Publications

2024

★ Chromatin accessibility during human first-trimester neurodevelopment Mannens CCA, Hu L, Lönnerberg P, Schipper M, Reagor CC, Li X, He X, Barker RA, Sundström E, Posthuma D, Linnarsson S.

Published in Nature (PDF)

Supporting data and visualizations.

The commitment of the human cell atlas to humanity Amit I, Ardlie K, Arzuaga F, Awandare G, Bader G, Bernier A, Carninci P, Donnelly S, Eils R, Forrest ARR, Greely HT, Guigo R, Hacohen N, Haniffa M, Kirby ES, Knoppers BM, Kriegstein A, Lein ES, Linnarsson S, Majumder PP, Merad M, Meyer K, Mhlanga MM, Nolan G, Ntusi NAB, Pe'er D, Prabhakar S, Raven-Adams M, Regev A, Rozenblatt-Rosen O, Saha S, Saltzman A, Shalek AK, Shin JW, Stunnenberg H, Teichmann SA, Tickle T, Villani AC, Wells C, Wold B, Yang H, Zhuang X.

Published in Nat Commun (PDF)

High-parametric protein maps reveal the spatial organization in early-developing human lung Sariyar S, Sountoulidis A, Hansen JN, Marco Salas S, Mardamshina M, Martinez Casals A, Ballllosera Navarro F, Andrusivova Z, Li X, Czarnewski P, Lundeberg J, Linnarsson S, Nilsson M, Sundström E, Samakovlis C, Lundberg E, Ayoglu B.

Published in Nat Commun (PDF)

GABAergic neuronal lineage development determines clinically actionable targets in diffuse hemispheric glioma, H3G34-mutant Liu I, Alencastro Veiga Cruzeiro G, Bjerke L, Rogers RF, Grabovska Y, Beck A, Mackay A, Barron T, Hack OA, Quezada MA, Molinari V, Shaw ML, Perez-Somarriba M, Temelso S, Raynaud F, Ruddle R, Panditharatna E, Englinger B, Mire HM, Jiang L, Nascimento A, LaBelle J, Haase R, Rozowsky J, Neyazi S, Baumgartner AC, Castellani S, Hoffman SE, Cameron A, Morrow M, Nguyen QD, Pericoli G, Madlener S, Mayr L, Dorfer C, Geyeregger R, Rota C, Ricken G, Ligon KL, Alexandrescu S, Cartaxo RT, Lau B, Uphadhyaya S, Koschmann C, Braun E, Danan-Gotthold M, Hu L, Siletti K, Sundström E, Hodge R, Lein E, Agnihotri S, Eisenstat DD, Stapleton S, King A, Bleil C, Mastronuzzi A, Cole KA, Waanders AJ, Montero Carcaboso A, Schüller U, Hargrave D, Vinci M, Carceller F, Haberler C, Slavc I, Linnarsson S, Gojo J, Monje M, Jones C, Filbin MG.

Published in Cancer Cell (PDF)

Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells Carrelha J, Mazzi S, Winroth A, Hagemann-Jensen M, Ziegenhain C, Högstrand K, Seki M, Brennan MS, Lehander M, Wu B, Meng Y, Markljung E, Norfo R, Ishida H, Belander Strålin K, Grasso F, Simoglou Karali C, Aliouat A, Hillen A, Chari E, Siletti K, Thongjuea S, Mead AJ, Linnarsson S, Nerlov C, Sandberg R, Yoshizato T, Woll PS, Jacobsen SEW.

Published in Nat Immunol (PDF)

2023

★ Comprehensive cell atlas of the first-trimester developing human brain Braun E, Danan-Gotthold M, Borm LE, Lee KW, Vinsland E, Lönnerberg P, Hu L, Li X, He X, Andrusivová Ž, Lundeberg J, Barker RA, Arenas E, Sundström E, Linnarsson S.

Published in Science (PDF)

★ Transcriptomic diversity of cell types across the adult human brain Siletti K, Hodge R, Mossi Albiach A, Lee KW, Ding SL, Hu L, Lönnerberg P, Bakken T, Casper T, Clark M, Dee N, Gloe J, Hirschstein D, Shapovalova NV, Keene CD, Nyhus J, Tung H, Yanny AM, Arenas E, Lein ES, Linnarsson S.

