Publications

Preprints 2024


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 Sacals A, Ballllosera Navarro F, Andrusivova Z, Li X, Czarnewski P, Lundeberg J, Linnarsson S, Nilsson M, Sundstrom E, Samakovlis C, Lundberg E, Ayoglu B
bioRxiv, 25 Jan 2024

2023


Gene expression of single cells mapped in tissue sections
Ståhl PL
Nature (13 Dec 2023)

Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics
Engblom C, Thrane K, Lin Q, Andersson A, Toosi H, Chen X, Steiner E, Lu C, Mantovani G, Hagemann-Jensen M, Saarenpää S, Jangard M, Saez-Rodriguez J, Michaëlsson J, Hartman J, Lagergren J, Mold JE, Lundeberg J, Frisén J
Science (8 Dec 2023)

Lokatt: A hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network
Xu X, Bhalla N, Ståhl PL, Jaldén J
BMC Bioinformatics (7 Dec 2023) (bioRxiv, July 2022)

Spatial metatranscriptomics resolves host–bacteria–fungi interactomes
Saarenpää S, Shalev O, Ashkenazy H, Carlos V, Severi Lundberg D, Weigel D, Giacomello S
Nature Biotechnology (20 Nov 2023) (bioRxiv, July 2022)

Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections
Sounart H, Lázár E, Masarapu Y, Wu J, Várkonyi T, Glasz T, Kiss A, Borgström E, Hill A, Rezene S, Gupta S, Jurek A, Niesnerová A, Druid H, Bergmann O, Giacomello S
Genome Biology (19 Oct 2023) (bioRxiv, Mar 2022)

Semla: A versatile toolkit for spatially resolved transcriptomics analysis and visualization
Larsson L, Franzén L, Ståhl PL, Lundeberg J
Bioinformatics (16 Oct 2023)

Miniature spatial transcriptomics for studying parasite-endosymbiont relationships at the micro scale
Sounart H, Voronin D, Masarapu Y, Chung M, Saarenpää S, Ghedin E, Giacomello S
Nature Communication (14 Oct 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
Science (13 Oct 2023)

Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues
Vicari M, Mirzazadeh R, Nilsson A, Shariatgorji R, Bjärterot P, Larsson L, Lee H, Nilsson M, Foyer J, Ekvall M, Czarnewski P, Zhang X, Svenningsson P, Käll L, Andrén PE, Lundeberg J
Nature Biotechnology (4 Sept 2023) (bioRxiv, 27 Jan 2023)

Enhancing European capabilities for application of multi-omics studies in biology and biomedicine space research
Manzano A, Weging S, Bezdan D, Borg J, Cahill T, Carnero-Diaz E, Cope H, Deane CS, Etheridge T, Giacomello S, Hardiman G, Leys N, Madrigal P, Mastroleo F, Medina FJ, Mieczkowski J, Fernandez-Rojo MA, Siew K, Szewczyk NJ, Walsh SB, da Silveira WA, Herranz R 
iScience (12 July 2023)

Spatial transcriptomics of human placentas reveal distinct RNA patterns associated with morphology and preeclampsia
Bhalla N, Franzén L, Scheynius A, Papadogiannakis N, Hansson SR, Lager S, Ståhl PL
Placenta (05 July 2023)

Expansion Spatial Transcriptomics
Fan Y, Andrusivová Ž, Wu Y, Chai C, Larsson L, He M, Luo L, Lundeberg J, Wang B
Nature Methods (22 Jun 2023) (bioRxiv, 25 Oct 2022)

Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells
Thrane K, Winge MCG, Wang H, Chen L, Guo MG, Andersson A, Abalo XM, Yang X, Kim DS, Longo SK, Soong BY, Meyers JM, Reynolds DL, McGeever A, Demircioglu D, Hasson D, Mirzazadeh R, Rubin AJ, Bae GH, Karkanias J, Rieger K, Lundeberg J, Ji AL
J Invest Dermatol (2 May 2023)

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin
Li X, Andrusivová Ž, 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
Nature Neuroscience (24 Apr 2023) (bioRxiv, 3 Sept 2022)

The spatial landscape of gene expression isoforms in tissue sections
Lebrigand K, Bergenstråhle J, Thrane K, Mollbrink A, Meletis K, Barbry P, Waldmann R, Lundeberg J
Nucleic Acids Research (17 Mar 2023) (bioRxiv, Jan 2022)

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 LAbalo 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)

High cardiomyocyte diversity in human early prenatal heart development
Sylvén C, Wärdell E, Månsson-Broberg A, Cingolani E, Ampatzis K, Larsson L, Björklund Å, Giacomello S
iScience (20 Jan 2023)

