Gisela Gabernet
Associate Research Scientist
New Haven, Connecticut, United States
Summary
🤩
Rockstar🎓
Top SchoolGisela Gabernet is an Associate Research Scientist at Yale with nine years of interdisciplinary experience at the intersection of computational biology, bioinformatics, and data-driven clinical research. Trained at ETH Zurich and TU Dresden, she has led research development and data science teams and supported molecular tumor boards and multiomics clinical studies, applying machine learning for precision medicine. She is an active contributor to the nf-core community, improving Nextflow scRNA-seq pipelines and testing tools to strengthen reproducible single-cell workflows used widely in genomics. Comfortable bridging clinic and code, she combines rigorous academic training with practical DevOps and pipeline engineering skills to make complex analyses robust and production-ready. An under-the-radar strength is her focus on automation and dependency management, which reduces friction for collaborative, large-scale computational experiments.
9 years of coding experience
8 years of employment as a software developer
Bachelor's degree, Biotechnology, Bachelor's degree, Biotechnology at Universitat Autònoma de BarcelonaMaster of Science (M.Sc.), Molecular Bioengineering, Master of Science (M.Sc.), Molecular Bioengineering at Technische Universität DresdenDoctor of Science - Dr. Sc., Doctor of Science - Dr. Sc. at ETH Zurich
English, German, Catalan, Spanish
Github Skills (21)
github-ci10
docker10
pytest10
groovy10
pipelining10
dockers10
nextflow10
automation10
pipe10
pipeline10
linter10
linting10
workflow-management10
automations10
githubaction-workflow10
Programming languages (12)
Github contributions (5)
nf-core/tools
Dec 2019 - Nov 2022
Python package with helper tools for the nf-core community.
Role in this project:
DevOps Engineer & Test Automation Engineer
DevOps Engineer & Test Automation EngineerContributions:56 reviews, 152 commits, 35 PRs in 3 years
Contributions summary:Gisela primarily contributed to the improvement of the `nf-core/tools` repository, which contains helper tools for the nf-core community. The user's work focused on enhancing the testing infrastructure by adding and modifying tests, specifically related to GitHub Actions workflows and linting checks. They also made several changes to the tests to improve the overall test coverage of the repository.
nf-corelinterpythonpipelinelinting
nf-core/scrnaseq
Mar 2021 - Jun 2022
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
Role in this project:DevOps Engineer & Pipeline Developer
DevOps Engineer & Pipeline DeveloperContributions:23 reviews, 27 commits, 8 PRs in 1 year 3 months
Contributions summary:Gisela's contributions focused on maintaining and improving the nf-core scRNA-seq pipeline. They primarily updated the Nextflow workflow files, specifically addressing linting issues, fixing groovy function errors, and replacing software modules. The user also worked on updating the schema and managing module versions to ensure compatibility and efficient pipeline execution. These changes indicate a strong focus on automation, pipeline structure, and dependency management.
nf-core10xrnaseqpipelinegenomics-data
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