Tim Treis
PhD Student Division Of ML In Single-cell Genomics, Prof. Theis, Helmholtz AI at Helmholtz Munich
Munich, Bavaria, Germany
Summary
👤
Senior🎓
Top SchoolTim Treis is a PhD researcher in computational biology at Helmholtz Munich with eight years of applied experience building reproducible ML and bioinformatics tools for single-cell and spatial multi-omics. As a core developer for scverse projects like SpatialData and Squidpy, he blends software engineering rigor with domain expertise to shape community data standards and analysis pipelines. His background spans industry and academic stints—from Roche and Novartis to EMBL and the Broad—where he delivered novel probabilistic factor modeling work later published from his DKFZ master’s project. Tim is fluent in Python and R, has experience deploying modular probabilistic frameworks (Pyro), and teaches best practices through package development and internal workshops. Based in Munich, he combines hands-on engineering with research curiosity, often translating complex experimental assays into robust, shareable software. An early interest in automation and imaging instrumentation also surfaces in his work on automated microscopes and high-throughput analysis pipelines.
8 years of coding experience
6 years of employment as a software developer
Bachelor of Science (B.Sc.) Molecular biology (B.Sc.), Bachelor of Science (B.Sc.) Molecular biology (B.Sc.) at Bielefeld UniversityMaster of Science - MS Molecular Biotechnology (bioinformatics track), Master of Science - MS Molecular Biotechnology (bioinformatics track) at Heidelberg University
German, English, Spanish
Stackoverflow
1reputation
0reached
0answers
0questions
Github Skills (71)
python10
spatial-transcriptomics10
forge10
transcriptomics10
spatial10
image-analysis10
gradient-boosting10
single-cell-analysis10
data-visualization10
shap10
spatial-data10
scanpy10
scales10
single-cell-genomics10
visualization10
Programming languages (8)
Github contributions (5)
openpharma/visR
Aug 2020 - Jul 2022
A package to wrap functionality for plots, tables and diagrams adhering to graphical principles.
Contributions:75 reviews, 320 commits, 88 PRs in 1 year 10 months
diagramspythonprincipleswrapgraphical
scverse/spatialdata-plot
Jan 2023 - Apr 2025
Static plotting for spatialdata
Contributions:7 releases, 61 reviews, 185 PRs in 2 years 3 months
spatialdatadata-visualizationplottingvisualization
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