapting to what is best for the team.
Profiles
Education
University of California, Irvine
B.S. • 3.9 GPA, Honors
Biochemistry & Molecular Biology; Chemistry
Aug 2013 – Jun 2017
Harvard Medical School
Ph.D. • 3.9 GPA
Biological and Biomedical Sciences
Aug 2017 – Nov 2022
Work Experience
Vertex Pharmaceuticals
Boston, MA
Computational Genomics Research Scientist
Dec 2022 – Present
•
Developed and deployed internal software tools to simplify and enhance analysis documentation and archiving.
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Progressed research projects in key disease areas by designing gene-editing experiments and data analyses in collaboration with experimental scientists.
Research Experience
Computational biology and bioinformatics
Aug 2017 – Nov 2022
•
Designed and executed novel research projects to address open questions in cancer genetics leading to 2 first-author publications (one in preparation) and 2+ co-authorships.
•
Developed Bayesian models to extract insights from large, complex, high-dimensional “omics” datasets.
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Constructed efficient pipelines to streamline data-processing for lab members.
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Presented my findings to audiences of diverse backgrounds and expertise.
Microbiology and immunology
Aug 2014 – Jun 2017
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Conducted experiments to investigate the molecular processes by which Toxoplasma gondii alters the behavior of its host white blood cell post-infection.
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Communicated the results and conclusions of my research in a first-authored publication and many conferences.
Neurobiology
Jun 2014 – Aug 2014
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Performed qPCR and neuronal imaging on samples from multiple brain regions of genetically engineered mice to quantify the spatial composition of axon-guidance machinery under different developmental conditions.
•
My work contributed to 2 publications, and I was listed as a co-author on one.
Select Publications
Functional and biological heterogeneity of KRASQ61 mutations
Aug. 9, 2022
Science Signaling
Minh V. Huynh, ..., Joshua H. Cook, ..., Kevin M. Haigis, ..., Channing J. Der.
The origins and genetic interactions of KRAS mutations are allele- and tissue-specific
Mar 22, 2021
Nature Communications
Joshua H. Cook, Giorgio E. M. Melloni, Doga C. Gulhan, Peter J. Park, Kevin M. Haigis.
Tissue-Specific Oncogenic Activity of KRASA146T
June 3, 2019
Cancer Discovery
Emily J. Poulin, …, Joshua H. Cook, …, Kevin M. Haigis.