Joshua Cook, Ph.D.

Computational Genomics Research Scientist

Vertex Pharmaceuticals

Biography

I am a computational biologist at Vertex Pharmaceuticals in Boston, MA.

In my free time, I enjoy learning about programming and computer science. Off the computer, my hobbies include running 🏃🏻‍♂️, exercising 🏋🏻, caring for my plants 🌵, baking bread 🍞, and fishing 🎣.

Interests

Bayesian data analysis
Python, R, and Rust programming
Swift and iOS development

Education

PhD in Computational Biology & Cancer Genetics, 2022
Harvard Medical School
BS in Biochemistry and Molecular Biology, 2017
University of California, Irvine
BS in Chemistry, 2017
University of California, Irvine

Skills

Python

Proficient

Rust

Intermediate

Proficient

Bayesian modeling

Proficient

Machine Learning

Intermediate

Data Visualization

Proficient

Linux

Sufficient

iOS, macOS & watchOS

Hobbiest

Raspberry Pi & Arduino

Hobbiest

Recent Accomplishments

Started at Vertex Pharmaceuticals

Vertex Pharmaceuticals Dec 2022

I have joined Vertex Pharmaceuticals as a Computational Genomics Research Scientist.

Defended my Ph.D. dissertation

Harvard University Nov 2022

Earned my Ph.D. from Harvard Medical School with my dissertation on “Studying the tissue-specificity of cancer drive genes through KRAS and genetic dependency screens.”

tumoroscope-pymc Python package

PyPI Oct 2022

Python package of the ‘Tumoroscope’ model implemented in PyMC.

Publications

Studying the Tissue Specificity of Cancer Driver Genes Through KRAS and Genetic Dependency Screens

Joshua Cook

Functional and biological heterogeneity of KRAS Q61 mutations

Huynh, Minh V and Hobbs, G Aaron and Schaefer, Antje and Pierobon, Mariaelena and Carey, Leiah M and Diehl, J Nathaniel and DeLiberty, Jonathan M and Thurman, Ryan D and Cooke, Adelaide R and Goodwin, Craig M and Cook, Joshua H and Lin, Lin and Waters, Andrew M and Rashid, Naim U and Petricoin, 3rd, Emanuel F and Campbell, Sharon L and Haigis, Kevin M and Simeone, Diane M and Lyssiotis, Costas A and Cox, Adrienne D and Der, Channing J

The origins and genetic interactions of KRAS mutations are allele- and tissue-specific

Joshua H. Cook, Giorgio E. M. Melloni, Doga C. Gulhan, Peter J. Park, Kevin M. Haigis

Tissue-specific oncogenic activity of KRAS A146T

Emily J. Poulin, Asim K. Bera, Jia Lu, Yi-Jang Lin, Samantha Dale Strasser, Joao A. Paulo, Tannie Q. Huang, Carolina Morales, Wei Yan, Joshua Cook, Jonathan A. Nowak, Douglas K. Brubaker, Brian A. Joughin, Christian W. Johnson, Rebecca A. DeStefanis, Phaedra C. Ghazi, Sudershan Gondi, Thomas E. Wales, Roxana E. Iacob, Lana Bogdanova, Jessica J. Gierut, Yina Li, John R. Engen, Pedro A. Perez-Mancera, Benjamin S. Braun, Steven P. Gygi, Douglas A. Lauffenburger, Kenneth D. Westover, Kevin M. Haigis

Toxoplasma gondii disrupts $\beta1$-integrin signaling and focal adhesion formation during monocyte hypermotility

Joshua H. Cook, Norikyo Ueno, Melissa B. Lodoen

See all publications

Projects

Click to see all of my projects!

Last updated on Dec 3, 2023 Fishing

Fishing 🎣

Spending a lot of my free time outdoors along the water trying to trick fish.

Last updated on Jun 24, 2023 Package

nciraspw

The NCI Ras Initiative’s Ras Pathway 2.0 exposed as a NetworkX object.

Last updated on Jun 24, 2023 Package

tumoroscope-pymc

Tumoroscope, a generative model of spatial transcriptomics clonality, implemented in PyMC.

Last updated on Jun 24, 2023 Programming

Comparing ML/AI summarizations of papers

Automatically download and parse research articles then summarize them with various ML and AI models.

Last updated on Jun 24, 2023 Hobbies

Reading

The books I have read along with my ratings and the rare review.

Last updated on Dec 3, 2023 Bread

Bread (and pizza!)

Just pictures and descriptions of some of the bread and pizza I’ve made.

Joshua Cook, Ph.D.

Last updated on Jun 24, 2023 R Packages

boston311

Python package for interfacing with Boston 311 API.

Last updated on Jun 24, 2023 Bayesian Data Analysis

Bayesian Data Analysis

The steps I have taken to learn how to conduct Bayesian data analysis.

Last updated on Jun 24, 2023 Applications

Counting Coffee

A suite of projects for tracking my coffee consumption.

Last updated on Jun 24, 2023 Data Analysis

Bayesian analysis of the 'Facial Feedback Hypothesis'

My own visualization and statistical analysis of the data from a replication study of this famous phsycology paper.

Last updated on Jun 24, 2023 Programming

Exploration of the latent input space of a Progressive Growing GAN

We trained a Progressive Growing GAN to produce realistic, yet novel, hand radiographs and explored its latent input space to identify an embedding of bone age.

Last updated on Jun 24, 2023 Programming

Text Summarization App

A web application that summarizing text down to an adjustable percentage of the the most important sentences.

Last updated on Jun 24, 2023 Programming

Sudoku Solver

A web application that solves [Sudoku puzzles] using linear integer programming.

Joshua Cook, Ph.D.

Last updated on Jun 24, 2023

Advent of Code (2020)

This links to my repository with my solutions to the Advent of Code 2020 programming challenges.

Joshua Cook, Ph.D.

Last updated on Jun 24, 2023 Data Analysis

Tidy Tuesday

This links to my repository of #TidyTuesday submissions. This is a series of notebooks and scripts that analyze a different dataset each week where I experiment with various modeling and data visualization techniques.

Joshua Cook, Ph.D.

Last updated on Jun 24, 2023 Swift Packages

textrank

A Swift package for summarizing long text into the most important sentences or words.

Last updated on Jun 24, 2023 Applications

WaterMe

An iPhone app for tracking when plants have been watered. There is also an Apple Watch app that makes work in the garden a bit easier. (demo GIFs)

Last updated on Jun 24, 2023 Applications

Apple Watch Telemetry Recorder

An Apple Watch application for recording telemetry data during a workout and uploading the data to iCloud Drive. Mathematical models are then fit to the data to identify the various stages of the exercise (e.g. the down and up positions of a push-up).

Last updated on Jun 24, 2023 Applications

Workout Spinner Apple Watch App

An Apple Watch application that randomly selects quick exercises using a Wheel-of-Fortune-like spinning wheel.

Joshua Cook, Ph.D.

Last updated on Jun 24, 2023 R Packages

mustashe

A simple system for saving and loading objects in R. Long running computations can be stashed after the first run and then reloaded the next time. Dependencies can be added to ensure that a computation is re-run if any of its dependencies or inputs have changed.

Joshua Cook, Ph.D.

Last updated on Jun 24, 2023 Plants