John Didion - Associate Director, Research Bioinformatics, Women's And Organ Health

John Didion

Associate Director, Research Bioinformatics, Women's And Organ Health

Livermore, California, United States

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Summary

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John Didion is a computational biologist and seasoned software leader with 25+ years of engineering experience and a PhD in Bioinformatics driving cloud-native genomics and diagnostics. Currently Associate Director of Research Bioinformatics and Data Science at Natera, he builds pipelines and methods for next-generation women's and organ health diagnostics, having previously led bioinformatics teams at Apton (acquired by PacBio), DNAnexus, and Fulcrum. He combines hands-on systems programming in Rust, Scala, Python and R with deep expertise in NGS, clinical bioinformatics, and machine learning to turn complex experimental designs into reproducible, benchmarked cloud workflows. A contributor to high-profile open standards and tools—helping author the WDL spec and improving parsers and core libraries like cutadapt—he bridges research and production with a pragmatic focus on performance and data streaming. Based in Livermore, CA, he pairs scientific rigor (a record of NIH and ADA fellowships and publications) with product-minded engineering, including inventing a binary streaming format and automated benchmarking dashboards.

11 years of coding experience

13 years of employment as a software developer

BS Computer Science, BS Computer Science at Northwestern University

Diploma, Diploma at Cambridge High School

Doctor of Philosophy (Ph.D.) Bioinformatics and Computational Biology, Doctor of Philosophy (Ph.D.) Bioinformatics and Computational Biology at UNC School of Medicine

Stackoverflow

Stats

31reputation

3kreached

1answer

0questions

Github Skills (22)

sequence-analysis10

parser10

lexer10

python10

parsing10

parse10

fileio10

antlr10

file-processing10

file-handling10

bioinformatics10

wdl10

file-access10

lex10

reproducible-science9

Programming languages (22)

JavaC++RustCTeXMakefileScalaGo

Github contributions (5)

openwdl/wdl

Apr 2020 - Dec 2022

Specification for the Workflow Description Language (WDL).

Role in this project:

Backend Developer

Contributions:7 releases, 176 reviews, 162 commits in 2 years 8 months

Contributions summary:John primarily contributed to the development of the Workflow Description Language (WDL) specification by modifying and adding to the ANTLR grammar files. Their work included updating the lexer for version 1.0, adding a draft 2 parser, and replacing tabs with spaces for code formatting. These changes suggest a focus on improving the language's parsing and validation capabilities, specifically for different WDL versions.

implementationsworkflow-description-languageincrementalopenwdlspecification-language

marcelm/cutadapt

Mar 2016 - Mar 2016

Cutadapt removes adapter sequences from sequencing reads

Role in this project:

Back-end Developer

Contributions:7 commits, 19 PRs, 15 comments in 3 days

Contributions summary:John primarily contributed to the `cutadapt` repository by implementing and refactoring core components related to sequence input/output. They introduced a `buffer_size` parameter for file I/O operations, enhancing flexibility and potentially improving performance. The user also added new classes for writing sequence records, enhancing the functionality of the library. Furthermore, the user added a `match_info` attribute to the sequence classes to improve flexibility.

sequencepythonbiocondafastasequencing

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