Author

Simon Haendeler

University of ViennaORCID 0000-0003-0442-3177Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Developmental Biology· 2 Evolutionary Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:benchmarking· 2 Research Focus:cell type annotation· 2 Approach:experimental assay· 2 Assay:bulk RNA-seq· 1 Assay:CRISPR screen· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Arndt von HaeseleriD· 2 shared Christopher EskiD· 2 shared Alison DeyettiD· 1 shared Amra Mujadzic· 1 shared ANNA CASCIO· 1 shared Aranxa Torres-Caballero· 1 shared Clara Schmidt· 1 shared Daniel ReumanniD· 1 shared

Activity by Year

2023-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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2 shared papersEvolutionary Biology

Arndt von HaeselerORCID

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4 papers

Recent·Most cited

Developmental BiologybioRxivPreprintOct 27, 2026

An improved CRISPR-LICHT screen of 120 Tdark genes illuminates new biologically relevant SOX2 targets in human brain organoids

Giorgia Pozzolini, Simon Haendeler, Salma Amin…·Silvia K. Nicolis

The paper uses CRISPR-LICHT to screen SOX2 targets in human brain organoids, identifying 28 new genes involved in neural progenitor lineage expansion and survival.

DOI 10.64898/2026.10.23.761353

humanCRISPR screen

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Evolutionary BiologyMolecular Biology and EvolutionPeer-reviewedAug 1, 2026

Phylo-Movies: Animating Phylogenetic Trees from Sliding-Window Analyses

Enes Sakalli, Simon Haendeler, Arndt von Haeseler, Heiko A. Schmidt

Phylo-Movies animates phylogenetic tree changes across genomic windows to identify recombination breakpoints and rogue taxa in norovirus genomes.

DOI 10.1093/molbev/msag194

virusproteomics

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Systems BiologyPLoS Computational BiologyPeer-reviewedApr 22, 2024

Neutral competition explains the clonal composition of neural organoids

Florian Pflug, Simon Haendeler, Christopher Esk…·Arndt von Haeseler

The paper explains the clonal composition of neural organoids using a neutral competition model that accounts for observed lineage size variability.

1 citation

humanbulk RNA-seq

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Developmental BiologyCellPeer-reviewedNov 28, 2023

Multi-chamber cardioids unravel human heart development and cardiac defects

Clara Schmidt, Alison Deyett, Tobias Ilmer…·Sasha Mendjan

This paper develops a multi-chamber cardioid platform to study human heart development and defects by generating compartment-specific gene expression, morphology, and function.

205 citationstop 1%

humanexperimental assay

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