Sten Linnarsson

Sten Linnarsson is professor of molecular systems biology at Karolinska Institutet and co-founder of the Eukaryotic Single-cell Genomics national infrastructure at SciLifeLab.

He has pioneered single-cell RNA sequencing and recently completed a single-cell RNA expression atlas of the mouse nervous system.

He is also a member of the Organizing Committee of the international Human Cell Atlas Initiative.

External homepage: http://linnarssonlab.org


Key publications:

Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, Deutsch GH, Dutra J, Gaulton KJ, Holden-Wiltse J, Huyck HL, Mariani TJ, Misra RS, Poole C, Preissl S, Pryhuber GS, Rogers L, Sun X, Wang A, Whitsett JA, Xu Y, Alladina J, Banovich NE, Barbry P, Beane JE, Bhattacharyya RP, Black KE, Brazma A, Campbell JD, Cho JL, Collin J, Conrad C, de Jong K, Desai T, Ding DZ, Eickelberg O, Eils R, Ellinor PT, Faiz A, Falk CS, Farzan M, Gellman A, Getz G, Glass IA, Greka A, Haniffa M, Hariri LP, Hennon MW, Horvath P, Hübner N, Hung DT, Huyck HL, Janssen WJ, Juric D, Kaminski N, Koenigshoff M, Koppelman GH, Krasnow MA, Kropski JA, Kuhnemund M, Lafyatis R, Lako M, Lander ES, Lee H, Lenburg ME, Marquette CH, Metzger RJ, Linnarsson S, Liu G, Lo YMD, Lundeberg J, Marioni JC, Mazzilli SA, Medoff BD, Meyer KB, Miao Z, Misharin AV, Nawijn MC, Nikolić MZ, Noseda M, Ordovas-Montanes J, Oudit GY, Pe’er D, Powell JE, Quake SR, Rajagopal J, Tata PR, Rawlins EL, Regev A, Reid ME, Reyfman PA, Rieger-Christ KM, Rojas M, Rozenblatt-Rosen O, Saeb-Parsy K, Samakovlis C, Sanes JR, Schiller HB, Schultze JL, Schwarz RF, Segre AV, Seibold MA, Seidman CE, Seidman JG, Shalek AK, Shepherd DP, Sinha R, Spence JR, Spira A, Sun X, Sundström E, Teichmann SA, Theis FJ, Tsankov AM, Vallier L, van den Berge M, Van Zyl TA, Villani AC, Weins A, Xavier RJ, Yildirim AÖ, Zaragosi LE, Zerti D, Zhang H, Zhang K, Zhang X. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. (2021) Nature medicine

Rozenblatt-Rosen O, Shin JW, Rood JE, Hupalowska A, Regev A, Heyn H, Ardlie K, Clatworthy M, Carninci P, Enard W, Greenleaf W, Heyn H, Lein E, Levin JZ, Linnarsson S, Lundberg E, Meyer K, Navin N, Nolan G, Teichmann S, Voet T, Zhuang X. Building a high-quality Human Cell Atlas. (2021) Nature biotechnology

