2021

  • ★ A multimodal cell census and atlas of the mammalian primary motor cortex BRAIN Initiative Cell Census Network (BICCN)

    Published in Nature (PDF)

    Supporting data and visualizations.

  • ★ Comparative cellular analysis of motor cortex in human, marmoset and mouse Trygve E Bakken, Nikolas L Jorstad, Qiwen Hu, Blue B Lake, Wei Tian, Brian E Kalmbach, Megan Crow, Rebecca D Hodge, Fenna M Krienen, Staci A Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D Aevermann, Andrew I Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G Castanon, Kirsten Crichton, Tanya L Daigle, Rachel Dalley, Nick Dee, Nikolai Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T Graybuck, Brian R Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S Liu, Hanqing Liu, Jacinta D Lucero, Anup Mahurkar, Delissa McMillen, Jeremy A Miller, Marmar Moussa, Joseph R Nery, Philip R Nicovich, Sheng-Yong Niu, Joshua Orvis, Julia K Osteen, Scott Owen, Carter R Palmer, Thanh Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M Reed, Christine Rimorin, Angeline Rivkin, William J Romanow, Adriana E Sedeño-Cortés, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A Ament, M Margarita Behrens, Hector Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R Hof, Thomas Höllt, Gregory D Horwitz, C Dirk Keene, Peter V Kharchenko, Andrew L Ko, Boudewijn P Lelieveldt, Chongyuan Luo, Eran A Mukamel, António Pinto-Duarte, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H Scheuermann, Kimberly Smith, William J Spain, Owen R White, Christof Koch, Michael Hawrylycz, Bosiljka Tasic, Evan Z Macosko, Steven A McCarroll, Jonathan T Ting, Hongkui Zeng, Kun Zhang, Guoping Feng, Joseph R Ecker, Sten Linnarsson, Ed S Lein

    Published in Nature (PDF)

    Supporting data and visualizations.

  • ★ Molecular architecture of the developing mouse brain Gioele La Manno, Kimberly Siletti, Alessandro Furlan, Daniel Gyllborg, Elin Vinsland, Alejandro Mossi Albiach, Christoffer Mattsson Langseth, Irina Khven, Alex R Lederer, Lisa M Dratva, Anna Johnsson, Mats Nilsson, Peter Lönnerberg, Sten Linnarsson

    Published in Nature (PDF)

    Supporting data and visualizations.

  • A roadmap for the Human Developmental Cell Atlas Muzlifah Haniffa, Deanne Taylor, Sten Linnarsson, Bruce J Aronow, Gary D Bader, Roger A Barker, Pablo G Camara, J Gray Camp, Alain Chédotal, Andrew Copp, Heather C Etchevers, Paolo Giacobini, Berthold Göttgens, Guoji Guo, Ania Hupalowska, Kylie R James, Emily Kirby, Arnold Kriegstein, Joakim Lundeberg, John C Marioni, Kerstin B Meyer, Kathy K Niakan, Mats Nilsson, Bayanne Olabi, Dana Pe'er, Aviv Regev, Jennifer Rood, Orit Rozenblatt-Rosen, Rahul Satija, Sarah A Teichmann, Barbara Treutlein, Roser Vento-Tormo, Simone Webb, Human Cell Atlas Developmental Biological Network

    Published in Nature (PDF)

