John Blischak

I am a postdoctoral researcher with Professor Matthew Stephens in the Department of Human Genetics at the University of Chicago. Currently I am focusing on the following projects:

  1. develop software to facilitate open and reproducible computational research
  2. build bioinformatics pipelines to analyze single-cell RNA sequencing data
  3. teach scientists how to use software development tools like version control
workflowr hex sticker

The workflowr R package combines R Markdown and version control (Git) to create a website containing time-stamped, versioned, and documented results.

Release Source Video

Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells


Blischak JD*, Tailleux L*, Myrthil M, Charlois C, Bergot E, Dinh A, Morizot G, Chény O, Platen CV, Herrmann JL, Brosch R, Barreiro LB, and Gilad Y

PubMed Code Data

Batch effects and the effective design of single-cell gene expression studies


Tung PY*, Blischak JD*, Hsiao CJ*, Knowles DA, Burnett JE, Pritchard JK, and Gilad Y

PubMed Code Data

A quick introduction to version control with Git and GitHub


Blischak JD, Davenport ER, and Wilson G

PubMed Code

Mycobacterial infection induces a specific human innate immune response


Blischak JD, Tailleux L, Mitrano A, Barreiro LB, and Gilad Y

PubMed Code Data

The workflowr R package: a framework for reproducible and collaborative data science

useR! 2018

Brisbane, QLD

Jul 2018

Introduction to the conda package manager for R users

Greater Cleveland R Group

Independence, OH

Dec 2018