Published in Science (PDF)

★ Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH Borm LE, Mossi Albiach A, Mannens CCA, Janusauskas J, Özgün C, Fernández-García D, Hodge R, Castillo F, Hedin CRH, Villablanca EJ, Uhlén P, Lein ES, Codeluppi S, Linnarsson S.

Published in Nat Biotechnol (PDF)

Supporting data and visualizations.

A comparative atlas of single-cell chromatin accessibility in the human brain Li YE, Preissl S, Miller M, Johnson ND, Wang Z, Jiao H, Zhu C, Wang Z, Xie Y, Poirion O, Kern C, Pinto-Duarte A, Tian W, Siletti K, Emerson N, Osteen J, Lucero J, Lin L, Yang Q, Zhu Q, Zemke N, Espinoza S, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Hodge RD, Linnarsson S, Bakken T, Levi B, Keene CD, Shang J, Lein E, Wang A, Behrens MM, Ecker JR, Ren B.

Published in Science (PDF)

Transcriptomic cytoarchitecture reveals principles of human neocortex organization Jorstad NL, Close J, Johansen N, Yanny AM, Barkan ER, Travaglini KJ, Bertagnolli D, Campos J, Casper T, Crichton K, Dee N, Ding SL, Gelfand E, Goldy J, Hirschstein D, Kiick K, Kroll M, Kunst M, Lathia K, Long B, Martin N, McMillen D, Pham T, Rimorin C, Ruiz A, Shapovalova N, Shehata S, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Callaway EM, Hof PR, Keene CD, Levi BP, Linnarsson S, Mitra PP, Smith K, Hodge RD, Bakken TE, Lein ES.

Published in Science (PDF)

Single-cell DNA methylation and 3D genome architecture in the human brain Tian W, Zhou J, Bartlett A, Zeng Q, Liu H, Castanon RG, Kenworthy M, Altshul J, Valadon C, Aldridge A, Nery JR, Chen H, Xu J, Johnson ND, Lucero J, Osteen JK, Emerson N, Rink J, Lee J, Li YE, Siletti K, Liem M, Claffey N, O'Connor C, Yanny AM, Nyhus J, Dee N, Casper T, Shapovalova N, Hirschstein D, Ding SL, Hodge R, Levi BP, Keene CD, Linnarsson S, Lein E, Ren B, Behrens MM, Ecker JR.

Published in Science (PDF)

Comparative transcriptomics reveals human-specific cortical features Jorstad NL, Song JHT, Exposito-Alonso D, Suresh H, Castro-Pacheco N, Krienen FM, Yanny AM, Close J, Gelfand E, Long B, Seeman SC, Travaglini KJ, Basu S, Beaudin M, Bertagnolli D, Crow M, Ding SL, Eggermont J, Glandon A, Goldy J, Kiick K, Kroes T, McMillen D, Pham T, Rimorin C, Siletti K, Somasundaram S, Tieu M, Torkelson A, Feng G, Hopkins WD, Höllt T, Keene CD, Linnarsson S, McCarroll SA, Lelieveldt BP, Sherwood CC, Smith K, Walsh CA, Dobin A, Gillis J, Lein ES, Hodge RD, Bakken TE.

Published in Science (PDF)

Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration Munguba H, Nikouei K, Hochgerner H, Oberst P, Kouznetsova A, Ryge J, Muñoz-Manchado AB, Close J, Batista-Brito R, Linnarsson S, Hjerling-Leffler J.

Published in Neuron (PDF)

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin Li X, Andrusivova Z, Czarnewski P, Langseth CM, Andersson A, Liu Y, Gyllborg D, Braun E, Larsson L, Hu L, Alekseenko Z, Lee H, Avenel C, Kallner HK, Åkesson E, Adameyko I, Nilsson M, Linnarsson S, Lundeberg J, Sundström E.

Published in Nat Neurosci (PDF)

RNAget: an API to securely retrieve RNA quantifications Upchurch S, Palumbo E, Adams J, Bujold D, Bourque G, Nedzel J, Graham K, Kagda MS, Assis P, Hitz B, Righi E, Guigó R, Wold BJ; GA4GH RNA-Seq Task Team.

