Jens Reeder
Director Bioinformatics
South San Francisco, California, United States
Summary
👤
Senior🎓
Top SchoolJens Reeder is a Director of Bioinformatics in South San Francisco with 16 years of experience building scalable genomics platforms and leading large teams to translate high-dimensional 'omics data into therapeutic insights. He has driven strategy and engineering at Genentech—from sequencing thousands of clinical genomes to launching reproducible, FAIR data workflows—and currently oversees a 50-person department and multi-million dollar budget. Technically grounded in algorithm development and software engineering, Jens contributes to well-known open-source projects such as QIIME and scikit-bio, where his work improved OTU picking and test reliability. A published scientist with 20+ papers and a PhD in Computer Science/Bioinformatics, he combines deep domain expertise in microbiome and single-cell analysis with a pragmatic focus on organizational effectiveness and career development.
16 years of coding experience
10 years of employment as a software developer
PhD Computer Science/Bioinformatics, PhD Computer Science/Bioinformatics at Bielefeld University
Github Skills (8)
unit-testing10
bioinformatics10
python10
numpy10
test-automation10
testing10
unit-test9
computational-biology9
Programming languages (4)
Github contributions (5)
biocore/qiime
Oct 2009 - Aug 2013
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Role in this project:
Back-end Developer
Back-end DeveloperContributions:131 commits in 3 years 10 months
Contributions summary:Jens contributed a new Trie-based OTU picker and added it to the QIIME 1 software repository. This implementation, along with its corresponding test case, enhanced the existing pick_otus module. The user also added a script for denoising using the pyroNoise method, contributing to functionality for noise removal and sequence analysis. These changes improve the software's capabilities in the analysis of microbiome data.
qiimeanalysismicrobiomeqiime2
scikit-bio/scikit-bio
May 2014 - Nov 2014
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Role in this project:QA Engineer / Test Automation Engineer
QA Engineer / Test Automation EngineerContributions:9 commits, 2 comments in 5 months
Contributions summary:Jens's contributions primarily focused on testing and quality assurance within the scikit-bio library. They added real tests for the `lladser_ci` and `lladser_pe` functions, using simulated data to validate their functionality. The user also addressed test-related issues, including fixing function name mismatches and reforming tests to satisfy testing requirements. Furthermore, the user improved tests by removing stochastic behavior by setting seeds, ensuring consistent and reliable testing.
scikitlicensedpythondata-sciencealgorithms-and-data-structures
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