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, Clevers H, De Strooper B, Eggert A, Ellenberg J, Fernández XM, Figlerowicz M, Gasser SM, Hubner N, Kjems J, Knoblich JA, Krabbe G, Lichter P, Linnarsson S, Marine JC, Marioni JC, Marti-Renom MA, Netea MG, Nickel D, Nollmann M, Novak HR, Parkinson H, Piccolo S, Pinheiro I, Pombo A, Popp C, Reik W, Roman-Roman S, Rosenstiel P, Schultze JL, Stegle O, Tanay A, Testa G, Thanos D, Theis FJ, Torres-Padilla ME, Valencia A, Vallot C, van Oudenaarden A, Vidal M, Voet T, Alberi L, Alexander S, Alexandrov T, Arenas E, Bagni C, Balderas R, Bandelli A, Becher B, Becker M, Beerenwinkel N, Benkirame M, Beyer M, Bickmore W, Biessen EEAL, Blomberg N, Blumcke I, Bodenmiller B, Borroni B, Boumpas DT, Bourgeron T, Bowers S, Braeken D, Brooksbank C, Brose N, Bruining H, Bury J, Caporale N, Cattoretti G, Chabane N, Chneiweiss H, Cook SA, Curatolo P, de Jonge MI, Deplancke B, De Strooper B, de Witte P, Dimmeler S, Draganski B, Drews A, Dumbrava C, Engelhardt S, Gasser T, Giamarellos-Bourboulis EJ, Graff C, Grün D, Gut I, Hansson O, Henshall DC, Herland A, Heutink P, Heymans SRB, Heyn H, Huch M, Huitinga I, Jackowiak P, Jongsma KR, Journot L, Junker JP, Katz S, Kehren J, Kempa S, Kirchhof P, Klein C, Koralewska N, Korbel JO, Kühnemund M, Lamond AI, Lauwers E, Le Ber I, Leinonen V, Tobon AL, Lundberg E, Lunkes A, Maatz H, Mann M, Marelli L, Matser V, Matthews PM, Mechta-Grigoriou F, Menon R, Nielsen AF, Pagani M, Pasterkamp RJ, Pitkänen A, Popescu V, Pottier C, Puisieux A, Rademakers R, Reiling D, Reiner O, Remondini D, Ritchie C, Rohrer JD, Saliba AE, Sanchez-Valle R, Santosuosso A, Sauter A, Scheltema RA, Scheltens P, Schiller HB, Schneider A, Seibler P, Sheehan-Rooney K, Shields D, Sleegers K, Smit AB, Smith KGC, Smolders I, Synofzik M, Tam WL, Teichmann S, Thom M, Turco MY, van Beusekom HMM, Vandenberghe R, Van den Hoecke S, Van de Poel I, van der Ven A, van der Zee J, van Lunzen J, van Minnebruggen G, van Oudenaarden A, Van Paesschen W, van Swieten J, van Vught R, Verhage M, Verstreken P, Villa CE, Vogel J, von Kalle C, Walter J, Weckhuysen S, Weichert W, Wood L, Ziegler AG, Zipp F. LifeTime and improving European healthcare through cell-based interceptive medicine. (2020) Nature

Wang Y, Wu H, Fontanet P, Codeluppi S, Akkuratova N, Petitpré C, Xue-Franzén Y, Niederreither K, Sharma A, Da Silva F, Comai G, Agirman G, Palumberi D, Linnarsson S, Adameyko I, Moqrich A, Schedl A, La Manno G, Hadjab S, Lallemend F. A cell fitness selection model for neuronal survival during development. (2019) Nature communications

Goodridge JP, Jacobs B, Saetersmoen ML, Clement D, Hammer Q, Clancy T, Skarpen E, Brech A, Landskron J, Grimm C, Pfefferle A, Meza-Zepeda L, Lorenz S, Wiiger MT, Louch WE, Ask EH, Liu LL, Oei VYS, Kjällquist U, Linnarsson S, Patel S, Taskén K, Stenmark H, Malmberg KJ. Remodeling of secretory lysosomes during education tunes functional potential in NK cells. (2019) Nature communications

Codeluppi S, Borm LE, Zeisel A, La Manno G, van Lunteren JA, Svensson CI, Linnarsson S. Spatial organization of the somatosensory cortex revealed by osmFISH. (2018) Nature methods

Mezger A, Klemm S, Mann I, Brower K, Mir A, Bostick M, Farmer A, Fordyce P, Linnarsson S, Greenleaf W. High-throughput chromatin accessibility profiling at single-cell resolution. (2018) Nature communications