Published in Bioinformatics (PDF)

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung Sountoulidis A, Marco Salas S, Braun E, Avenel C, Bergenstråhle J, Theelke J, Vicari M, Czarnewski P, Liontos A, Abalo X, Andrusivová Ž, Mirzazadeh R, Asp M, Li X, Hu L, Sariyar S, Martinez Casals A, Ayoglu B, Firsova A, Michaëlsson J, Lundberg E, Wählby C, Sundström E, Linnarsson S, Lundeberg J, Nilsson M, Samakovlis C.

Published in Nat Cell Biol (PDF)

Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation Nishimura K, Yang S, Lee KW, Ásgrímsdóttir ES, Nikouei K, Paslawski W, Gnodde S, Lyu G, Hu L, Saltó C, Svenningsson P, Hjerling-Leffler J, Linnarsson S, Arenas E.

Published in Stem Cell Reports (PDF)

2022

Single-cell RNA-sequencing of mammalian brain development: insights and future directions Vinsland E, Linnarsson S.

Published in Development (PDF)

Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation Liu R, Pisco AO, Braun E, Linnarsson S, Zou J.

Published in J Mol Biol (PDF)

Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis van Bruggen D, Pohl F, Langseth CM, Kukanja P, Lee H, Albiach AM, Kabbe M, Meijer M, Linnarsson S, Hilscher MM, Nilsson M, Sundström E, Castelo-Branco G.

Published in Dev Cell (PDF)

Single nucleus multi-omics identifies human cortical cell regulatory genome diversity Luo C, Liu H, Xie F, Armand EJ, Siletti K, Bakken TE, Fang R, Doyle WI, Stuart T, Hodge RD, Hu L, Wang BA, Zhang Z, Preissl S, Lee DS, Zhou J, Niu SY, Castanon R, Bartlett A, Rivkin A, Wang X, Lucero J, Nery JR, Davis DA, Mash DC, Satija R, Dixon JR, Linnarsson S, Lein E, Behrens MM, Ren B, Mukamel EA, Ecker JR.

Published in Cell Genom (PDF)

Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preiss S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, et al.

Published in Nature (PDF)

2021

★ Molecular architecture of the developing mouse brain La Manno G, Siletti K, Furlan A, Gyllborg D, Vinsland E, Mossi Albiach A, Mattsson Langseth C, Khven I, Lederer AR, Dratva LM, Johnsson A, Nilsson M, Lönnerberg P, Linnarsson S.

Published in Nature (PDF)

Supporting data and visualizations.

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 Bakken TE, Jorstad NL, Hu Q, Lake BB, Tian W, Kalmbach BE, Crow M, Hodge RD, Krienen FM, Sorensen SA, Eggermont J, Yao Z, Aevermann BD, Aldridge AI, Bartlett A, Bertagnolli D, Casper T, Castanon RG, Crichton K, Daigle TL, Dalley R, Dee N, Dembrow N, Diep D, Ding SL, Dong W, Fang R, Fischer S, Goldman M, Goldy J, Graybuck LT, Herb BR, Hou X, Kancherla J, Kroll M, Lathia K, van Lew B, Li YE, Liu CS, Liu H, Lucero JD, Mahurkar A, McMillen D, Miller JA, Moussa M, Nery JR, Nicovich PR, Niu SY, Orvis J, Osteen JK, Owen S, Palmer CR, Pham T, Plongthongkum N, Poirion O, Reed NM, Rimorin C, Rivkin A, Romanow WJ, Sedeño-Cortés AE, Siletti K, Somasundaram S, Sulc J, Tieu M, Torkelson A, Tung H, Wang X, Xie F, Yanny AM, Zhang R, Ament SA, Behrens MM, Bravo HC, Chun J, Dobin A, Gillis J, Hertzano R, Hof PR, Höllt T, Horwitz GD, Keene CD, Kharchenko PV, Ko AL, Lelieveldt BP, Luo C, Mukamel EA, Pinto-Duarte A, Preissl S, Regev A, Ren B, Scheuermann RH, Smith K, Spain WJ, White OR, Koch C, Hawrylycz M, Tasic B, Macosko EZ, McCarroll SA, Ting JT, et al.