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)

Preprints 2023

Translational mapping of spatially resolved transcriptomes in human and mouse pulmonary fibrosis
Franzén L, Olsson Lindvall M, Hühn M, Ptasinski V, Setyo L, Keith B, Collin A, Oag S, Volckaert T, Borde A, Lundeberg J, Lindgren J, Belfield G, Jackson S, Ollerstam A, Stamou M, Ståhl PL, Hornberg JJ
bioRxiv, 22 Dec 2023

Host-Pathogen Interactions in the Plasmodium-Infected Mouse Liver at Spatial and Single-Cell Resolution
Hildebrandt F, Urrutia-Iturritza M, Zwicker C, Vanneste B, Van Hul N, Semle E, Pascini T, Saarenpää S, He M, Andersson ER, Scott L, Vega-Rodriguez J, Lundeberg J, Ankarklev J
bioRxiv, 22 Dec 2023

snPATHO-seq: unlocking the pathology archives
Taopeng Wang, Kate Harvey, Javier Escudero Morlanes, Beata Kiedik, Ghamdan Al-Eryani, Alissa Greenwald, Nikolaos Kalavros, Felipe Segato Dezem, Yuling Ma, Yered H. Pita-Juarez, Kellie Wise, Cyril Degletagne, Anna Elz, Azi Hadadianpour, Jack Johanneson, Fiona Pakiam, Heeju Ryu, Evan W. Newell, Laurie Tonon, Andrew Kohlway, Tingsheng Drennon, Jawad Abousoud, Ryan Stott, Paul Lund, Jens Durruthy, Andres F Vallejo, Dominik Kaczorowski, Joanna Warren, Lisa M. Butler, Sandra O’Toole, Jasmine Plummer, Ioannis S Vlachos, Joakim Lundeberg, Alexander Swarbrick, Luciano Martelotto
bioRxiv, 8 Dec 2023

Spatially resolved multiomics on the neuronal effects induced by spaceflight
Yuvarani Masarapu, Egle Cekanaviciute, Zaneta Andrusivova, Jakub Orzechowski Westholm, Åsa Björklund, Robin Fallegger, Pau Badia-i-Mompel, Valery Boyko, Shubha Vasisht, Amanda Saravia-Butler, Samrawit Gebre, Enikö Lázár, Olaf Bergmann, Deanne Taylor, Douglas Wallace, Christer Sylvén, Julio Saez Rodriguez, Jonathan Galazka, Sylvain Costes, Stefania Giacomello
Research Square, 30 May 2023

Spatial landmark detection and tissue registration with deep learning
Ekvall M, Bergenstråhle L, Andersson A, Czarnewski P, Olegård J, Käll L, Lundeberg J
bioRxiv, 26 Aug 2023

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton
Vesna Grujcic, Sami Saarenpää, John Sundh, Bengt Sennblad, Benjamin Norgren, Meike Latz, Stefania Giacomello, Rachel A Foster, Anders F Andersson
bioRxiv, 29 March 2023

Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of heterogeneity on genomic signature scoring
Sandy Figiel, Wencheng Yin, Dimitrios Doultsinos, Andrew Erickson, Ninu Poulose, Reema Singh, Anette Magnussen, Thineskrishna Anbarasan, Renuka Teague, Mengxiao He, Joakim Lundeberg, Massimo Loda, Clare Verrill, Richard Colling, Pelvender S. Gill, Richard J. Bryant, Freddie C. Hamdy, Dan J. Woodcock, Ian G. Mills, Olivier Cussenot, Alastair D. Lamb
bioRxiv, 10 March 2023

Learning Stationary Markov Processes with Contrastive Adjustment
Ludvig Bergenstråhle, Jens Lagergren, Joakim Lundeberg
arXiv, 9 March 2023

2022


Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight
Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S
Cell Reports Methods (31 Oct 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
Luecken MD, Zaragosi LE, Madissoon E, Sikkema L, Firsova AB, De Domenico E, Kümmerle L, Saglam A, Berg M, Gay ACA, Schniering J, Mayr CH, Abalo XM, Larsson L, Sountoulidis A, Teichmann SA, van Eunen K, Koppelman GH, Saeb-Parsy K, Leroy S, Powell P, Sarkans U, Timens W, Lundeberg J, van den Berge M, Nilsson M, Horváth P, Denning J, Papatheodorou I, Schultze JL, Schiller HB, Barbry P, Petoukhov I, Misharin AV, Adcock IM, von Papen M, Theis FJ, Samakovlis C, Meyer KB, Nawijn MC
European Respiratory Journal (18 Aug 2022)

