Joakim Lundeberg


Professor Joakim Lundeberg is part of the Department of Gene Technology, KTH and the National Genomics Infrastructure at SciLifeLab.

He developed Spatial Transcriptomics, a technology that uses spatially barcoded microarrays to enable whole-transcriptome spatially resolved RNA-sequencing in human tissues.

External homepage: https://www.spatialresearch.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

Larsson L, Frisén J, Lundeberg J. Spatially resolved transcriptomics adds a new dimension to genomics. (2021) Nature methods

Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, Köhler P, Künstner A, Rosati E, Aschenbrenner AC, Bacher P, Baran N, Boysen T, Brandt B, Bruse N, Dörr J, Dräger A, Elke G, Ellinghaus D, Fischer J, Forster M, Franke A, Franzenburg S, Frey N, Friedrichs A, Fuß J, Glück A, Hamm J, Hinrichsen F, Hoeppner MP, Imm S, Junker R, Kaiser S, Kan YH, Knoll R, Lange C, Laue G, Lier C, Lindner M, Marinos G, Markewitz R, Nattermann J, Noth R, Pickkers P, Rabe KF, Renz A, Röcken C, Rupp J, Schaffarzyk A, Scheffold A, Schulte-Schrepping J, Schunk D, Skowasch D, Ulas T, Wandinger KP, Wittig M, Zimmermann J, Busch H, Hoyer BF, Kaleta C, Heyckendorf J, Kox M, Rybniker J, Schreiber S, Schultze JL, Rosenstiel P, Banovich NE, Desai T, Eickelberg O, Haniffa M, Horvath P, Kropski JA, Lafyatis R, Lundeberg J, Meyer K, Nawijn MC, Nikolic M, Ordovas Montanes J, Pe’er D, Tata PR, Rawlins E, Regev A, Reyfman P, Samakovlis C, Schultze J, Shalek A, Shepherd D, Spence J, Teichmann S, Theis F, Tsankov A, van den Berge M, von Papen M, Whitsett J, Zaragosi LE, Angelov A, Bals R, Bartholomäus A, Becker A, Bezdan D, Bonifacio E, Bork P, Clavel T, Colme-Tatche M, Diefenbach A, Dilthey A, Fischer N, Förstner K, Frick JS, Gagneur J, Goesmann A, Hain T, Hummel M, Janssen S, Kalinowski J, Kallies R, Kehr B, Keller A, Kim-Hellmuth S, Klein C, Kohlbacher O, Korbel JO, Kurth I, Landthaler M, Li Y, Ludwig K, Makarewicz O, Marz M, McHardy A, Mertes C, Nöthen M, Nürnberg P, Ohler U, Ossowski S, Overmann J, Peter S, Pfeffer K, Poetsch AR, Pühler A, Rajewsky N, Ralser M, Rieß O, Ripke S, Nunes da Rocha U, Rosenstiel P, Saliba AE, Sander LE, Sawitzki B, Schiffer P, Schulte EC, Schultze JL, Sczyrba A, Stegle O, Stoye J, Theis F, Vehreschild J, Vogel J, von Kleist M, Walker A, Walter J, Wieczorek D, Ziebuhr J. Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. (2020) Immunity

Llorens-Bobadilla E, Chell JM, Le Merre P, Wu Y, Zamboni M, Bergenstråhle J, Stenudd M, Sopova E, Lundeberg J, Shupliakov O, Carlén M, Frisén J. A latent lineage potential in resident neural stem cells enables spinal cord repair. (2020) Science (New York, N.Y.)

Ji AL, Rubin AJ, Thrane K, Jiang S, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. (2020) Cell

Tucker NR, Chaffin M, Bedi KC, Papangeli I, Akkad AD, Arduini A, Hayat S, Eraslan G, Muus C, Bhattacharyya RP, Stegmann CM, Margulies KB, Ellinor PT, Banovich NE, Barbry P, Black KE, Brazma A, Collin J, Conrad C, Desai T, Duong TE, Eickelberg O, Eils R, Faiz A, Falk C, Farzan M, Glass I, Haniffa M, Horvath P, Hubner N, Hung D, Kaminski N, Koppelman G, Krasnow M, Kropski JA, Kuhnemund M, Lafyatis R, Lako M, Lee H, Leroy S, Linnarson S, Lundeberg J, Medoff B, Meyer K, Miao C, Misharin A, Nawijn M, Nikolic M, Noseda M, Montanes JO, Oudit G, Pe’er D, Powell J, Quake S, Rajagopal J, Rao Tata P, Rawlins E, Regev A, Reyfman P, Rojas M, Rosenblatt-Rosen O, Saeb-Parsy K, Samakovlis C, Schiller H, Schultze J, Schwarz R, Segre A, Seibold M, Seidman J, Seidman C, Shalek A, Shepherd D, Spence J, Spira A, Sun X, Sundström E, Teichmann S, Theis F, Tsankov A, Vallier L, van den Berge M, Whitsett J, Xavier R, Xu Y, Zaragosi LE, Zerti D, Zhang K, Zhang H. NA (2020) Circulation

