John Kern
Senior Bioinformatics Engineer
Cincinnati, Ohio, United States
Summary
👤
Senior🎓
Top SchoolJohn Kern is a Senior Bioinformatics Engineer with 13 years of experience applying software engineering to genomics, currently building and deploying NGS secondary analysis pipelines at AccuraGen. He blends deep systems and cloud expertise—Python, AWS, Ansible, SGE—with hands-on web and LIMS development (Django, MySQL) to move sequencing data from instrument to actionable results. His background spans low-level systems and platform engineering (Sun, Synopsys, Numerical Technologies) through developer advocacy at Symbian, giving him rare fluency across C/C++ toolchains, CI and modern cloud-native pipelines. An active open-source contributor, he has improved usability and integrations in respected bioinformatics projects like bcbio-nextgen and helped clarify documentation for Elasticluster, signaling a pragmatic focus on reproducibility and user experience. Based in Cincinnati, he also brings GIS training and a demonstrated interest in languages and education technology, revealing a multidisciplinary curiosity that informs how he designs data-driven solutions.
13 years of coding experience
22 years of employment as a software developer
Certificate GIS, Certificate GIS at San Francisco State Universitynon-Matriculating workshops GIS GPS and remote sensing, non-Matriculating workshops GIS GPS and remote sensing at University of California, BerkeleyBS MS Computer Science, BS MS Computer Science at Michigan State University
English, Portuguese
Stackoverflow
1reputation
0reached
0answers
0questions
Github Skills (15)
bioinformatics10
python10
documentation10
git8
version-control8
hadoop3
spark3
cluster-computing3
azure3
ansible3
ansible-galaxy3
clustering3
cloud-computing3
slurm3
microsoft-azure3
Programming languages (10)
Github contributions (5)
bcbio/bcbio-nextgen
Apr 2014 - Sep 2014
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Role in this project:
Backend Developer
Backend DeveloperContributions:38 commits, 10 comments, 4 issues in 5 months
Contributions summary:John primarily contributed to the bcbio-nextgen repository by fixing typos in documentation, improving clarity, and updating URLs. Additionally, the user made code changes related to the integration of the Chanjo tool for coverage analysis, as well as modifications to system configuration files. These contributions suggest a focus on refining existing code, improving documentation, and adding new features or integrations to the system.
scalablecallingrnaseqvariant-callinggenomics
elasticluster/elasticluster
Sep 2014 - Sep 2014
Create clusters of VMs on the cloud and configure them with Ansible.
Role in this project:Technical Writer
Technical WriterContributions:6 commits, 3 comments, 6 issues in 1 day
Contributions summary:John's contributions primarily involved fixing formatting issues within the documentation files. These fixes included correcting typos, adjusting code snippets, and improving the overall presentation of the configuration instructions. The edits were consistently made to the `docs/configure.rst` file, suggesting a focus on improving the clarity and accuracy of the documentation for users. This work directly enhances the usability of the Elasticluster project.
gcppythonclustersconfigureslurm
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