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Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals
Coleman Jri, Bryois J, Gaspar Ha, Jansen Pr, Savage Je, Skene N, et al
Molecular psychiatry 2019;24(2):182-197

Remodeling of secretory lysosomes during education tunes functional potential in NK cells
Goodridge Jp, Jacobs B, Saetersmoen Ml, Clement D, Hammer Q, Clancy T, et al
Nature communications 2019;10(1):514-

Classes and continua of hippocampal CA1 inhibitory neurons revealed by single-cell transcriptomics
Harris Kd, Hochgerner H, Skene Ng, Magno L, Katona L, Bengtsson Gonzales C, et al
PLoS biology 2018;16(6):e2006387-

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing
Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S
Nature neuroscience 2018;21(2):290-299

Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq
Muñoz-manchado Ab, Bengtsson Gonzales C, Zeisel A, Munguba H, Bekkouche B, Skene Ng, et al
Cell reports 2018;24(8):2179-2190.e7

Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)
Kjällquist U, Erlandsson R, Tobin Np, Alkodsi A, Ullah I, Stålhammar G, et al
BMC cancer 2018;18(1):174-

Genetic identification of brain cell types underlying schizophrenia
Major Depressive Disorder Working Group Of The Psychiatric Genomics Consortium, Skene Ng, Bryois J, Bakken Te, Breen G, Crowley Jj, et al
Nature genetics 2018;50(6):825-833

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence
Savage Je, Jansen Pr, Stringer S, Watanabe K, Bryois J, De Leeuw Ca, et al
Nature genetics 2018;50(7):912-919

High-throughput chromatin accessibility profiling at single-cell resolution
Mezger A, Klemm S, Mann I, Brower K, Mir A, Bostick M, et al
Nature communications 2018;9(1):3647-

Meta-analysis of genome-wide association studies for neuroticism in 449,484 individuals identifies novel genetic loci and pathways
23andme Research Team, Nagel M, Jansen Pr, Stringer S, Watanabe K, De Leeuw Ca, et al
Nature genetics 2018;50(7):920-927

Molecular Architecture of the Mouse Nervous System
Zeisel A, Hochgerner H, Lönnerberg P, Johnsson A, Memic F, Van Der Zwan J, et al
Cell 2018;174(4):999-1014.e22

Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types
Häring M, Zeisel A, Hochgerner H, Rinwa P, Jakobsson Jet, Lönnerberg P, et al
Nature neuroscience 2018;21(6):869-880

RNA velocity of single cells
La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, et al
Nature 2018;560(7719):494-498

Spatial organization of the somatosensory cortex revealed by osmFISH
Codeluppi S, Borm Le, Zeisel A, La Manno G, Van Lunteren Ja, Svensson Ci, et al
Nature methods 2018;15(11):932-935

A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA
Lake Bb, Codeluppi S, Yung Yc, Gao D, Chun J, Kharchenko Pv, et al
Scientific reports 2017;7(1):6031-

Alternative TSSs are co-regulated in single cells in the mouse brain
Karlsson K, Lönnerberg P, Linnarsson S
Molecular systems biology 2017;13(5):930-

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells
Boström J, Sramkova Z, Salašová A, Johard H, Mahdessian D, Fedr R, et al
PloS one 2017;12(12):e0188772-

Constitutively Active SMAD2/3 Are Broad-Scope Potentiators of Transcription-Factor-Mediated Cellular Reprogramming
Ruetz T, Pfisterer U, Di Stefano B, Ashmore J, Beniazza M, Tian Tv, et al
Cell stem cell 2017;21(6):791-805.e9

Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model
Rivetti Di Val Cervo P, Romanov Ra, Spigolon G, Masini D, Martín-montañez E, Toledo Em, et al
Nature biotechnology 2017;35(5):444-452

Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders
Nguyen Ht, Bryois J, Kim A, Dobbyn A, Huckins Lm, Munoz-manchado Ab, et al
Genome medicine 2017;9(1):114-

Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses
Niklasson M, Maddalo G, Sramkova Z, Mutlu E, Wee S, Sekyrova P, et al
Cancer research 2017;77(7):1741-1752

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes
Romanov Ra, Zeisel A, Bakker J, Girach F, Hellysaz A, Tomer R, et al
Nature neuroscience 2017;20(2):176-188

Single-cell mRNA isoform diversity in the mouse brain
Karlsson K, Linnarsson S
BMC genomics 2017;18(1):126-

STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array
Hochgerner H, Lönnerberg P, Hodge R, Mikes J, Heskol A, Hubschle H, et al
Scientific reports 2017;7(1):16327-

The Human Cell Atlas
Human Cell Atlas Meeting Participants, Regev A, Teichmann Sa, Lander Es, Amit I, Benoist C, et al
eLife 2017;6():-

