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Mats Nilsson

Stockholm University

63H-index
457Paper Count
1.7WCitation Count
Published Papers 140
Publication Date
Identifying 3D signal overlaps in spatial transcriptomics data with ovrlpy
err2026-02-10
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PREAI
errSebastian Tiesmeyer; Niklas Müller-Bötticher; Alexander Malt; Leyao Ma; Sergio Marco-Salas; Paul Kiessling; Paul Horn; Adrien Guillot; Louis B. Kuemmerle; Frank Tacke; Fabian J. Theis; Christoph Kuppe; Mats Nilsson; Roland Eils; Brian Long; Naveed Ishaque
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Spatial single-cell atlas reveals regional variations in healthy and diseased human lung
err2025-11-05
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errOAAI
errAlexandra B. Firsova; Sergio Marco Salas; Louis B. Kuemmerle; Xesús M. Abalo; Alexandros Sountoulidis; Ludvig Larsson; Krishnaa T. Mahbubani; Jonas Theelke; Zaneta Andrusivova; Leire Alonso Galicia; Andreas Liontos; Tamás Balassa; Ferenc Kovacs; Peter Horvath; Yuexin Chen; Janine Gote-Schniering; Mircea-Gabriel Stoleriu; Jürgen Behr; Kerstin B. Meyer; Wim Timens; Herbert B. Schiller; Malte D. Luecken; Fabian J. Theis; Joakim Lundeberg; Mats Nilsson; Martijn C. Nawijn; Christos Samakovlis
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Spatiotemporal gene expression and cellular dynamics of the developing human heart
err2025-10-29
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errOAAI
errEnikő Lázár; Raphaël Mauron; Žaneta Andrusivová; Julia Foyer; Mengxiao He; Ludvig Larsson; Nick Shakari; Sergio Marco Salas; Christophe Avenel; Sanem Sariyar; Jan Niklas Hansen; Marco Vicari; Paulo Czarnewski; Emelie Braun; Xiaofei Li; Olaf Bergmann; Christer Sylvén; Emma Lundberg; Sten Linnarsson; Mats Nilsson; Erik Sundström; Igor Adameyko; Joakim Lundeberg
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Oligodendroglia vulnerability in the human dorsal striatum in Parkinson's disease
err2025-05-05
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errOAAI
errBarba-Reyes, JM; Harder, L; Salas, SM; Jaisa-aad, M; Muñoz-Castro, C; Garma, LD; Rafati, N; Nilsson, M; Hyman, BT; Serrano-Pozo, A; Muñoz-Manchado, AB
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Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap
err2025-05-01
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errOAAI
errRuiz-Moreno, Cristian; Salas, Sergio Marco; Samuelsson, Erik; Minaeva, Mariia; Ibarra, Ignacio; Grillo, Marco; Brandner, Sebastian; Roy, Ananya; Forsberg-Nilsson, Karin; Kranendonk, Mariette E. G.; Theis, Fabian J.; Nilsson, Mats; Stunnenberg, Hendrik G.
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A systematic implementation of padlock probing-based rolling circle amplification in an integrated microfluidic device for quantitative biomolecular analyses
err2025-02-01
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PREAI
errCaneira, Catarina R. F.; Rosa, Rafaela R.; Chu, Virginia; Nilsson, Mats; Madaboosi, Narayanan; Soares, Ruben R. G.; Conde, Joao P.
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Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology
err2024-08-29
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errOAAI
errLee, Hower; Langseth, Christoffer Mattsson; Salas, Sergio Marco; Sariyar, Sanem; Metousis, Andreas; Rueda-Alana, Eneritz; Bekiari, Christina; Lundberg, Emma; Garcia-Moreno, Fernando; Grillo, Marco; Nilsson, Mats
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Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim
err2024-07-25
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errOAAI
errAndersson, Axel; Escriva Conde, Maria; Surova, Olga; Vermeulen, Peter; Wahlby, Carolina; Nilsson, Mats; Nystrom, Hanna
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Interneuron diversity in the human dorsal striatum
err2024-07-22
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errOAAI
errGarma, Leonardo D.; Harder, Lisbeth; Barba-Reyes, Juan M.; Marco Salas, Sergio; Diez-Salguero, Monica; Nilsson, Mats; Serrano-Pozo, Alberto; Hyman, Bradley T.; Munoz-Manchado, Ana B.
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A community effort to track commercial single-cell and spatial 'omic technologies and business trends
err2024-07-17
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PREAI
errDe Jonghe, Joachim; Opzoomer, James W.; Vilas-Zornoza, Amaia; Crane, Peter; Nilges, Benedikt S.; Vicari, Marco; Lee, Hower; Lara-Astiaso, David; Gross, Torsten; Morf, Joerg; Schneider, Kim; Cudini, Juliana; Ramos-Mucci, Lorenzo; Mooijman, Dylan; Tiklova, Katarina; Salas, Sergio Marco; Langseth, Christoffer Mattsson; Kashikar, Nachiket D.; Roberts, Charles E. S.; Lundeberg, Joakim; Nilsson, Mats; Shalek, Alex K.; Cribbs, Adam P.; Taylor-King, Jake P.
