Jan Hoinka
Staff Scientist at National Center for Biotechnology Information (NCBI)
Bethesda, Maryland, United States
Summary
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Senior🎓
Top SchoolJan Hoinka is a Staff Scientist and computational biologist with a decade of experience turning complex biological questions into reproducible, production-ready bioinformatics solutions. Based at NCBI, he develops neural-network approaches to detect non-canonical bases from raw Nanopore signals and previously advanced interpretable deep convolutional models for ribosome profiling. He combines strong software engineering—Python, R, Java, Scala, C++, Unix—with high-performance computing and end-to-end pipeline design to move research from data to insight. His academic work produced widely used tools for HT-SELEX and aptamer discovery (AptaSUITE, AptaBlocks, AptaPlex) and novel algorithms like locality-sensitive hashing for rapid motif extraction. Jan’s background spans theoretical algorithm development to web and GUI toolchains, making him equally comfortable in low-level C++ performance work and user-facing software. Colleagues rely on him for rigorous, reproducible solutions that bridge machine learning innovation with practical genomics applications.
10 years of coding experience
13 years of employment as a software developer
Doctor of Philosophy - PhD, Biomathematics, Bioinformatics, and Computational Biology, Doctor of Philosophy - PhD, Biomathematics, Bioinformatics, and Computational Biology at The University of FreiburgMaster of Science - MS, Biomathematics, Bioinformatics, and Computational Biology, Master of Science - MS, Biomathematics, Bioinformatics, and Computational Biology at Saarland University
German, Spanish, English
Github Skills (111)
genomics10
computational-biology10
clustering10
java10
graphical-user-interface10
bioinformatics10
deep-learning9
intellij9
deploying9
jgitver8
backup8
maven-extension8
itunes8
keras-tensorflow8
id38
Programming languages (7)
Github contributions (5)
drivenbyentropy/aptasuite
Sep 2016 - May 2022
A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.
Contributions:33 releases, 233 commits, 3 PRs in 5 years 8 months
full-featuredsequence-structure-motifdnaht-selexin-vitro-selection
drivenbyentropy/drivenbyentropy.github.io
Feb 2018 - Aug 2020
Contributions:156 pushes in 2 years 6 months
stylishjekylljekyll-theme
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