Preprint

  • ★ RNA velocity in single cells Gioele La Manno, Ruslan Soldatov, Hannah Hochgerner, Amit Zeisel, Viktor Petukhov, Maria Kastriti, Peter Lonnerberg, Alessandro Furlan, Jean Fan, Zehua Liu, David van Bruggen, Jimin Guo, Erik Sundstrom, Goncalo Castelo-Branco, Igor Adameyko, Sten Linnarsson, Peter Kharchenko

    Published in bioRxiv (PDF)

    Supporting data and visualizations.

2018

  • ★ Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing. Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S.

    Published in Nature Neuroscience (PDF)

    Supporting data and visualizations.

  • 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, Karlsson E, Hatschek T, Hartman J, Linnarsson S, Bergh J.

    Published in BMC Cancer(PDF)

2017

  • ★ The human cell atlas. Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

    Published in ELife (PDF)

  • ★ 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, Lin P, Picelli S, La Manno G, Ratz M, Dunne J, Husain S, Lein E, Srinivasan M, Zeisel A, Linnarsson S.

    Published in Scientific Reports (PDF)

  • ★ The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing Ed Lein, Lars Borm, Sten Linnarsson

    Published in Science (PDF)

  • ★ Alternative TSSs are co-regulated in single cells in the mouse brain. Karlsson K, Lönnerberg P, Linnarsson S.

    Published in Molecular Systems Biology (PDF)

  • 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, La Manno G, Feyder M, Pifl C, Ng YH, Sánchez SP, Linnarsson S, Wernig M, Harkany T, Fisone G, Arenas E.

    Published in Nature Biotechnology (PDF)

  • 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, Ruderfer DM, Genovese G, Fromer M, Xu X, Pinto D, Linnarsson S, Verhage M, Smit AB, Hjerling-Leffler J, Buxbaum JD, Hultman C, Sklar P, Purcell SM, Lage K, He X, Sullivan PF, Stahl EA.

    Published in Genome Medicine(PDF)

  • 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, Marks C, Medalová J, Souček K, Lundberg E, Linnarsson S, Bryja V, Sekyrova P, Altun M, Andäng M.

    Published in PLoS One(PDF)

  • 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, Kaemena DF, Tosti L, Tan W, Manning JR, Chantzoura E, Ottosson DR, Collombet S, Johnsson A, Cohen E, Yusa K, Linnarsson S, Graf T, Parmar M, Kaji K.

    Published in Cell Stem Cell(PDF)

  • 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, Linnarsson S, Zhang K.

    Published in Scientific Reports(PDF)

  • Single-cell mRNA isoform diversity in the mouse brain. Karlsson K, Linnarsson S.

    Published in BMC Genomics(PDF)

  • 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, Schmidt L, Fritz N, Dehnisch I, Kyriatzis G, Krafcikova M, Carson BB, Feenstra JM, Marinescu VD, Segerman A, Haraldsson M, Gustavsson AL, Hammarström LG, Jenmalm Jensen A, Uhrbom L, Altelaar AF, Linnarsson S, Uhlén P, Trantirek L, Vincent CT, Nelander S, Enger PØ, Andäng M.

    Published in Cancer Research(PDF)

2016

  • ★ Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Salto, Amit Zeisel, Lars E. Borm, Simon R.W. Stott, Enrique M. Toledo, J. Carlos Villaescusa, Peter Lönnerberg, Jesper Ryge, Roger A. Barker, Ernest Arenas, and Sten Linnarsson

    Published in Cell (PDF)

    Supporting data and visualizations.

  • ★ Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity Simon Joost, Amit Zeisel, Tina Jacob, Xiaoyan Sun, Gioele La Manno, Peter Lönnerberg, Sten Linnarsson*, Maria Kasper*

    Published in Cell Systems (PDF)

    Supporting data and visualizations.

  • ★ Visceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle control Alessandro Furlan, Gioele La Manno, Moritz Lübke, Martin Häring, Hind Abdo, Hannah Hochgerner, Jussi Kupari, Dmitry Usoskin, Matti S Airaksinen, Guillermo Oliver, Sten Linnarsson* and Patrik Ernfors*

    Published in Nature Neuroscience (PDF)

    Supporting data and visualizations.

  • Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J.

    Published in Science (PDF)

  • Origin, fate and dynamics of macrophages at central nervous system interfaces. Goldmann T, Wieghofer P, Jordão MJ, Prutek F, Hagemeyer N, Frenzel K, Amann L, Staszewski O, Kierdorf K, Krueger M, Locatelli G, Hochgerner H, Zeiser R, Epelman S, Geissmann F, Priller J, Rossi FM, Bechmann I, Kerschensteiner M, Linnarsson S, Jung S, Prinz M.

