Author

Tim Treis

Helmholtz MunichORCID 0000-0002-9686-4799Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:database / resource· 3 Research Focus:software / tool· 3 Research Focus:benchmarking· 2 Research Focus:deconvolution· 2 Assay:scRNA-seq· 2 Assay:spatial transcriptomics· 2 Approach:statistical model· 2 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Fabian Joachim TheisiD· 3 shared Giovanni PallaiD· 2 shared Alexander DietrichiD· 1 shared Anna Christina SchaariD· 1 shared Benjamin RombautiD· 1 shared Bernard Eder· 1 shared Elyas HeidariiD· 1 shared Francesca FinotelloiD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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3 shared papersBioinformatics

Fabian Joachim TheisORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Rectangle: robust and scalable multiscale deconvolution informed by single-cell RNA sequencing data

Bernard Eder, Irene Rigato, Alexander Dietrich, Lorenzo Merotto, Gregor Sturm, Tim Treis, Markus List, Fabian Joachim Theis, Francesca Finotello

Rectangle provides a scalable deconvolution framework for bulk RNA-seq using single-cell data, achieving high accuracy and robustness across diverse benchmarks.

bioRxiv · Jul 9, 2026 · PreprintBioinformatics

GraphCompass: Spatial metrics for differential analyses of cell organization across conditions

Mayar Ali, Merel Kuijs, Soroor Hediyeh-zadeh, Tim Treis, Karin Hrovatin, Giovanni Palla, Anna Christina Schaar, Fabian Joachim Theis

GraphCompass provides graph analysis methods to compare cell spatial organization across conditions using spatial omics data.

Bioinformatics · Apr 25, 2024Peer-reviewedBioinformatics

SpatialData: an open and universal data framework for spatial omics

Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Wouter-Michiel Vierdag, Marcella Toth, Sonja Stockhaus, Rahul Shrestha, Benjamin Rombaut, Lotte Pollaris, Laurens Lehner, Harald S. Vöhringer, Ilia Kats, , Oliver Stegle

SpatialData, a Zarr/OME-NGFF-based format plus Python library, unifies images, labels, points, shapes and tables across spatial omics platforms with coordinate alignment, lazy loading and cross-modal aggregation.

Nature Methods · Mar 20, 2024Peer-reviewedBioinformatics✦ In-depth digest