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Single-cell RNA-seq measurements provide a powerful approach for studying complex biological tissues. Some of the more interesting contexts involve dynamic processes, such as development or disease progression. However single-cell measurements only capture a snapshot of a transcriptional state at a single point in time.

Several approaches have been developed to infer dynamic processes, such as branching lineages, from this scRNA-seq. Usually those methods require …


Outreach and popular science

Midbrain study gives boost to Parkinson’s research

Two research teams at Karolinska Institutet have identified the dopamine-producing cells in the midbrain of mice and humans. They have also developed a method of assessing the quality of in-vitro cultured dopamine-producing cells, which can be of great benefit to research on Parkinson’s disease. The results are published in the academic journal Cell.

Special nerve cells cause goose bumps and nipple erection

The sympathetic nerve system has long been thought to respond the same regardless of the physical or emotional stimulus triggering it. However, in a new study from Karolinska Institutet published in the journal Nature Neuroscience, scientists show that the system comprises different neurons that regulate specific physiological functions, such as erectile muscle control.

Selected Publications

We discover: Species differences in developmental timing and cell proliferation. Multiple radial glia subtypes biased toward distinct fates. Adult dopaminergic neuron subtypes emerge postnatally. A machine learning method to score dopaminergic differentiation of stem cells
Cell, 2016

We explored the heterogeneity of mouse stellate and thoracic ganglia and found an unexpected variety of cell types. We identified specialized populations of nipple- and pilo-erector muscle neurons. Our results provide compelling evidence for a highly sophisticated organization of the sympathetic nervous system into discrete outflow channels that project to well-defined target tissues and offer mechanistic insight into how diversity and connectivity are established during development.
Nature Neuroscience, 2016


. STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array. Scientific Reports, 2017.

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. RNA velocity in single cells. bioarxiv, 2017.

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. Molecular analysis of the midbrain dopaminergic niche during neurogenesis. bioarxiv, 2017.

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. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model. Nature Biotechnology, 2017.


. Molecular diversity of midbrain development in mouse, human, and stem cells. Cell, 2016.

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. Visceral motor neuron diversity delineates a cellular basis for nipple-and pilo-erection muscle control. Nature Neuroscience, 2016.

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. Single-cell transcriptomics reveals that differentiation and spatial signatures shape epidermal and hair follicle heterogeneity. Cell Systems, 2016.


. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science, 2016.

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. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science, 2015.

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. Quantitative single-cell RNA-seq with unique molecular identifiers. Nature methods, 2014.

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