  • Single-cell meta-analysis of SARS-CoV- entry genes across tissues and demographics Christoph Muus, Malte D Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, Graham Heimberg, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smillie, Karthik A Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L Haber, Hattie Chung, Daniel T Montoro, Taylor Adams, Hananeh Aliee, Samuel J Allon, Zaneta Andrusivova, Ilias Angelidis, Orr Ashenberg, Kevin Bassler, Christophe Bécavin, Inbal Benhar, Joseph Bergenstråhle, Ludvig Bergenstråhle, Liam Bolt, Emelie Braun, Linh T Bui, Steven Callori, Mark Chaffin, Evgeny Chichelnitskiy, Joshua Chiou, Thomas M Conlon, Michael S Cuoco, Anna S E Cuomo, Marie Deprez, Grant Duclos, Denise Fine, David S Fischer, Shila Ghazanfar, Astrid Gillich, Bruno Giotti, Joshua Gould, Minzhe Guo, Austin J Gutierrez, Arun C Habermann, Tyler Harvey, Peng He, Xiaomeng Hou, Lijuan Hu, Yan Hu, Alok Jaiswal, Lu Ji, Peiyong Jiang, Theodoros S Kapellos, Christin S Kuo, Ludvig Larsson, Michael A Leney-Greene, Kyungtae Lim, Monika Litviňuková, Leif S Ludwig, Soeren Lukassen, Wendy Luo, Henrike Maatz, Elo Madissoon, Lira Mamanova, Kasidet Manakongtreecheep, Sylvie Leroy, Christoph H Mayr, Ian M Mbano, Alexi M McAdams, Ahmad N Nabhan, Sarah K Nyquist, Lolita Penland, Olivier B Poirion, Sergio Poli, CanCan Qi, Rachel Queen, Daniel Reichart, Ivan Rosas, Jonas C Schupp, Conor V Shea, Xingyi Shi, Rahul Sinha, Rene V Sit, Kamil Slowikowski, Michal Slyper, Neal P Smith, Alex Sountoulidis, Maximilian Strunz, Travis B Sullivan, Dawei Sun, Carlos Talavera-López, Peng Tan, Jessica Tantivit, Kyle J Travaglini, Nathan R Tucker, Katherine A Vernon, Marc H Wadsworth, Julia Waldman, Xiuting Wang, Ke Xu, Wenjun Yan, William Zhao, Carly G K Ziegler, NHLBI LungMap Consortium; Human Cell Atlas Lung Biological Network

    Published in Nature Medicine (PDF)

  • Building a high-quality Human Cell Atlas Orit Rozenblatt-Rosen, Jay W Shin, Jennifer E Rood, Anna Hupalowska, Human Cell Atlas Standards and Technology Working Group; Aviv Regev, Holger Heyn

    Published in Nature biotechnology (PDF)

2020

  • Effects of In Vivo Gluten Challenge on PBMC Gene Expression Profiles in Diet Treated Celiac Disease Dawit A Yohannes, Andrea de Kauwe, Katri Kaukinen, Kalle Kurppa, Markku Mäki, Robert P Anderson, Sten Linnarsson, Dario Greco, Päivi Saavalainen

    Published in Frontiers in Immunology (PDF)

  • LifeTime and improving European healthcare through cell-based interceptive medicine Nikolaus Rajewsky, Geneviève Almouzni, Stanislaw A Gorski, Stein Aerts, Ido Amit, Michela G Bertero, Christoph Bock, Annelien L Bredenoord, Giacomo Cavalli, Susanna Chiocca, Hans Clevers, Bart De Strooper, Angelika Eggert, Jan Ellenberg, Xosé M Fernández, Marek Figlerowicz, Susan M Gasser, Norbert Hubner, Jørgen Kjems, Jürgen A Knoblich, Grietje Krabbe, Peter Lichter, Sten Linnarsson, Jean-Christophe Marine, John C Marioni, Marc A Marti-Renom, Mihai G Netea, Dörthe Nickel, Marcelo Nollmann, Halina R Novak, Helen Parkinson, Stefano Piccolo, Inês Pinheiro, Ana Pombo, Christian Popp, Wolf Reik, Sergio Roman-Roman, Philip Rosenstiel, Joachim L Schultze, Oliver Stegle, Amos Tanay, Giuseppe Testa, Dimitris Thanos, Fabian J Theis, Maria-Elena Torres-Padilla, Alfonso Valencia, Céline Vallot, Alexander van Oudenaarden, Marie Vidal, Thierry Voet, LifeTime Community Working Groups