Zeisel A, Hochgerner H, Lönnerberg P, Johnsson A, Memic F, van der Zwan J, Häring M, Braun E, Borm LE, La Manno G, Codeluppi S, Furlan A, Lee K, Skene N, Harris KD, Hjerling-Leffler J, Arenas E, Ernfors P, Marklund U, Linnarsson S. Molecular Architecture of the Mouse Nervous System. (2018) Cell

La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, Lönnerberg P, Furlan A, Fan J, Borm LE, Liu Z, van Bruggen D, Guo J, He X, Barker R, Sundström E, Castelo-Branco G, Cramer P, Adameyko I, Linnarsson S, Kharchenko PV. RNA velocity of single cells. (2018) Nature

Savage JE, Jansen PR, Stringer S, Watanabe K, Bryois J, de Leeuw CA, Nagel M, Awasthi S, Barr PB, Coleman JRI, Grasby KL, Hammerschlag AR, Kaminski JA, Karlsson R, Krapohl E, Lam M, Nygaard M, Reynolds CA, Trampush JW, Young H, Zabaneh D, Hägg S, Hansell NK, Karlsson IK, Linnarsson S, Montgomery GW, Muñoz-Manchado AB, Quinlan EB, Schumann G, Skene NG, Webb BT, White T, Arking DE, Avramopoulos D, Bilder RM, Bitsios P, Burdick KE, Cannon TD, Chiba-Falek O, Christoforou A, Cirulli ET, Congdon E, Corvin A, Davies G, Deary IJ, DeRosse P, Dickinson D, Djurovic S, Donohoe G, Conley ED, Eriksson JG, Espeseth T, Freimer NA, Giakoumaki S, Giegling I, Gill M, Glahn DC, Hariri AR, Hatzimanolis A, Keller MC, Knowles E, Koltai D, Konte B, Lahti J, Le Hellard S, Lencz T, Liewald DC, London E, Lundervold AJ, Malhotra AK, Melle I, Morris D, Need AC, Ollier W, Palotie A, Payton A, Pendleton N, Poldrack RA, Räikkönen K, Reinvang I, Roussos P, Rujescu D, Sabb FW, Scult MA, Smeland OB, Smyrnis N, Starr JM, Steen VM, Stefanis NC, Straub RE, Sundet K, Tiemeier H, Voineskos AN, Weinberger DR, Widen E, Yu J, Abecasis G, Andreassen OA, Breen G, Christiansen L, Debrabant B, Dick DM, Heinz A, Hjerling-Leffler J, Ikram MA, Kendler KS, Martin NG, Medland SE, Pedersen NL, Plomin R, Polderman TJC, Ripke S, van der Sluis S, Sullivan PF, Vrieze SI, Wright MJ, Posthuma D. Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence. (2018) Nature genetics

Nagel M, Jansen PR, Stringer S, Watanabe K, de Leeuw CA, Bryois J, Savage JE, Hammerschlag AR, Skene NG, Muñoz-Manchado AB, White T, Tiemeier H, Linnarsson S, Hjerling-Leffler J, Polderman TJC, Sullivan PF, van der Sluis S, Posthuma D, Agee M, Alipanahi B, Auton A, Bell RK, Bryc K, Elson SL, Fontanillas P, Furlotte NA, Hinds DA, Hromatka BS, Huber KE, Kleinman A, Litterman NK, McIntyre MH, Mountain JL, Noblin ES, Northover CAM, Pitts SJ, Sathirapongsasuti JF, Sazonova OV, Shelton JF, Shringarpure S, Tian C, Tung JY, Vacic V, Wilson CH. Meta-analysis of genome-wide association studies for neuroticism in 449,484 individuals identifies novel genetic loci and pathways. (2018) Nature genetics

Skene NG, Bryois J, Bakken TE, Breen G, Crowley JJ, Gaspar HA, Giusti-Rodriguez P, Hodge RD, Miller JA, Muñoz-Manchado AB, O’Donovan MC, Owen MJ, Pardiñas AF, Ryge J, Walters JTR, Linnarsson S, Lein ES, Sullivan PF, Hjerling-Leffler J. Genetic identification of brain cell types underlying schizophrenia. (2018) Nature genetics

