Graduate Student

Harvard Medical School

Biography

Josh is a computational biologist pursuing his PhD. at Harvard Medical School. There, he is co-advised by Professor Kevin Haigis and Professor Peter Park as he studies cancer genetics and evolution. Specifically, he is working to understand the tissue-specific impacts of KRAS mutations on the behavior of cancers.

In his free time, Josh enjoys learning about programming and computer science - his current project is creating an iOS app in Swift. Off the computer, his hobbies include running and caring for his plants.

Interests

  • Cancer genetics and evolution
  • Swift and iOS development

Education

  • BS in Biochemistry and Molecular Biology, 2017

    University of California, Irvine

  • BS in Chemistry, 2017

    University of California, Irvine

Skills

R

Proficient

Python

Intermediate

Swift

Intermediate

Linux

Sufficient

Statistics

Intermediate

iOS & watchOS

Intermediate

All Publications

Quickly discover relevant content by filtering publications.
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
PDF Code Dataset DOI PubMed Nat. Comm.
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
PDF Code DOI PubMed Cancer Discov.
Toxoplasma gondii disrupts $\beta1$-integrin signaling and focal adhesion formation during monocyte hypermotility
Joshua H. Cook, Norikyo Ueno, Melissa B. Lodoen
PDF DOI PubMed JBC
Loss of Magel2 impairs the development of hypothalamic Anorexigenic circuits
Julien Maillard, Soyoung Park, Sophie Croizier, Charlotte Vanacker, Joshua H. Cook, Vincent Prevot, Maithe Tauber, Sebastien G. Bouret
PDF DOI PubMed Hum Mol Genet.

Projects

.js-id-application
Applications Packages Data Analysis Plants

Text Summarization App

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

Sudoku Solver

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

Advent of Code (2020)

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

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.

textrank

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

Bayesian Data Analysis

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

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)

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).

Workout Spinner Apple Watch App

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

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.

Frailea castanea from seed

My attempt at growing Frailea castanea from seed.

Germination Tracker iOS App

A simple app to help me record data on my seedlings.

Growing Lithops from seed

Documenting my journey from seed to Lithops.

ggasym (“gg-awesome”)

‘ggasym’ (pronounced “gg-awesome”) plots a symmetric matrix with three different fill aesthetics.

Plant Tracker iOS App

An app to help my mom keep track of and care for her plants.

Recent Posts

Click to see all of my posts!

Xcode Logger Notes

A few useful notes for using the logging system in Swift apps on Apple platforms.
Last updated on Mar 24, 2021 4 min read Programming, Swift
Xcode Logger Notes

Creating a Streamlit web app, building with Docker + GitHub Actions, and hosting on Heroku

A step-by-step tutorial on creating a web application with Streamlit, building a Docker image with GitHub Actions, and hosting on Heroku.
Last updated on Dec 31, 2020 9 min read Programming
Creating a Streamlit web app, building with Docker + GitHub Actions, and hosting on Heroku

Fitting a spline with PyMC3

How to fit a spline using the Bayesian modeling framework PyMC3.
Josh Cook
Last updated on Nov 15, 2020 9 min read Programming
Fitting a spline with PyMC3

Colorize black-and-white photos

How to use DeepAI’s Image Colorization API to colorize black-and-white photos using Python.
Josh Cook
Last updated on Nov 14, 2020 4 min read Programming
Colorize black-and-white photos

Riddler: Can You Beat MLB Recods?

A simple statistical solution to this Riddler accompanied by descriptive simulations.
Last updated on Jan 27, 2021 6 min read Programming
Riddler: Can You Beat MLB Recods?
See all posts

Accomplish­ments

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

Nature Communications Mar 2021
We have published our analysis on the genetic interactions of KRAS alleles in four different cancer types in Nature Communications.

Completed Advent of Code 2020

Advent of Code Dec 2020
I completed both coding puzzles released on each of the 25 days before Christmas as a part of the Advent of Code challenge.

Completed Hacktoberfest 2020

Hacktoberfest Oct 2020
I opened four pull requests to open source projects to complete the Hacktoberfest challenge. The first two added iPhone-to-Watch connectivity and Workout Session capabilities to my Apple Watch telemetry-recording application (1, 2). The third PR added the Workout Session capability to my Workout Spinner Apple Watch app (3). Finally, the fourth PR merged the resubmission branch of the KRAS comutation project code repository (4).

mustashe

CRAN Mar 2020
My R package, ‘mustashe’, has been accepted to CRAN. It is ‘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.’

100 Days of Python

GitHub Oct 2019 – Jan 2020
To become comfortable with Python, I completed an hour (usually more) of deliberate practice. I primarily followed data science-centered tutorials, namely Python for Data Analysis and Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow. I also followed the tutorials for the common plotting libraries, Matplotlib, Seaborn, and Plotly. I recorded my progress at the linked GitHub repository. I did not finish the Hands on ML book in the 100 days, but I continued working through it afterwords.

Completed Hacktoberfest 2019

Hacktoberfest Oct 2019
I opened four pull requests to open source projects to complete the Hacktoberfest challenge. I merged large features into my Germination and Plant Tracker apps (1, 2, 3). Also, I made a pull request to add documentation for a statsitcal test using by Hierarchical HotNet (Reyna, et al.. Bioinformatics. 2018) from the Raphael Lab at Princton University (4).

100 Days of Swift

GitHub Jun 2019 – Sep 2019
I challenged myself to do at least an hour of Swift every day for 100 days. I recorded my progress at the linked GitHub repository. Towards the end of the challenge, I started developing two iOS apps, a Plant Tracker and a Germinaton Tracker.

Tissue-specific oncogenic activity of KRAS A146T

Cancer Discovery Jun 2019
The Haigis Lab published on a biochemical, signaling, and computational description of the KRAS A146T allele.

Honorable Mention NSF GRFP

NSF Apr 2019
I have been awarded an Honorable Mention in the 2019 National Science Foundation (NSF) Graduate Research Fellowship Program competition

ggasym

CRAN Mar 2019
My R package, ‘ggasym’, has been accepted to CRAN. It was further promoted by RStudio in their March edition of Top 40 New CRAN Packages and R Weekly (March 18, 2019).

Toxoplasma gondii disrupts β1 integrin signaling and focal adhesion formation during monocyte hypermotility

Journal of Biological Chemistry Jan 2018
My undergraduate reseach in the Lodoen Lab at UC Irvine on the interactions between the single-celled parasite, T. gondii, and human monocytes was accepted by JBC.

Contact

  • Boston, MA 02215