    Published in Nature (PDF)

  • Srebf Controls Midbrain Dopaminergic Neurogenesis Enrique M Toledo, Shanzheng Yang, Daniel Gyllborg, Kim E van Wijk, Indranil Sinha, Manuel Varas-Godoy, Christopher L Grigsby, Peter Lönnerberg, Saiful Islam, Knut R Steffensen, Sten Linnarsson, Ernest Arenas

    Published in Cell reports (PDF)

2019

  • A cell fitness selection model for neuronal survival during development Yiqiao Wang , Haohao Wu , Paula Fontanet , Simone Codeluppi , Natalia Akkuratova , Charles Petitpré , Yongtao Xue-Franzén , Karen Niederreither , Anil Sharma , Fabio Da Silva , Glenda Comai , Gulistan Agirman , Domenico Palumberi , Sten Linnarsson , Igor Adameyko, Aziz Moqrich , Andreas Schedl , Gioele La Manno , Saida Hadjab , François Lallemend

    Published in Nature communications (PDF)

  • Remodeling of secretory lysosomes during education tunes functional potential in NK cells. Jodie P Goodridge, Benedikt Jacobs, Michelle L Saetersmoen, Dennis Clement, Quirin Hammer, Trevor Clancy, Ellen Skarpen, Andreas Brech, Johannes Landskron, Christian Grimm, Aline Pfefferle, Leonardo Meza-Zepeda, Susanne Lorenz, Merete Thune Wiiger, William E Louch, Eivind Heggernes Ask, Lisa L Liu, Vincent Yi Sheng Oei, Una Kjällquist, Sten Linnarsson, Sandip Patel, Kjetil Taskén, Harald Stenmark, Karl-Johan Malmberg

    Published in Nature communications (PDF)

2018

  • ★ Spatial organization of the somatosensory cortex revealed by osmFISH. Codeluppi S, Borm LE, Zeisel A, La Manno G, van Lunteren JA, Svensson CI, Linnarsson S.

    Published in Nature Methods (PDF)

    Supporting data and visualizations.

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

    Published in Nature Communications (PDF)

  • ★ RNA velocity of single cells 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.

    Published in Nature (PDF)

    Supporting data and visualizations.

  • 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, Lönnerberg P, Ryge J, Harris KD, Linnarsson S, Hjerling-Leffler J.

    Published in Cell Reports (PDF)

  • 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, Somogyi P, Kessaris N, Linnarsson S, Hjerling-Leffler J.

    Published in PLoS Biology (PDF)

  • ★ 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, La Manno G, Sharma N, Borgius L, Kiehn O, Lagerström MC, Linnarsson S, Ernfors P.

    Published in Nature Neuroscience (PDF)

    Supporting data and visualizations.

  • ★ Molecular architecture of the mouse nervous system 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.

    Published in Cell (PDF)

    Supporting data and visualizations.

  • ★ 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.

  • 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, 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.

    Published in Nature Genetics (PDF)

  • Meta-analysis of genome-wide association studies for neuroticism in 449,484 individuals identifies novel genetic loci and pathways. Nagel M, Jansen PR, Stringer S, Watanabe K, de Leeuw CA, Bryois J, Savage JE, Hammerschlag AR, Skene NG, Muñoz-Manchado AB; 23andMe Research Team, White T, Tiemeier H, Linnarsson S, Hjerling-Leffler J, Polderman TJC, Sullivan PF, van der Sluis S, Posthuma D.

    Published in Nature Genetics (PDF)

  • Genetic identification of brain cell types underlying schizophrenia. 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; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Sullivan PF, Hjerling-Leffler J.

    Published in Nature Genetics (PDF)

  • 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)

  • 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, Plomin R, Muñoz-Manchado AB, Linnarsson S, Crawford G, Hjerling-Leffler J, Sullivan PF, Posthuma D, Breen G.

    Published in Molecular Psychiatry (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