Häring M, Zeisel A, Hochgerner H, Rinwa P, Jakobsson JET, Lönnerberg P, La Manno G, Sharma N, Borgius L, Kiehn O, Lagerström MC, Linnarsson S, Ernfors P. Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types. (2018) Nature neuroscience

Coleman JRI, Bryois J, Gaspar HA, Jansen PR, Savage JE, Skene N, Plomin R, Muñoz-Manchado AB, Linnarsson S, Crawford G, Hjerling-Leffler J, Sullivan PF, Posthuma D, Breen G. Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals. (2018) Molecular psychiatry

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

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. Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders. (2017) Genome medicine

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. Constitutively Active SMAD2/3 Are Broad-Scope Potentiators of Transcription-Factor-Mediated Cellular Reprogramming. (2017) Cell stem cell

Lein E, Borm LE, Linnarsson S. The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing. (2017) Science (New York, N.Y.)

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. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model. (2017) Nature biotechnology

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. Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. (2016) Nature neuroscience

La Manno G, Gyllborg D, Codeluppi S, Nishimura K, Salto C, Zeisel A, Borm LE, Stott SRW, Toledo EM, Villaescusa JC, Lönnerberg P, Ryge J, Barker RA, Arenas E, Linnarsson S. Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. (2016) Cell

Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula SP, Codeluppi S, Reyes AP, Linnarsson S, Sandberg R, Lanner F. Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos. (2016) Cell

Furlan A, La Manno G, Lübke M, Häring M, Abdo H, Hochgerner H, Kupari J, Usoskin D, Airaksinen MS, Oliver G, Linnarsson S, Ernfors P. Visceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle control. (2016) Nature neuroscience

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. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. (2016) Science (New York, N.Y.)

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 A, 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. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. (2016) Science (New York, N.Y.)

Linnarsson S, Teichmann SA. Single-cell genomics: coming of age. (2016) Genome biology

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. Origin, fate and dynamics of macrophages at central nervous system interfaces. (2016) Nature immunology

Petropoulos S, Edsgärd D, Reinius B, Deng Q, Panula SP, Codeluppi S, Plaza Reyes A, Linnarsson S, Sandberg R, Lanner F. Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos. (2016) Cell

Fuzik J, Zeisel A, Máté Z, Calvigioni D, Yanagawa Y, Szabó G, Linnarsson S, Harkany T. Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes. (2015) Nature biotechnology

Linnarsson S. NEUROSCIENCE. A tree of the human brain. (2015) Science (New York, N.Y.)

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. Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development. (2015) Nature communications

Linnarsson S. Sequencing Single Cells Reveals Sequential Stem Cell States. (2015) Cell stem cell

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. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. (2015) Science (New York, N.Y.)

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. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. (2014) Nature neuroscience

Zechel S, Zajac P, Lönnerberg P, Ibáñez CF, Linnarsson S. Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. (2014) Genome biology

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. Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo. (2014) Cancer cell

Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S. Quantitative single-cell RNA-seq with unique molecular identifiers. (2013) Nature methods

O’Malley J, Skylaki S, Iwabuchi KA, Chantzoura E, Ruetz T, Johnsson A, Tomlinson SR, Linnarsson S, Kaji K. High-resolution analysis with novel cell-surface markers identifies routes to iPS cells. (2013) Nature

Linnarsson S. Single-cell biology meeting marks rebirth of an old science. (2013) Genome biology

Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S. Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing. (2012) Nature protocols

Linnarsson S. Magnetic sequencing. (2012) Nature methods

Kivioja T, Vähärautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, Taipale J. Counting absolute numbers of molecules using unique molecular identifiers. (2011) Nature methods

Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. (2011) Genome research