This study shows that clonal memory in human embryonic stem cells influences fate potential during endoderm differentiation by heritable chromatin states.

bioRxiv · Sep 3, 2026 · PreprintDevelopmental Biology

Identifying Spatial Co-occurrence in Healthy and InflAmed tissues (ISCHIA)

Atefeh Lafzi, Costanza Borrelli, Simona Baghai Sain, Karsten Bach, Jonas A. Kretz, Kristina Handler, Daniel Regan-Komito, Xenia Ficht, Andreas P. Frei, Andreas E. Moor

ISCHIA identifies spatial co-occurrence patterns in healthy and inflamed human tissues using spatial transcriptomics data.

Molecular Systems Biology · Jan 15, 2024Peer-reviewedSystems Biology

A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons

Martin Mikl, Davide Eletto, Malak Nijim, Minkyoung Lee, Atefeh Lafzi, Farah Mhamedi, Orit David, Simona Baghai Sain, Kristina Handler, Andreas E. Moor

The paper uses a massively parallel reporter assay to identify RNA localization signals in neurons, revealing focused and broadly encoded motifs that influence mRNA localization to neurites and soma.

Nucleic Acids Research · Sep 8, 2022Peer-reviewedGenomics

Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects

Elisabetta Mereu, Atefeh Lafzi, Cátia Moutinho, Christoph Ziegenhain, Davis James McCarthy, Adrián Álvarez-Varela, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad D. Sanada, Aik Teong Ooi, Robert C. Jones, Kelly A. Kaihara, , Holger Heyn

This study benchmarks 13 scRNA-seq protocols to evaluate their effectiveness in characterizing cell types and states for cell atlas projects.

Nature Biotechnology · Apr 6, 2020Peer-reviewedGenomics