Spatially resolved clonal copy number alterations in benign and malignant tissue
Erickson A, He M, Berglund E, Marklund M, Mirzazadeh R, Schultz N, Kvastad L, Andersson A, Bergenstråhle L, Bergenstråhle J, Larsson L, Alonso Galicia L, Shamikh A, Basmaci E, Díaz De Ståhl T, Rajakumar T, Doultsinos D, Thrane K, Ji AL, Khavari PA, Tarish F, Tanoglidi A, Maaskola J, Colling R, Mirtti T, Hamdy FC, Woodcock DJ, Helleday T, Mills IG, Lamb AD, Lundeberg J
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)

Preprints 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)

2021


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)

Preprints 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)

2020


A New Era for Space Life Science: International Standards for Space Omics Processing
Rutter L, Barker R, Bezdan D, Cope H, Costes SV, Degoricija L, Fisch KM, Gabitto MI, Gebre S, Giacomello S, Gilroy S, Green SJ, Mason CE, Reinsch SS, Szewczyk NJ, Taylor DM, Galazka JM, Herranz R, Muratani M
Patterns (11 Dec 2020)

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)

2019


A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart
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
Cell (12 December 2019)

Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Carlberg K, Korotkova M, Larsson L, Catrina AI, Ståhl PL, Malmström V
Scientific Reports (12 December 2019)

A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection
Poux C, Dondalska A, Bergenstråhle J, Pålsson S, Contreras V, Arasa C, Järver P, Albert J, Busse DC, LeGrand R, Lundeberg J, Tregoning JS, Spetz AL
Frontiers in Immunology (12 September 2019)

High-density spatial transcriptomics arrays for in situ tissue profiling
Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Äijö T, Bonneau R, Bergenstråhle L, Fernandéz Navarro J, Gould J, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL
Nature Methods (9 September 2019)

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivova Z, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H
Science (5 April 2019)

ST Viewer: A tool for analysis and visualization of Spatial Transcriptomics datasets
Fernández Navarro J, Lundeberg J and Ståhl PL
Bioinformatics (15 March 2019)

2018


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

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

Dissecting genetic heterogeneity in Stage III cutaneous malignant melanoma with spatially resolved transcriptomics
Thrane K, Eriksson H, Maaskola J, Hansson J, and Lundeberg J
Cancer Research (2018)

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

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics
Lundmark A, Gerasimcik N, Båge T, Jemt A, Mollbrink A, Salmén F, Lundeberg J, Yucel-Lindberg T
Scientific Reports (2018)

ST Spot Detector: a web-based application for automatic spot and tissue detection for Spatial Transcriptomics image data sets
Wong K, Navarro JF, Bergenstråhle L, Ståhl PL, Lundeberg J
Bioinformatics (2018)

Preprints 2018

Charting Tissue Expression Anatomy by Spatial Transcriptome Deconvolution
Maaskola J, Bergenstråhle L, Jurek A, Fernández Navarro J, Lagergren J, & Lundeberg J
Available at bioRxiv (2018)

Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Salmén F, Vickovic S, Larsson L, Stenbeck L, Vallon-Christersson J, Ehinger A, Häkkinen J, Borg Å, Frisén J, Ståhl PL & Lundeberg J
Available at bioRxiv (2018)

2017


Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Asp M, Salmén F, Ståhl PL, Vickovic S, Felldin U, Löfling M, Navarro JF, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J
Scientific Reports (2017)

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
Navarro J F, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL
Bioinformatics (2017)

Spatially resolved transcriptome profiling in model plant species
Giacomello S, Salmén F, Terebieniec B K, Vickovic S, Navarro J F, Alexeyenko A, Reimegård J, McKee L S, Mannapperuma C, Bulone V, Ståhl P L, Sundström J F, Street N R, Lundeberg J
Nature Plants (2017)

2016


An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Jemt A, Salmén F, Lundmark A, Mollbrink A, Fernández Navarro J, Ståhl PL, Tülay YL, Lundeberg J
Scientific Reports (2016)

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

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
Ståhl PL, Salmén F, Vickovic S, Lundmark A, Fernández Navarro J, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, PI Costea, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J
Science (2016)

2015


Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring
Kvastad L, Werne Solnestam B, Johansson E, Nygren AO, Laddach N, Sahlén P, Vickovic S, Bendigtsen SC, Aaserud M, Floer L, Borgen E, Schwind C, Himmelreich R, Latta D, Lundeberg J
Scientific Reports (2015)

Toward Rare Blood Cell Preservation for RNA Sequencing
Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J
The Journal of Molecular Diagnostics (2015)

2014


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

2013


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