Michael Ratz's Group

We study mammalian brain development by using and building novel molecular tools such as cellular barcoding and spatial transcriptomics.

A tree with yellow, red and blue cells on it.
Artistic illustration showing how uniquely barcoded progenitor cells (bottom) develop into a range of diverse cell types (top). Image: Lesya Adamchuk (Ella Maru Studio, Inc.).

We are interested in understanding the principles that govern the formation and function of the mammalian brain across scales ranging from genes to neural circuits:

  • What is the molecular and cellular architecture of neural circuits in the mammalian brain?
  • How do single neurons choose specific synaptic partners from many potential targets during brain development?
  • How do mutations in risk genes lead to neurodevelopmental disorders (e.g. autism spectrum disorder)?


To tackle those questions, we employ and develop cutting edge technologies with a special focus on the following areas:

  • Cellular barcodes for lineage and/or synaptic connectivity tracking in vivo
  • Spatial transcriptomics to decode gene expression with 3D resolution in situ 
  • Bioinformatic methods for exploratory data analysis of large genomic datasets 
  • Genome engineering in cells and animals for scalable studies of gene function
A man smiling for the portrait.
Michael Ratz, Department of Cell and Molecular Biology. Photo: Linda Lindell

Research support

  • SSMF Starting Grant
  • VR Starting Grant
  • StratNeuro Startup Grant


Group Members

Selected Publications

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, Martin M, Westholm JO, La Manno G, Lundeberg J, Frisén J
Nat Neurosci 2022 Mar;25(3):285-294

Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin.
Kameneva P, Artemov AV, Kastriti ME, Faure L, Olsen TK, Otte J, Erickson A, Semsch B, Andersson ER, Ratz M, Frisén J, Tischler AS, de Krijger RR, Bouderlique T, Akkuratova N, Vorontsova M, Gusev O, Fried K, Sundström E, Mei S, Kogner P, Baryawno N, Kharchenko PV, Adameyko I
Nat Genet 2021 May;53(5):694-706

Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis.
von Berlin L, Westholm JO, Ratz M, Frisén J
Hippocampus 2023 Apr;33(4):391-401

Enhanced photon collection enables four dimensional fluorescence nanoscopy of living systems.
Masullo LA, Bodén A, Pennacchietti F, Coceano G, Ratz M, Testa I
Nat Commun 2018 Aug;9(1):3281

CRISPR/Cas9-mediated endogenous protein tagging for RESOLFT super-resolution microscopy of living human cells.
Ratz M, Testa I, Hell SW, Jakobs S
Sci Rep 2015 Apr;5():9592

Linda Lindell