Jan Oppelt
Bioinformatics Core Unit Team Leader
Vienna, Austria
Summary
👤
Senior🎓
Top SchoolJan Oppelt is a bioinformatics leader with a decade of experience designing and running analyses for high-throughput sequencing, specializing in RNA-Seq, smallRNA-Seq, variant calling and genome/transcriptome assembly. Based in Vienna, he currently leads the Bioinformatics Core Unit at St. Anna CCRI, where he combines hands-on pipeline development with experimental design guidance, teaching, and team management. His background spans academic and industry research—from a PhD in Biomolecular Chemistry and postdoctoral method development at UPenn (including a novel direct RNA sequencing method) to product-focused bioinformatics for CNV and structural variant detection that outperformed commercial pipelines. Jan routinely bridges wet-lab and computational teams, translating biological questions into robust, IVDR-aware workflows and reproducible software. He brings both people-management experience from leading multi-member teams and deep technical craftsmanship in workflow prototyping and validation. An uncommon strength is his track record of pairing novel RNA-method development with practical diagnostic pipeline delivery.
10 years of coding experience
10 years of employment as a software developer
Doctor of Philosophy (PhD), Biomolecular Chemistry, Doctor of Philosophy (PhD), Biomolecular Chemistry at Masaryk University BrnoBiochemistry, Biophysics and Molecular Biology, Biochemistry, Biophysics and Molecular Biology at Stockholm University
English, Czech, Slovak
Github Skills (52)
next-generation-sequencing9
genome-assembly9
libtorch9
genomics9
rna-seq9
sequencing8
chip-seq8
bioinformatics8
vcf-files7
decay7
python6
science5
immunology5
periodicity4
nvidia-docker4
Programming languages (9)
Github contributions (5)
opplatek/utils
Sep 2019 - Dec 2023
Contributions:78 pushes, 1 branch in 4 years 3 months
BiCU-CCRI/running_rstudio_or_jupyterlab
Jan 2025 - Feb 2026
Collection of scripts to run Rstudio or Jupyterlab on the CeMM cluster
Contributions:1 review, 6 PRs, 20 pushes in 1 year 1 month
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