    Published in Nature Immunology (PDF)

    Supporting data and visualizations.

  • ★ 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, Li H, Häring M, Hochgerner H, Romanov RA, Gyllborg D, Muñoz-Manchado AB, La Manno G, Lönnerberg P, Floriddia EM, Rezayee F, Ernfors P, Arenas E, Hjerling-Leffler J, Harkany T, Richardson WD, Linnarsson S*, Castelo-Branco G*.

    Published in Science (PDF)

    Supporting data and visualizations.

  • 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, Plaza Reyes A, Linnarsson S, Sandberg R, Lanner F.

    Published in Cell (PDF)

  • ★ 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, Linnarsson S*, Harkany T*.

    Published in Nature Biotechnology (PDF)

  • ★ Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Romanov RA, Zeisel A, Bakker J, Girach F, Hellysaz A, Tomer R, Alpár A, Mulder J, Clotman F, Keimpema E, Hsueh B, Crow AK, Martens H, Schwindling C, Calvigioni D, Bains JS, Máté Z, Szabó G, Yanagawa Y, Zhang MD, Rendeiro A, Farlik M, Uhlén M, Wulff P, Bock C, Broberger C, Deisseroth K, Hökfelt T, Linnarsson S, Horvath TL, Harkany T.

    Published in Nature Neuroscience(PDF)

  • Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos. Madissoon E, Jouhilahti EM, Vesterlund L, Töhönen V, Krjutškov K, Petropoulous S, Einarsdottir E, Linnarsson S, Lanner F, Månsson R, Hovatta O, Bürglin TR, Katayama S, Kere J.

    Published in Scientific Reports(PDF)

  • 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, Kaiser K, Islam S, Gyllborg D, Laguna-Goya R, Landreh M, Lönnerberg P, Falk A, Bergman T, Barker RA, Linnarsson S, Selleri L, Arenas E.

    Published in EMBO Journal(PDF)

  • Single-cell genomics: coming of age. Linnarsson S, Teichmann SA.

    Published in Genome Biology(PDF)

  • 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, Sormunen R, Johnsson A, Linnarsson S, Suomela S, Kankuri E, Kere J, Elomaa O.

    Published in Scientific Reports(PDF)

2015

  • A tree of the human brain. Linnarsson S.

    Published in Science (PDF)

  • Sequencing Single Cells Reveals Sequential Stem Cell States. Linnarsson S.

    Published in Cell Stem Cell (PDF)

  • ★ 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, Marques S, Munguba H, He L, Betsholtz C, Rolny C, Castelo-Branco G, Hjerling-Leffler J, Linnarsson S.

    Published in Science (PDF)

    Supporting data and visualizations.

  • A secretagogin locus of the mammalian hypothalamus controls stress hormone release. Romanov RA, Alpár A, Zhang MD, Zeisel A, Calas A, Landry M, Fuszard M, Shirran SL, Schnell R, Dobolyi Á, Oláh M, Spence L, Mulder J, Martens H, Palkovits M, Uhlen M, Sitte HH, Botting CH, Wagner L, Linnarsson S, Hökfelt T, Harkany T.

    Published in EMBO Journal (PDF)

  • ★ Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Usoskin D, Furlan A, Islam S, Abdo H, Lönnerberg P, Lou D, Hjerling-Leffler J, Haeggström J, Kharchenko O, Kharchenko PV, Linnarsson S*, Ernfors P.*

    Published in Nature Neuroscience (PDF)

    Supporting data and visualizations.

  • Dynamics of Lgr6⁺ Progenitor Cells in the Hair Follicle, Sebaceous Gland, and Interfollicular Epidermis. Füllgrabe A, Joost S, Are A, Jacob T, Sivan U, Haegebarth A, Linnarsson S, Simons BD, Clevers H, Toftgård R, Kasper M.

    Published in Stem Cell Reports(PDF)

  • 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, Filippini-Cattaneo G, Jaconi M, Johnsson A, Bürglin TR, Linnarsson S, Hovatta O, Kere J.

    Published in Nature Communications(PDF)

  • Reprogramming Roadblocks Are System Dependent. Chantzoura E, Skylaki S, Menendez S, Kim SI, Johnsson A, Linnarsson S, Woltjen K, Chambers I, Kaji K.