Published in Nature (PDF)

Supporting data and visualizations.

A roadmap for the Human Developmental Cell Atlas Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe'er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S; Human Cell Atlas Developmental Biological Network.

Published in Nature (PDF)

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine 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; LifeTime Community Working Groups.

Published in Nature (PDF)

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics 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, Torlai Triglia E, 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, et al.

Published in Nat Med (PDF)

Building a high-quality Human Cell Atlas Rozenblatt-Rosen O, Shin JW, Rood JE, Hupalowska A; Human Cell Atlas Standards and Technology Working Group; Regev A, Heyn H.

Published in Nat Biotechnol (PDF)

2020

Effects of In Vivo Gluten Challenge on PBMC Gene Expression Profiles in Diet Treated Celiac Disease Yohannes DA, de Kauwe A, Kaukinen K, Kurppa K, Mäki M, Anderson RP, Linnarsson S, Greco D, Saavalainen P.

Published in Front Immunol (PDF)

LifeTime and improving European healthcare through cell-based interceptive medicine 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; LifeTime Community Working Groups.

Published in Nature (PDF)

Srebf1 Controls Midbrain Dopaminergic Neurogenesis Toledo EM, Yang S, Gyllborg D, van Wijk KE, Sinha I, Varas-Godoy M, Grigsby CL, Lönnerberg P, Islam S, Steffensen KR, Linnarsson S, Arenas E.

Published in Cell Rep (PDF)

2019

A cell fitness selection model for neuronal survival during development 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.

Published in Nat Commun (PDF)

Remodeling of secretory lysosomes during education tunes functional potential in NK cells 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.

Published in Nat Commun (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 Mol Psychiatry (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 Nat Methods (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.

★ 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.

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 Nat Neurosci (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 Nat Neurosci (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 Nat Commun (PDF)

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 Rep (PDF)

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, et al.

Published in Nat Genet (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 Nat Genet (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 Biol (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 Nat Genet (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)

2017

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 Sci Rep (PDF)

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing Lein E, Borm LE, Linnarsson S.

Published in Science (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 Med (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)

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)

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 Sci Rep (PDF)

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

Published in Mol Syst Biol (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 Nat Biotechnol (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 Res (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 Nat Neurosci (PDF)

2016

★ Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells 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.

Published in Cell (PDF)

Supporting data and visualizations.

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, Linnarsson S, Kasper M.

Published in Cell Syst (PDF)

Supporting data and visualizations.

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, Kupari J, Usoskin D, Airaksinen MS, Oliver G, Linnarsson S, Ernfors P.

Published in Nat Neurosci (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 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.

Published in Science (PDF)

Supporting data and visualizations.

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 Nat Biotechnol (PDF)

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, Reyes AP, Linnarsson S, Sandberg R, Lanner F.

Published in Cell (PDF)

Corrigendum: 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, Petropoulos S, Einarsdottir E, Linnarsson S, Lanner F, Månsson R, Hovatta O, Bürglin TR, Katayama S, Kere J.

Published in Sci Rep (PDF)

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, Petropoulos S, Månsson R, Linnarsson S, Bürglin T, Lanner F, Hovatta O, Katayama S, Kere J.

Published in Development (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, Petropoulos S, Einarsdottir E, Linnarsson S, Lanner F, Månsson R, Hovatta O, Bürglin TR, Katayama S, Kere J.

Published in Sci Rep (PDF)

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)

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 J (PDF)

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

Published in Genome Biol (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 Nat Immunol (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)

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 Sci Rep (PDF)

2015

NEUROSCIENCE. 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)

★ 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, 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.

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)

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 Nat Neurosci (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 Nat Commun (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 J Biol Chem (PDF)

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 J (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 Biol (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 Nat Methods (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)

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)

2013

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)

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

Published in Nat Rev Genet (PDF)

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

Published in Genome Biol (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)

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)

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 Nat Protoc (PDF)

Magnetic sequencing Linnarsson S.

Published in Nat 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 J (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 Nat 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 Res (PDF)

2010

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

Published in Exp Cell Res (PDF)

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 Proc Natl Acad Sci U S A (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 Nat Biotechnol (PDF)

Older papers are available from PubMed