Publications

Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues
Marco Vicari, Reza Mirzazadeh, Anna Nilsson, Reza Shariatgorji, Patrik Bjärterot, Ludvig Larsson, Hower Lee, Mats Nilsson, Julia Foyer, Markus Ekvall, Paulo Czarnewski, Xiaoqun Zhang, Per Svenningsson, Per E. Andrén, Joakim Lundeberg
Available at bioRxiv (27 Jan 2023)

An integrated single cell and spatial transcriptomic map of human white adipose tissue
Massier L, Jalkanen J, Elmastas M, Zhong J, Wang T, Nono Nankam PA, Frendo-Cumbo S, Bäckdahl J, Subramanian N, Sekine T, Kerr AG, Tseng BTP, Laurencikiene J, Buggert M, Lourda M, Kublickiene K, Bhalla N, Andersson A, Valsesia A, Astrup A, Blaak EE, Ståhl PL, Viguerie N, Langin D, Wolfrum C, Blüher M, Rydén M, Mejhert N
Nature Communications (15 Mar 2023)

Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
Mirzazadeh R, Andrusivova Z, Larsson L, Newton P, Alonso Galicia L,  Abalo XM, Avijgan M, Kvastad L, Denadai-Souza A, Stakenborg N, Firsova AB, Shamikh A, Jurek A, Schultz N, Nister M, Samakovlis C, Boeckxstaens G, Lundeberg J
Nature Communications (31 Jan 2023) (bioRxiv 2022)

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
Nature Cell Biology (16 Jan 2023) (bioRxiv 2022)

Solid-phase capture and profiling of open chromatin by spatial atac
Llorens-Bobadilla E, Zamboni M, Marklund M, Bhalla N, Chen X, Hartman J, Frisén J, Ståhl PL
Nature Biotechnology (5 Jan 2023) (bioRxiv 2022)

Expansion Spatial Transcriptomics
Yuhang Fan, Žaneta Andrusivová, Yunming Wu, Chew Chai, Ludvig Larsson, Mengxiao He, Liqun Luo, Joakim Lundeberg, Bo Wang
Available at bioRxiv (25 Oct 2022)

Decoding spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
Li X, Andrusivova Z, Czarnewski P, Mattsson Langseth C, Andersson A, Liu Y, Gyllborg D, Braun E, Larsson L, Hu L, Alekseenko Z, Lee H, Avenel C, Kopp Kallner H, Åkesson E, Adameyko I, Nilsson M, Linnarsson S, Lundeberg J, Sundström E
Available at bioRxiv (3 Sept 2022)

Spatially resolved host-bacteria-fungi interactomes via spatial metatranscriptomics
Sami Saarenpää, Or Shalev, Haim Ashkenazy, Vanessa de Oliveira-Carlos, Derek Severi Lundberg, Detlef Weigel, Stefania Giacomello
Available at bioRxiv (July 2022)

Lokatt: A hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network
Xuechun Xu, Nayanika Bhalla, Patrik Ståhl, Joakim Jaldén
Available at bioRxiv (July 2022)

Integration of single-cell RNA and protein data identifies novel clinically-relevant lymphocyte phenotypes in breast cancers
Al-Eryani G, Bartonicek N, Chan CL, Anderson A, Harvey K, Wu SZ, Roden D, Wang T, Reeves J, Yeung BZ, Masle-Farquhar E,  Goodnow CC, Ma C, Phan TG, Lundeberg J, Junankar S, Swarbrick A
Available at bioRxiv (31 May 2022)

Dual spatially resolved transcriptomics for SARS-CoV-2 host-pathogen colocalization studies in humans
Sounart H, Lázár E, Masarapu Y, Wu J, Várkonyi T, Glasz T, Kiss A, Borgström E, Hill A, Jurek A, Niesnerová A, Druid H, Bergmann O, Giacomello S
Available at bioRxiv (15 Mar 2022)

The spatial landscape of gene expression isoforms in tissue sections
Lebrigand K, Bergenstråhle J, Thrane K, Mollbrink A, Barbry P, Waldmann R, & Lundeberg J
Available at bioRxiv (Jan 2022)

Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones
Marklund M, Schultz N, Friedrich S, Berglund E, Tarish F, Tanoglidi A, Liu Y, Bergenstråhle L, Erickson A, Helleday T, Lamb AD, Sonnhammer E, Lundeberg J.
Nature Communication (17 Sep 2022)

The discovAIR project: a roadmap towards the Human Lung Cell Atlas
Malte D. Luecken, Laure-Emmanuelle Zaragosi, Elo Madissoon, Lisa Sikkema, Alexandra B. Firsova, Elena De Domenico, Louis Kümmerle, Adem Saglam, Marijn Berg, Aurore C.A. Gay, Janine Schniering, Christoph H. Mayr, Xesús M. Abalo, Ludvig Larsson, Alexandros Sountoulidis, Sarah A. Teichmann, Karen van Eunen, Gerard H. Koppelman, Kourosh Saeb-Parsy, Sylvie Leroy, Pippa Powell, Ugis Sarkans, Wim Timens, Joakim Lundeberg, Maarten van den Berge, Mats Nilsson, Peter Horváth, Jessica Denning, Irene Papatheodorou, Joachim L. Schultze, Herbert B. Schiller, Pascal Barbry, Ilya Petoukhov, Alexander V. Misharin, Ian M. Adcock, Michael von Papen, Fabian J. Theis, Christos Samakovlis, Kerstin B. Meyer, Martijn C. Nawijn
European Respiratory Journal (18 Aug 2022)

The spatial landscape of clonal somatic mutations in benign and malignant tissue
Andrew Erickson, Emelie Berglund, Mengxiao He, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Ludvig Bergenstråhle, Linda Kvastad, Alma Andersson, Joseph Bergenstråhle, Ludvig Larsson, Alia Shamikh, Elisa Basmaci, Teresita Diaz De Ståhl, Timothy Rajakumar, Kim Thrane, Andrew L Ji, Paul A Khavari, Firaz Tarish, Anna Tanoglidi, Jonas Maaskola, Richard Colling, Tuomas Mirtti, Freddie C Hamdy, Dan J Woodcock, Thomas Helleday, Ian G. Mills, Alastair D Lamb, Joakim Lundeberg
Nature (10 Aug 2022) (bioRxiv, 2021)

SnapShot: Spatial transcriptomics
Larsson L, Bergenstråhle L, He M, Andrusivova Z, Lundeberg J
Cell (21 Jul 2022)

Identification of early neurodegenerative pathways in progressive multiple sclerosis
Kaufmann M, Schaupp AL, Sun R, Coscia F, Dendrou CA, Cortes A, Kaur G, Evans HG, Mollbrink A, Navarro JF, Sonner JK, Mayer C, DeLuca GC, Lundeberg J, Matthews PM, Attfield KE, Friese MA, Mann M, Fugger L
Nature Neuroscience (20 Jul 2022)

Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis
Hardt U, Carlberg K, Af Klint E, Sahlström P, Larsson L, van Vollenhoven A, Hernandez Machado S, Israelsson L, Amara K, Chemin K, Korotkova M, Karlsson Hedestam GB, Catrina AI, Teichmann SA, Ståhl PL, Malmström V
Scientific Reports (13 Jul 2022)

Enabling automated and reproducible spatially resolved transcriptomics at scale
Stenbeck L, Taborsak-Lines F, Giacomello S
Heliyon (11 Jun 2022)

Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
Ratz M, von Berlin L, Larsson L, Martin M, Orzechowski Westholm J, La Manno G, Lundeberg J, Frisén J
Nature Neuroscience (24 Feb 2022) (bioRxiv 2021)

Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium
Vickovic S, Schapiro D, Carlberg K, Lötstedt B, Larsson L, Hildebrandt F, Korotkova M, Hensvold AH, Catrina AI, Sorger PK, Malmström V, Regev A, Ståhl PL
Communications Biology (11 Feb 2022)

The spatial transcriptomic landscape of the healing intestine following damage
Parigi SM, Larsson L, Das S, Ramirez Flores RO, Frede A, Tripathi KP, Diaz OE, Selin K, Morales RA, Luo X, Monasterio G, Engblom C, Gagliani N, Saez-Rodriguez J, Lundeberg J, Villablanca EJ
Nature Communications (11 Feb 2022)