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing
Lein E, Borm Le, Linnarsson S
Science (New York, N.Y.) 2017;358(6359):64-69

A PBX1 transcriptional network controls dopaminergic neuron development and is impaired in Parkinson's disease
Villaescusa Jc, Li B, Toledo Em, Rivetti Di Val Cervo P, Yang S, Stott Sr, et al
The EMBO journal 2016;35(18):1963-78

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes
Fuzik J, Zeisel A, Máté Z, Calvigioni D, Yanagawa Y, Szabó G, et al
Nature biotechnology 2016;34(2):175-183

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells
La Manno G, Gyllborg D, Codeluppi S, Nishimura K, Salto C, Zeisel A, et al
Cell 2016;167(2):566-580.e19

NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis
Tervaniemi Mh, Katayama S, Skoog T, Siitonen Ha, Vuola J, Nuutila K, et al
Scientific reports 2016;6():22745-

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system
Marques S, Zeisel A, Codeluppi S, Van Bruggen D, Mendanha Falcão A, Xiao L, et al
Science (New York, N.Y.) 2016;352(6291):1326-1329

Origin, fate and dynamics of macrophages at central nervous system interfaces
Goldmann T, Wieghofer P, Jordão Mj, Prutek F, Hagemeyer N, Frenzel K, et al
Nature immunology 2016;17(7):797-805

Single-cell genomics: coming of age
Linnarsson S, Teichmann Sa
Genome biology 2016;17():97-

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula Sp, Codeluppi S, et al
Cell 2016;165(4):1012-26

Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity
Joost S, Zeisel A, Jacob T, Sun X, La Manno G, Lönnerberg P, et al
Cell systems 2016;3(3):221-237.e9

The human PRD-like homeobox gene LEUTX has a central role in embryo genome activation
Jouhilahti Em, Madissoon E, Vesterlund L, Töhönen V, Krjutškov K, Plaza Reyes A, et al
Development (Cambridge, England) 2016;143(19):3459-3469

Visceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle control
Furlan A, La Manno G, Lübke M, Häring M, Abdo H, Hochgerner H, et al
Nature neuroscience 2016;19(10):1331-40

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
Ståhl Pl, Salmén F, Vickovic S, Lundmark A, Navarro Jf, Magnusson J, et al
Science (New York, N.Y.) 2016;353(6294):78-82

Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations
Karlsson K, Sahlin E, Iwarsson E, Westgren M, Nordenskjöld M, Linnarsson S
Genomics 2015;105(3):150-8

A secretagogin locus of the mammalian hypothalamus controls stress hormone release
Romanov Ra, Alpar A, Zhang Md, Zeisel A, Calas A, Landry M, et al
EMBO JOURNAL 2015;34(1):36-54

Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
Zeisel A, Muñoz-manchado Ab, Codeluppi S, Lönnerberg P, La Manno G, Juréus A, et al
Science (New York, N.Y.) 2015;347(6226):1138-42

Dynamics of Lgr6(+) Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis
Fullgrabe A, Joost S, Are A, Jacob T, Sivan U, Haegebarth A, et al
STEM CELL REPORTS 2015;5(5):843-855

Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control
Katayama S, Skoog T, Jouhilahti Em, Siitonen Ha, Nuutila K, Tervaniemi Mh, et al
BMC genomics 2015;16():476-

NEUROSCIENCE. A tree of the human brain
Linnarsson S
Science (New York, N.Y.) 2015;350(6256):37-

Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development
Töhönen V, Katayama S, Vesterlund L, Jouhilahti Em, Sheikhi M, Madissoon E, et al
Nature communications 2015;6():8207-

Reprogramming Roadblocks Are System Dependent
Chantzoura E, Skylaki S, Menendez S, Kim Si, Johnsson A, Linnarsson S, et al
Stem cell reports 2015;5(3):350-64

Rewired metabolism in drug-resistant leukemia cells: a metabolic switch hallmarked by reduced dependence on exogenous glutamine
Stäubert C, Bhuiyan H, Lindahl A, Broom Oj, Zhu Y, Islam S, et al
The Journal of biological chemistry 2015;290(13):8348-59

Sequencing Single Cells Reveals Sequential Stem Cell States
Linnarsson S
Cell stem cell 2015;17(3):251-2

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing
Usoskin D, Furlan A, Islam S, Abdo H, Lonnerberg P, Lou D, et al
NATURE NEUROSCIENCE 2015;18(1):145-53

Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo
Woll Ps, Kjällquist U, Chowdhury O, Doolittle H, Wedge Dc, Thongjuea S, et al
Cancer cell 2014;25(6):794-808