Chen WT, Lu A, Craessaerts K, Pavie B, Sala Frigerio C, Corthout N, Qian X, Laláková J, Kühnemund M, Voytyuk I, Wolfs L, Mancuso R, Salta E, Balusu S, Snellinx A, Munck S, Jurek A, Fernandez Navarro J, Saido TC, Huitinga I, Lundeberg J, Fiers M, De Strooper B. Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease. (2020) Cell

Ortiz C, Navarro JF, Jurek A, Märtin A, Lundeberg J, Meletis K. Molecular atlas of the adult mouse brain. (2020) Science advances

Ji AL, Rubin AJ, Thrane K, Jiang S, Reynolds DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhle J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Hollmig ST, Aasi SZ, Nolan GP, Lundeberg J, Khavari PA. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. (2020) Cell

He B, Bergenstråhle L, Stenbeck L, Abid A, Andersson A, Borg Å, Maaskola J, Lundeberg J, Zou J. Integrating spatial gene expression and breast tumour morphology via deep learning. (2020) Nature biomedical engineering

Ziegler CGK, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth MH, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Wang JP, Gras D, Plaisant M, Ansari M, Angelidis I, Adler H, Sucre JMS, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi LE, Barbry P, Leslie A, Kiem HP, Flynn JL, Fortune SM, Berger B, Finberg RW, Kean LS, Garber M, Schmidt AG, Lingwood D, Shalek AK, Ordovas-Montanes J, Banovich N, Barbry P, Brazma A, Desai T, Duong TE, Eickelberg O, Falk C, Farzan M, Glass I, Haniffa M, Horvath P, Hung D, Kaminski N, Krasnow M, Kropski JA, Kuhnemund M, Lafyatis R, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer K, Misharin A, Nawijn M, Nikolic MZ, Ordovas-Montanes J, Pe’er D, Powell J, Quake S, Rajagopal J, Tata PR, Rawlins EL, Regev A, Reyfman PA, Rojas M, Rosen O, Saeb-Parsy K, Samakovlis C, Schiller H, Schultze JL, Seibold MA, Shalek AK, Shepherd D, Spence J, Spira A, Sun X, Teichmann S, Theis F, Tsankov A, van den Berge M, von Papen M, Whitsett J, Xavier R, Xu Y, Zaragosi LE, Zhang K. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues. (2020) Cell

Sungnak W, Huang N, Bécavin C, Berg M, Queen R, Litvinukova M, Talavera-López C, Maatz H, Reichart D, Sampaziotis F, Worlock KB, Yoshida M, Barnes JL, Banovich NE, Barbry P, Brazma A, Collin J, Desai TJ, Duong TE, Eickelberg O, Falk C, Farzan M, Glass I, Gupta RK, Haniffa M, Horvath P, Hubner N, Hung D, Kaminski N, Krasnow M, Kropski JA, Kuhnemund M, Lako M, Lee H, Leroy S, Linnarson S, Lundeberg J, Meyer KB, Miao Z, Misharin AV, Nawijn MC, Nikolic MZ, Noseda M, Ordovas-Montanes J, Oudit GY, Pe’er D, Powell J, Quake S, Rajagopal J, Tata PR, Rawlins EL, Regev A, Reyfman PA, Rozenblatt-Rosen O, Saeb-Parsy K, Samakovlis C, Schiller HB, Schultze JL, Seibold MA, Seidman CE, Seidman JG, Shalek AK, Shepherd D, Spence J, Spira A, Sun X, Teichmann SA, Theis FJ, Tsankov AM, Vallier L, van den Berge M, Whitsett J, Xavier R, Xu Y, Zaragosi LE, Zerti D, Zhang H, Zhang K, Rojas M, Figueiredo F. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. (2020) Nature medicine

Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. (2019) Cell

Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL. High-definition spatial transcriptomics for in situ tissue profiling. (2019) Nature methods

Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivová Ž, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. (2019) Science (New York, N.Y.)