    Published in Stem Cell Reports(PDF)

  • 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, Vuola J, Johnsson A, Lönnerberg P, Linnarsson S, Elomaa O, Kankuri E, Kere J.

    Published in BMC Genomics(PDF)

  • 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, Linnarsson S, Lehtiö J, Nordström A.

    Published in Journal of Biological Chemistry(PDF)

  • 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.

    Published in Genomics(PDF)

2014

  • Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. Zechel S, Zajac P, Lönnerberg P, Ibáñez CF, Linnarsson S.

    Published in Genome Biology (PDF)

  • ★ 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, Erlandsson R, Ngara M, Anderson K, Deng Q, Mead AJ, Stenson L, Giustacchini A, Duarte S, Giannoulatou E, Taylor S, Karimi M, Scharenberg C, Mortera-Blanco T, Macaulay IC, Clark SA, Dybedal I, Josefsen D, Fenaux P, Hokland P, Holm MS, Cazzola M, Malcovati L, Tauro S, Bowen D, Boultwood J, Pellagatti A, Pimanda JE, Unnikrishnan A, Vyas P, Göhring G, Schlegelberger B, Tobiasson M, Kvalheim G, Constantinescu SN, Nerlov C, Nilsson L, Campbell PJ, Sandberg R, Papaemmanuil E, Hellström-Lindberg E, Linnarsson S, Jacobsen SE.

    Published in Cancer Cell (PDF)

  • Selective calcium sensitivity in immature glioma cancer stem cells. Wee S, Niklasson M, Marinescu VD, Segerman A, Schmidt L, Hermansson A, Dirks P, Forsberg-Nilsson K, Westermark B, Uhrbom L, Linnarsson S, Nelander S, Andäng M.

    Published in PLoS ONE(PDF)

2013

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

    Published in Nature Genetics (PDF)

  • 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, Tomlinson SR, Linnarsson S, Kaji K.

    Published in Nature (PDF)

  • ★ Quantitative single-cell RNA-seq with unique molecular identifiers. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S.

    Published in Nature Methods (PDF)

  • Base preferences in non-templated nucleotide incorporation by MMLV-derived reverse transcriptases. Zajac P, Islam S, Hochgerner H, Lönnerberg P, Linnarsson S.

    Published in PLoS ONE(PDF)

  • SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization. Katayama S, Töhönen V, Linnarsson S, Kere J.

    Published in Bioinformatics(PDF)

  • 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, Lundgren KT, Castelo-Branco G, Linnarsson S, Wedlich-Söldner R, Teixeira A, Andäng M.

    Published in PLoS ONE(PDF)

  • Single-cell biology meeting marks rebirth of an old science. Linnarsson S.

    Published in Genome Biology(PDF)

2012

  • Highly multiplexed and strand-specific single-cell RNA 5' end sequencing. Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.

    Published in Nature Protocols (PDF)

  • Magnetic sequencing. Linnarsson S.

    Published in Nature Methods (PDF)

  • 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, Villaescusa JC, Levanon D, Wang Y, Franck MC, Kharchenko O, Adameyko I, Linnarsson S, Groner Y, Turner E, Ernfors P.

    Published in EMBO Journal(PDF)

  • RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells. Jääger K, Islam S, Zajac P, Linnarsson S, Neuman T.

    Published in PLoS ONE(PDF)

  • Highly parallel genome-wide expression analysis of single mammalian cells. Fan JB, Chen J, April CS, Fisher JS, Klotzle B, Bibikova M, Kaper F, Ronaghi M, Linnarsson S, Ota T, Chien J, Laurent LC, Loring JF, Nisperos SV, Chen GY, Zhong JF.

    Published in PLoS ONE(PDF)

2011

  • ★ Counting absolute numbers of molecules using unique molecular identifiers. Kivioja T, Vähärautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J.

    Published in Nature Methods (PDF)

  • ★ Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.

    Published in Genome Research (PDF)

2010

  • En masse in vitro functional profiling of the axonal mechanosensitivity of sensory neurons. Usoskin D, Zilberter M, Linnarsson S, Hjerling-Leffler J, Uhlén P, Harkany T, Ernfors P.

    Published in PNAS(PDF)

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

    Published in Experimental Cell Research(PDF)

2009

2008

  • ★ Rapid genome sequencing with short universal tiling probes. Pihlak A, Baurén G, Hersoug E, Lönnerberg P, Metsis A, Linnarsson S.

    Published in Nature Biotechnology (PDF)

Older papers are available from PubMed