Quantitative single-cell RNA-seq with unique molecular identifiers
Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al
Nature methods 2014;11(2):163-6

Selective calcium sensitivity in immature glioma cancer stem cells
Wee S, Niklasson M, Marinescu Vd, Segerman A, Schmidt L, Hermansson A, et al
PloS one 2014;9(12):e115698-

Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq
Zechel S, Zajac P, Lonnerberg P, Ibanez Cf, Linnarsson S
GENOME BIOLOGY 2014;15(10):486-

Base preferences in non-templated nucleotide incorporation by MMLV-derived reverse transcriptases
Zajac P, Islam S, Hochgerner H, Lönnerberg P, Linnarsson S
PloS one 2013;8(12):e85270-

Erg channel is critical in controlling cell volume during cell cycle in embryonic stem cells
Abdelhady S, Kitambi Ss, Lundin V, Aufschnaiter R, Sekyrova P, Sinha I, et al
PloS one 2013;8(8):e72409-

High-resolution analysis with novel cell-surface markers identifies routes to iPS cells
O'malley J, Skylaki S, Iwabuchi Ka, Chantzoura E, Ruetz T, Johnsson A, et al
NATURE 2013;499(7456):88-91

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
Katayama S, Töhönen V, Linnarsson S, Kere J
Bioinformatics (Oxford, England) 2013;29(22):2943-5

Single-cell biology meeting marks rebirth of an old science
Linnarsson S
GENOME BIOLOGY 2013;14(4):305-

Single-cell sequencing-based technologies will revolutionize whole-organism science
Shapiro E, Biezuner T, Linnarsson S

Counting absolute numbers of molecules using unique molecular identifiers
Kivioja T, Vaharautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, et al
NATURE METHODS 2012;9(1):72-4

Highly multiplexed and strand-specific single-cell RNA 5 ' end sequencing
Islam S, Kjallquist U, Moliner A, Zajac P, Fan Jb, Lonnerberg P, et al
NATURE PROTOCOLS 2012;7(5):813-28

Highly Parallel Genome-Wide Expression Analysis of Single Mammalian Cells
Fan Jb, Chen J, April Cs, Fisher Js, Klotzle B, Bibikova M, et al
PLOS ONE 2012;7(2):e30794-

Magnetic sequencing
Linnarsson S
NATURE METHODS 2012;9(4):339-341

Positional differences of axon growth rates between sensory neurons encoded by Runx3
Lallemend F, Sterzenbach U, Hadjab-lallemend S, Aquino Jb, Castelo-branco G, Sinha I, et al
The EMBO journal 2012;31(18):3718-29

RNA-Seq Analysis Reveals Different Dynamics of Differentiation of Human Dermis- and Adipose-Derived Stromal Stem Cells
Jaager K, Islam S, Zajac P, Linnarsson S, Neuman T
PLOS ONE 2012;7(6):e38833-

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
Islam S, Kjallquist U, Moliner A, Zajac P, Fan Jb, Lonnerberg P, et al
GENOME RESEARCH 2011;21(7):1160-7

En masse in vitro functional profiling of the axonal mechanosensitivity of sensory neurons
Usoskin D, Zilberter M, Linnarsson S, Hjerling-leffler J, Uhlen P, Harkany T, et al

Recent advances in DNA sequencing methods - general principles of sample preparation
Linnarsson S

Rapid genome sequencing with short universal tiling probes
Pihlak A, Bauren G, Hersoug E, Lonnerberg P, Metsis A, Linnarsson S
NATURE BIOTECHNOLOGY 2008;26(6):676-84

Whole-genome expression profiling through fragment display and combinatorial gene identification
Metsis A, Andersson U, Bauren G, Ernfors P, Lonnerberg P, Montelius A, et al
NUCLEIC ACIDS RESEARCH 2004;32(16):e127-

Activation by GDNF of a transcriptional program repressing neurite growth in dorsal root ganglia
Linnarsson S, Mikaels A, Baudet C, Ernfors P

Cell death in regenerating populations of neurons in BDNF mutant mice
Linnarsson S, Willson Ca, Ernfors P

BDNF regulates Reelin expression and Cajal-Retzius cell development in the cerebral cortex
Ringstedt T, Linnarsson S, Wagner J, Lendahl U, Kokaia Z, Arenas E, et al
NEURON 1998;21(2):305-15

Learning deficit in BDNF mutant mice
Linnarsson S, Bjorklund A, Ernfors P

Prenatal and postnatal requirements of NT-3 for sympathetic neuroblast survival and innervation of specific targets
Elshamy Wm, Linnarsson S, Lee Kf, Jaenisch R, Ernfors P
DEVELOPMENT 1996;122(2):491-500

Kucera J, Fan Gp, Jaenisch R, Linnarsson S, Ernfors P

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