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Michael Ratz et al. Cell types and clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nature Neuroscience 2022. Nature Neuroscience | PubMed

Mold, Jeff E, et al. Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans. PubMed

Enric Llorens-Bobadilla, et al. A latent lineage potential in resident neural stem cells enables spinal cord repair. Science, 2020. PubMed | Science  

Latent potential in neural stem cells. Through the integration of different layers of genomic information in single cells, we found that the genetic program for oligodendrocyte generation is latently accessible in ependymal neural stem cells of the adult spinal cord. After injury, activating the latent potential by forced OLIG2 expression unfolds efficient oligodendrocyte generation, leading to enhanced myelin repair.

Zamboni, Margherita, et al. A Widespread Neurogenic Potential of Neocortical Astrocytes Is Induced by Injury. Cell Stem Cell, 2020. PubMed

Cortical injury, in combination with Notch signalling depletion, recruits parenchymal astrocytes into a neurogenic program to generate new interneurons. Transcriptional profiling of the astrocytes as they transition towards the neuronal lineage fate, revealed that silencing of Notch initiates a neural stem cell program in both injured and intact cortices, and that neurogenesis occurs after injury independently of reactive gliosis. Furthermore, comparison of transcriptional programs revealed that cortical and subventricular zone neurogenesis develop along similar molecular trajectories.

Magnusson, Jens P, et al. Activation of a neural stem cell transcriptional program in parenchymal astrocytes. Elife, 2020. PubMed | eLife
Santopolo, Giuseppe, et al. Blocking Notch-Signaling Increases Neurogenesis in the Striatum after Stroke. Cells, 2020. PubMed | PDF
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Hård, Joanna; Al Hakim, Ezeddin; Kindblom, Marie, et al. Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing. Genome Biology, 2019. PubMed | PDF

Somatic mutations label cells that share a recent common ancestry and can be used to trace cell lineage in humans. Identification of somatic mutations is challenging due to errors and biases in single cell DNA sequencing data. Conbase enables the identification of somatic mutations with high confidence and low false discovery rate by taking advantage of read phasing.

Kempermann, Gerd., et al. Human Adult Neurogenesis: Evidence and Remaining Questions. Cell Stem Cell, 2018. PubMed
Dias, David Oliveira, et al. Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury. Cell, 2018. PubMed Attenuation of the fibrotic scarring that is derived from a subpopulation of perivascular cells, termed type A pericytes, reduces fibrosis, astrogliosis and inflammation, and increases axon regeneration below the level of the lesion after spinal cord injury in mice. Mice with reduced fibrotic scarring showed improved functional recovery after injury. These findings identify pericyte-derived scarring as a target for therapies against spinal cord i​njury.
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Magnusson, Jens P., and Frisén, Jonas. Stars from the darkest night: unlocking the neurogenic potential of astrocytes in different brain regions. Development, 2016. PubMed | PDF
Bergmann, Olaf; Spalding, Kirsty L.; and Frisén, Jonas. Adult neurogenesis in humans. Cold Spring Harbor perspectives in biology, 2015. PubMed | PDF
Bergmann, Olaf, et al. Dynamics of cell generation and turnover in the human heart. Cell, 2015.
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Ernst, Aurélie, and Frisén, Jonas. Adult neurogenesis in humans-common and unique traits in mammals. PLoS Biology, 2015.

Stenudd, Moa et al. Role of endogenous neural stem cells in spinal cord injury and repair. JAMA Neurology, 2015.

Yeung, Maggie SY, et al. Dynamics of oligodendrocyte generation and myelination in the human brain. Cell, 2014.

Magnusson, Jens P., et al. A latent neurogenic program in astrocytes regulated by Notch signaling in the mouse. Science, 2014.

Astrocytes in the striatum of adult mice activate a neurogenic program in response to experimental stroke or  deletion of the Notch-mediating transcription factor Rbpj. They generate transit-amplifying cells that divide to generate ~40 neuroblasts per starting astrocyte. Some of the neuroblasts mature into neurons.

Huttner, Hagen B., et al. The age and genomic integrity of neurons after cortical stroke in humans. Nature Neuroscience, 2014.
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Spalding, Kirsty L.; Bergmann, Olaf, et al. Dynamics of hippocampal neurogenesis in adult humans. Cell, 2013.

Carbon-14 dating of hippocampal neurons in humans showed ongoing neurogenesis in adulthood. A closer look at the dynamics of hippocampal neuron renewal revealed that one-third of all hippocampal neurons may be subject to exchange in an adult human. The annual turnover rate of hippocampal neurons within the group of renewing neurons is 1.75%.

Bergmann, Olaf, and Frisén, Jonas. Why adults need new brain cells. Science, 2013.
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Bergmann, Olaf, et al. Identification of cardiomyocyte nuclei and assessment of ploidy for the analysis of cell turnover. Experimental Cell Research, 2011.
Nomura, Tadashi, et al. EphB Signaling Controls Lineage Plasticity of Adult Neural Stem Cell Niche Cells. Cell Stem Cell, 2010.
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Genander, Maria, et al. Ephrins negatively regulate cell proliferation in the epidermis and hair follicle. Stem Cells, 2010.
Genander, Maria, et al. Dissociation of EphB2 signaling pathways mediating progenitor cell proliferation and tumor suppression. Cell, 2009.
Bergmann, Olaf, et al. Evidence for cardiomyocyte renewal in humans. Science, 2009.
Carlén, Marie, et al. Forebrain ependymal cells are Notch-dependent and generate neuroblasts and astrocytes after stroke. Nature Neuroscience, 2009.
Meletis, Konstantinos, et al. Spinal cord injury reveals multilineage differentiation of ependymal cells. PLoS Biology, 2008.
Spalding, Kirsty, et al. Dynamics of fat cell turnover in humans. Nature, 2008.
Barnabé-Heider, Fanie, et al. Genetic manipulation of adult mouse neurogenic niches by in vivo electroporation. Nature Methods, 2008.
Bhardwaj, Ratan D., et al. Neocortical neurogenesis in humans is restricted to development. PNAS, 2006.
Holmberg, Johan, et al. EphB receptors coordinate migration and proliferation in the intestinal stem cell niche. Cell, 2006.
Meletis, Konstantinos, et al. p53 suppresses the self-renewal of adult neural stem cells. Development, 2006.
Carlén, Marie, et al. Genetic visualization of neurogenesis. Experimental Cell Research, 2006.
Spalding, Kirsty et al. Forensics: age written in teeth by nuclear tests. Nature, 2005.
Spalding, Kirsty et al. Retrospective birthdating of cells in humans. Cell, 2005.