Genome-wide spatial expression profiling in formalin-fixed tissues
Gracia Villacampa E, Larsson L, Mirzazadeh R, Kvastad L, Andersson A, Mollbrink A, Kokaraki G, Monteil V, Schultz N, Appelberg KS, Montserrat N, Zhang H, Penninger JM, Miesbach W, Mirazimi A, Carlson J & Lundeberg J
Cell Genomics (8 Dec 2021) (bioRxiv 2020)

Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver
Hildebrandt F, Andersson A, Saarenpää S, Larsson L, Van Hul N, Kanatani S, Masek J, Ellis E, Barragan A, Mollbrink A, Andersson ER, Lundeberg J, Ankarklev J
Nature Communications (2 Dec 2021)

Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma
Yang M, Johnsson P, Bräutigam L, Yang XR, Thrane K, Gao J, Tobin NP, Zhou Y, Yu R, Nagy N, Engström PG, Tuominen R, Eriksson H, Lundeberg J, Tucker MA, Goldstein AM, Egyhazi-Brage S, Zhao J, Cao Y, Höiom V
Genetic Medicine (30 Nov 2021)

Super-resolved spatial transcriptomics by deep data fusion
Bergenstråhle L, He B, Bergenstråhle J, Abalo X, Mirzazadeh R, Thrane K, Ji AL, Andersson A, Larsson L, Stakenborg N, Boeckxstaens G, Khavari P, Zou J, Lundeberg J, Maaskola J.
Nature Biotechnology (29 Nov 2021)

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
Andersson A, Larsson L, Stenbeck L, Salmén F, Ehinger A, Wu SZ, Al-Eryani G, Roden D, Swarbrick A, Borg Å, Frisén J, Engblom C, Lundeberg J
Nature Communications (14 Oct 2021)

Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer
Chelebian E, Avenel C, Kartasalo K, Marklund M, Tanoglidi A, Mirtti T, Colling R, Erickson A, Lamb AD, Lundeberg J, Wählby C
Cancers (28 Sep 2021)

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
Nature (Sep 2021)

A single-cell and spatially resolved atlas of human breast cancers
Wu SZ, Al-Eryani G, Roden DL, Junankar S, Harvey K, Andersson A, Thennavan A, Wang C, Torpy JR, Bartonicek N, Wang T, Larsson L, Kaczorowski D, Weisenfeld NI, Uytingco CR, Chew JG, Bent ZW, Chan CL, Gnanasambandapillai V, Dutertre CA, Gluch L, Hui MN, Beith J, Parker A, Robbins E, Segara D, Cooper C, Mak C, Chan B, Warrier S, Ginhoux F, Millar E, Powell JE, Williams SR, Liu XS, O’Toole S, Lim E, Lundeberg J, Perou CM, Swarbrick A
Nature Genetics (Sep 2021)

Vision, challenges and opportunities for a Plant Cell Atlas
Plant Cell Atlas Consortium, Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JA, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY
Elife (7 Sep 2021)

Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin
Bäckdahl J, Franzén L, Massier L, Li Q, Jalkanen J, Gao H, Andersson A, Bhalla N, Thorell A, Rydén M, Ståhl PL, Mejhert N
Cell Metabolism (10 Aug 2021)

Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans
Mold JE, Modolo L, Hård J, Zamboni M, Larsson AJM, Stenudd M, Eriksson CJ, Durif G, Ståhl PL, Borgström E, Picelli S, Reinius B, Sandberg R, Réu P, Talavera-Lopez C, Andersson B, Blom K, Sandberg JK, Picard F, Michaëlsson J, Frisén J
Cell Reports (25 May 2021)

Single cell and spatial transcriptomics in human tendon disease indicate dysregulated immune homeostasis
Akbar M, MacDonald L, Crowe LAN, Carlberg K, Kurowska-Stolarska M, Ståhl PL, Snelling SJB, McInnes IB, Millar NL
Ann Rheum Dis. (17 May 2021)

