Hello, I'm David - a scientific software developer currently working at the University of Zurich within the research group of Professor Mering. My current focus is on a significant project called MicrobeAtlas, which involves the aggregated analysis of a vast set of metagenomic sequenced samples. This pioneering work aims to enhance our understanding of microbial taxa in varying environments and infer their potential capabilities. By accumulating data on typical abundances and environmental conditions, our project supports microbial researchers in prioritizing taxa that are more relevant to their studies.


Work Experience

02/2024- PRESENT

Scientific Software Developer

University of Zürich

  1. -Maintanance and development of Microbeatlas, analysing and displaying millions of microbiome samples.
  • bioinformatics
  • databases
  • web-development
  • golang
  • svelte
  • distributed-systems
  • cloud-computing
12/2019- 12/2023

Ph.D. on algorithm-aided directed evolution

ZHAW Wädenswil / University of Greifswald

  1. -Ph.D. with a focus on computational protein engineering.
  2. -How can directed evolution techniques be augmented and advanced through simulations/machine learning.
  3. -Developed a novel pipeline that allows for the (significantly) faster and more efficient evolution of proteins.
  4. -Development of tools and websites to facilitate access to these concepts.
  • bioinformatics
  • machine-learning
  • databases
  • web-development
02/2019- 09/2019

Master thesis on the characterization of CARs

Forschungszentrum Jülich

  1. -Characterization of different enzyme variants.
  2. -Evaluation and application of different optimization techniques.
  • experiment-design
  • optimization

Publications

Research Article

Effective engineering of a ketoreductase for the biocatalytic synthesis of an ipatasertib precursor

Sumire Honda Malca, Nadine Duss, Jasmin Meierhofer, David Patsch, et al.

28 February 2024

Communications Chemistry

  • Python
  • git
  • NumPy
  • Pandas
  • scikit-learn

Research Article

LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries

David Patsch et al.

13 September 2023

Computational and Structural Biotechnology Journal

  • React
  • NextJs
  • TypeScript
  • Docker
  • GCP
  • serverless
  • Firebase
  • CSS
  • HTML
  • APIs

Review

Improving Enzyme Fitness with Machine Learning

David Patsch and Rebecca Buller

29 March 2023

Chimia

Research Article

Algorithm-aided engineering of aliphatic halogenase WelO5* for the asymmetric late-stage functionalization of soraphens

Johannes Büchler, Sumire Honda Malca, David Patsch, et al.

18 January 2022

Nature Communications

  • Python
  • git
  • NumPy
  • Pandas
  • scikit-learn

Research Article

Asymmetric Cation-Olefin Monocyclization by Engineered Squalene–Hopene Cyclases

Dr. Michael Eichenberger*, Sean Hüppi*, David Patsch*, et al.

04 August 2021

Angewandte Chemie

  • matplotlib
  • seaborn
  • molecular-docking

Application Note

AlphaDock - A molecular docking plugin for PyMol

David Patsch et al.

Manuscript in review

  • Python
  • PyQt
  • PyMol
  • molecular-docking
  • Docker

Research Article

Revolution of a Kemp Eliminase

David Patsch et al.

Manuscript in preperation

  • Rosetta
  • molecular-docking
  • molecular-dynamics

Kaggle Competitions

G2Net Gravitational Wave Detection

Find gravitational wave signals from binary black hole collisions

4/1219

gold

Bristol-Myers Squibb – Molecular Translation

Can you translate chemical images to text?

13/874

silver

Mechanisms of Action (MoA) Prediction

Can you improve the algorithm that classifies drugs based on their biological activity?

21/4373

silver

Google Brain - Ventilator Pressure Prediction

Simulate a ventilator connected to a sedated patient's lung

27/2605

silver

Full List

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