Dr. David Patsch

Scientific Software Developer

Scientific Software Developer at the University of Zurich, developing Microbeatlas - a comprehensive metagenomic data integration and analysis platform. Full-stack development across web interface, backend pipelines, and alignment tools for millions of microbiome samples. Kaggle Competition Master and Ph.D. in computational biology combining expertise in bioinformatics and software engineering.

Building and maintaining microbeatlas.org and nexis.bio

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Experience

Scientific Software Developer
University of Zürich
02/2024 - present
Core developer on MicrobeAtlas, a global microbiome data platform processing 2+ PB of sequencing data from 2.4M samples. Built scalable NGS data pipelines and contributed to full-stack development of the microbeatlas.org portal (Python backend, Svelte frontend).
PythonGoSvelteNextflowNGSHPCDockerGCP
Ph.D. on algorithm-aided directed evolution
ZHAW Wädenswil / University of Greifswald
12/2019 - 12/2023
Ph.D. in computational protein engineering, developing novel ML-augmented directed evolution pipelines to accelerate protein optimization. Built tools and web platforms to make these methods accessible to researchers.
PythonRMachine LearningBioinformaticsProtein Engineering
Master thesis on the characterization of CARs
Forschungszentrum Jülich
02/2019 - 09/2019
Master thesis characterizing enzyme variants and evaluating optimization techniques for carboxylic acid recductases (CARs) at Forschungszentrum Jülich.
OptimizationProtein EngineeringMachine Learning

Publications and Patents

Research Article
The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems
02 April 2026
Matias Rodrigues, J. F., Tackmann, J., Malfertheiner, L., Patsch, D. et al.
Cell
Patent
RNA ligase variants
07 August 2025
Collaboration with F. Hoffmann-La Roche Ag
Research Article
Enriching productive mutational paths accelerates enzyme evolution
11 September 2024
David Patsch, et al.
Nature Chemical Biology
Patent
Mutant ketoreductase with increased ketoreductase activity as well as methods and uses involving the same
08 August 2024
Collaboration with F. Hoffmann-La Roche Ag
Research Article
Effective engineering of a ketoreductase for the biocatalytic synthesis of an ipatasertib precursor
28 February 2024
Sumire Honda Malca, Nadine Duss, Jasmin Meierhofer, David Patsch, et al.
Communications Chemistry
Research Article
LibGENiE - A bioinformatic pipeline for the design of information-enriched enzyme libraries
13 September 2023
David Patsch et al.
Computational and Structural Biotechnology Journal
Review
Improving Enzyme Fitness with Machine Learning
29 March 2023
David Patsch and Rebecca Buller
Chimia
Research Article
Algorithm-aided engineering of aliphatic halogenase WelO5* for the asymmetric late-stage functionalization of soraphens
18 January 2022
Johannes Büchler, Sumire Honda Malca, David Patsch, et al.
Nature Communications
Research Article
Asymmetric Cation-Olefin Monocyclization by Engineered Squalene-Hopene Cyclases
04 August 2021
Dr. Michael Eichenberger*, Sean Hüppi*, David Patsch*, et al.
Angewandte Chemie

Kaggle Competitions

G2Net Gravitational Wave Detection
2021
Find gravitational wave signals from binary black hole collisions
4/1219
Bristol-Myers Squibb - Molecular Translation
2021
Can you translate chemical images to text?
13/874
Google Brain - Ventilator Pressure Prediction
2021
Simulate a ventilator connected to a sedated patient's lung
27/2605
Mechanisms of Action (MoA) Prediction
2020
Can you improve the algorithm that classifies drugs based on their biological activity?
21/4373
Full list