Newton PT, Li L, Zhou B, Schweingruber C, Hovorakova M, Xie M, Sun X, Sandhow L, Artemov AV, Ivashkin E, Suter S, Dyachuk V, El Shahawy M, Gritli-Linde A, Bouderlique T, Petersen J, Mollbrink A, Lundeberg J, Enikolopov G, Qian H, Fried K, Kasper M, Hedlund E, Adameyko I, Sävendahl L, Chagin AS. A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate. (2019) Nature

Giacomello S, Lundeberg J. Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays. (2018) Nature protocols

Salmén F, Ståhl PL, Mollbrink A, Navarro JF, Vickovic S, Frisén J, Lundeberg J. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections. (2018) Nature protocols

Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmén F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. (2018) Nature communications

Dias DO, Kim H, Holl D, Werne Solnestam B, Lundeberg J, Carlén M, Göritz C, Frisén J. Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury. (2018) Cell

Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J. Spatially resolved transcriptome profiling in model plant species. (2017) Nature plants

Zhu Y, Engström PG, Tellgren-Roth C, Baudo CD, Kennell JC, Sun S, Billmyre RB, Schröder MS, Andersson A, Holm T, Sigurgeirsson B, Wu G, Sankaranarayanan SR, Siddharthan R, Sanyal K, Lundeberg J, Nystedt B, Boekhout T, Dawson TL, Heitman J, Scheynius A, Lehtiö J. Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis. (2017) Nucleic acids research

Vickovic S, Ståhl PL, Salmén F, Giatrellis S, Westholm JO, Mollbrink A, Navarro JF, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J. Massive and parallel expression profiling using microarrayed single-cell sequencing. (2016) Nature communications

Linde C, Eriksson MJ, Hage C, Wallén H, Persson B, Corbascio M, Lundeberg J, Maret E, Ugander M, Persson H. Rationale and design of the PREFERS (Preserved and Reduced Ejection Fraction Epidemiological Regional Study) Stockholm heart failure study: an epidemiological regional study in Stockholm county of 2.1 million inhabitants. (2016) European journal of heart failure

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.)

Gréen H, Hasmats J, Kupershmidt I, Edsgärd D, de Petris L, Lewensohn R, Blackhall F, Vikingsson S, Besse B, Lindgren A, Brandén E, Koyi H, Peterson C, Lundeberg J. Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities. (2015) Clinical cancer research : an official journal of the American Association for Cancer Research

Stödberg T, McTague A, Ruiz AJ, Hirata H, Zhen J, Long P, Farabella I, Meyer E, Kawahara A, Vassallo G, Stivaros SM, Bjursell MK, Stranneheim H, Tigerschiöld S, Persson B, Bangash I, Das K, Hughes D, Lesko N, Lundeberg J, Scott RC, Poduri A, Scheffer IE, Smith H, Gissen P, Schorge S, Reith ME, Topf M, Kullmann DM, Harvey RJ, Wedell A, Kurian MA. Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures. (2015) Nature communications

Sahlén P, Abdullayev I, Ramsköld D, Matskova L, Rilakovic N, Lötstedt B, Albert TJ, Lundeberg J, Sandberg R. Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution. (2015) Genome biology

Huttner HB, Bergmann O, Salehpour M, Rácz A, Tatarishvili J, Lindgren E, Csonka T, Csiba L, Hortobágyi T, Méhes G, Englund E, Solnestam BW, Zdunek S, Scharenberg C, Ström L, Ståhl P, Sigurgeirsson B, Dahl A, Schwab S, Possnert G, Bernard S, Kokaia Z, Lindvall O, Lundeberg J, Frisén J. The age and genomic integrity of neurons after cortical stroke in humans. (2014) Nature neuroscience

Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin YC, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller M, Luthman J, Lysholm F, Niittylä T, Olson A, Rilakovic N, Ritland C, Rosselló JA, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu ZQ, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S. The Norway spruce genome sequence and conifer genome evolution. (2013) Nature

Akan P, Alexeyenko A, Costea PI, Hedberg L, Solnestam BW, Lundin S, Hällman J, Lundberg E, Uhlén M, Lundeberg J. Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines. (2012) Genome medicine

Ståhl PL, Lundeberg J. Toward the single-hour high-quality genome. (2012) Annual review of biochemistry

Bjursell MK, Blom HJ, Cayuela JA, Engvall ML, Lesko N, Balasubramaniam S, Brandberg G, Halldin M, Falkenberg M, Jakobs C, Smith D, Struys E, von Döbeln U, Gustafsson CM, Lundeberg J, Wedell A. Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function. (2011) American journal of human genetics

Seidel S, Garvalov BK, Wirta V, von Stechow L, Schänzer A, Meletis K, Wolter M, Sommerlad D, Henze AT, Nistér M, Reifenberger G, Lundeberg J, Frisén J, Acker T. A hypoxic niche regulates glioblastoma stem cells through hypoxia inducible factor 2 alpha. (2010) Brain : a journal of neurology