A new era for plant science: spatial single-cell transcriptomics
Giacomello S
Current Opinion in Plant Biology (26 Apr 2021)

sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling
Andersson A, Lundeberg J
Oxford Bioinformatics (11 March 2021)

The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
Kvastad L, Carlberg K, Larsson L, Villacampa EG, Stuckey A, Stenbeck L, Mollbrink A, Zamboni M, Magnusson JP, Basmaci E, Shamikh A, Prochazka G, Schaupp AL, Borg Å, Fugger L, Nistér M, Lundeberg J
Communications Biology (8 Jan 2021)

Spatially resolved transcriptomics adds a new dimension to genomics
Larsson L, Frisén J, Lundeberg J
Nature Methods (6 Jan 2021)

A Landmark-based Common Coordinate Framework for Spatial Transcriptomics Data
Andersson A, Andrusivová Z, Czarnewski P, Li X, Sundström E, Lundeberg J
Available at bioRxiv (Nov 2021)

Single-Stranded Oligonucleotide-Mediated Inhibition of Respiratory Syncytial Virus Infection
Pålsson SA, Dondalska A, Bergenstråhle J, Rolfes C, Björk A, Sedano L, Power UF, Rameix-Welti MA, Lundeberg J, Wahren-Herlenius M, Mastrangelo P, Eleouet JF, Le Goffic R, Galloux M, Spetz AL
Frontiers in Immunology (8 Dec 2020)

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography
Andersson A, Bergenstråhle J, Asp M, Bergenstråhle L, Jurek A, Fernández Navarro J, & Lundeberg J
Communiations Biology (9 Oct 2020)

A latent lineage potential in resident neural stem cells enables spinal cord repair
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
Science (2 Oct 2020)

Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease
Navarro JF, Croteau DL, Jurek A, Andrusivova Z, Yang B, Wang Y, Ogedegbe B, Riaz T, Støen M, Desler C, Rasmussen LJ, Tønjum T, Galas MC, Lundeberg J, Bohr VA
iScience (15 Sep 2020)

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease
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
Cell (20 Aug 2020)

Seamless integration of image and molecular analysis for spatial transcriptomics workflows
Bergenstråhle J, Larsson L, & Lundeberg J
BMC Genomics (14 July 2020)

Molecular Atlas Of The Adult Mouse Brain
Ortiz C, Navarro JF, Jurek A, Märtin A, Lundeberg J, & Meletis K.
Science advances (26 June 2020)

Integrating Spatial Gene Expression and Breast Tumour Morphology via Deep Learning
He B, Bergenstråhle L, Stenbeck L, Abid A, Andersson A, Borg Å, Maaskola J, Lundeberg J, & Zou J
Nature biomedical engineering (22 June 2020)

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Ji AL, Rubin AJ, Thrane K, Jiang S, Reynold DL, Meyers RM, Guo MG, George BM, Mollbrink A, Bergenstråhl J, Larsson L, Bai Y, Zhu B, Bhaduri A, Meyers JM, Rovira-Clavé X, Tyler Hollmig S, Aasi SZ, Nolan GP, Lundeberg J & Khavari PA
Cell (23 June 2020)

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration
Asp M, Bergenstråhle J & Lundeberg J
BioEssays (04 May 2020)

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
Bergenstråhle J, Bergenstråhle L & Lundeberg J
BMC Bioinformatics (29 April 2020)

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues
Berglund E, Saarenpää S, Jemt A, Gruselius J, Larsson L, Bergenstråhle L, Lundeberg J & Giacomello S
BMC Genomics (15 April 2020)

Identification and Transfer of Spatial Transcriptomics Signatures for Cancer Diagnosis
Yoosuf N, Navarro JF, Salmén F, Ståhl PL, Daub CO
Breast Cancer Res. (13 January 2020)

Sequencing degraded RNA addressed by 3′ tag counting
Sigurgeirsson B, Emanuelsson O, Lundeberg J
PLoS One (2014)

TagGD: fast and accurate software for DNA Tag generation and demultiplexing
Costea PI, Lundeberg J, Akan P
PLoS One (2013)