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Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
err2024-06-06
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errOAAI
errWernersson, Erik; Gelali, Eleni; Girelli, Gabriele; Wang, Su; Castillo, David; Langseth, Christoffer Mattsson; Verron, Quentin; Nguyen, Huy Q.; Chattoraj, Shyamtanu; Martinez Casals, Anna; Blom, Hans; Lundberg, Emma; Nilsson, Mats; Marti-Renom, Marc A.; Wu, Chao-ting; Crosetto, Nicola; Bienko, Magda
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Large scale, transcriptome-based analysis of TCR clonality reveals functional immunity in non-small cell lung cancer
err2024-03-22
err0
PREAI
errYu, Hui; Magoulopoulou, Anastasia; Hori, Masafumi; Lindberg, Amanda; Backman, Max; Brunstrom, Hans; Zuniga, Millaray Marincevic; Mattsson, Johanna; Saito, Akira; Leandersson, Karin; Nilsson, Mats; Amini, Rose-Marie; Micke, Patrick; Strell, Carina
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Spatial multimodal analysis of transcriptomes and metabolomes in tissues
err2023-09-04
err28
errOAAI
errVicari, Marco; Mirzazadeh, Reza; Nilsson, Anna; Shariatgorji, Reza; Bjaerterot, Patrik; Larsson, Ludvig; Lee, Hower; Nilsson, Mats; Foyer, Julia; Ekvall, Markus; Czarnewski, Paulo; Zhang, Xiaoqun; Svenningsson, Per; Kaell, Lukas; Andren, Per E.; Lundeberg, Joakim
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Highly multiplexed targeted sequencing strategy for infectious disease surveillance
err2023-08-23
err3
errOAAI
errHernandez-Neuta, Ivan; Magoulopoulou, Anastasia; Pineiro, Flor; Lisby, Jan Gorm; Gulberg, Mats; Nilsson, Mats
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Spatial tumour gene signature discriminates neoplastic from non-neoplastic compartments in colon cancer: unravelling predictive biomarkers for relapse
err2023-08-05
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errOAAI
errSallinger, Katja; Gruber, Michael; Mueller, Christin-Therese; Bonstingl, Lilli; Pritz, Elisabeth; Pankratz, Karin; Gerger, Armin; Smolle, Maria Anna; Aigelsreiter, Ariane; Surova, Olga; Svedlund, Jessica; Nilsson, Mats; Kroneis, Thomas; El-Heliebi, Amin
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A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
err2023-01-16
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errOAAI
errSountoulidis, Alexandros; Marco Salas, Sergio; Braun, Emelie; Avenel, Christophe; Bergenstrahle, Joseph; Theelke, Jonas; Vicari, Marco; Czarnewski, Paulo; Liontos, Andreas; Abalo, Xesus; Andrusivova, Zaneta; Mirzazadeh, Reza; Asp, Michaela; Li, Xiaofei; Hu, Lijuan; Sariyar, Sanem; Martinez Casals, Anna; Ayoglu, Burcu; Firsova, Alexandra; Michaelsson, Jakob; Lundberg, Emma; Waehlby, Carolina; Sundstroem, Erik; Linnarsson, Sten; Lundeberg, Joakim; Nilsson, Mats; Samakovlis, Christos
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The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location
err2022-12-05
err67
errOAAI
errLiu, Ilon; Jiang, Li; Samuelsson, Erik R.; Salas, Sergio Marco; Beck, Alexander; Hack, Olivia A.; Jeong, Daeun; Shaw, McKenzie L.; Englinger, Bernhard; LaBelle, Jenna; Mire, Hafsa M.; Madlener, Sibylle; Mayr, Lisa; Quezada, Michael A.; Trissal, Maria; Panditharatna, Eshini; Ernst, Kati J.; Vogelzang, Jayne; Gatesman, Taylor A.; Halbert, Matthew E.; Palova, Hana; Pokorna, Petra; Sterba, Jaroslav; Slaby, Ondrej; Geyeregger, Rene; Diaz, Aaron; Findlay, Izac J.; Dun, Matthew D.; Resnick, Adam; Suva, Mario L.; Jones, David T. W.; Agnihotri, Sameer; Svedlund, Jessica; Koschmann, Carl; Haberler, Christine; Czech, Thomas; Slavc, Irene; Cotter, Jennifer A.; Ligon, Keith L.; Alexandrescu, Sanda; Yung, W. K. Alfred; Arrillaga-Romany, Isabel; Gojo, Johannes; Monje, Michelle; Nilsson, Mats; Filbin, Mariella G.
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THE LANDSCAPE OF TUMOR CELL STATES AND SPATIAL ORGANIZATION IN H3-K27M MUTANT DIFFUSE MIDLINE GLIOMA ACROSS AGE AND LOCATION
err2022-09-05
err2
errOAAI
errLiu, I; Jiang, L.; Samuelsson, E.; Marco Salas, S.; Hack, O.; Jeong, D.; Shaw, M.; Englinger, B.; LaBelle, J.; Ernst, K.; Palova, H.; Pokorna, P.; Sterba, J.; Slaby, O.; Geyeregger, R.; Jones, D.; Koschmann, C.; Svedlund, J.; Resnick, A.; Diaz, A.; Haberler, C.; Czech, T.; Slavc, I; Cotter, J.; Ligon, K.; Alexandrescu, S.; Yung, W.; Arrillaga-Romany, I; Suva, M.; Beck, A.; Gojo, J.; Monje, M.; Nilsson, M.; Filbin, M.
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Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis
err2022-06-01
err27
errOAAI
errvan Bruggen, David; Pohl, Fabio; Langseth, Christoffer Mattsson; Kukanja, Petra; Lee, Hower; Albiach, Alejandro Mossi; Kabbe, Mukund; Meijer, Mandy; Linnarsson, Sten; Hilscher, Markus M.; Nilsson, Mats; Sundstrom, Erik; Castelo-Branco, Goncalo
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