| Year |
Citation |
Score |
| 2024 |
Ekvall M, Bergenstråhle L, Andersson A, Czarnewski P, Olegård J, Käll L, Lundeberg J. Spatial landmark detection and tissue registration with deep learning. Nature Methods. 21: 673-679. PMID 38438615 DOI: 10.1038/s41592-024-02199-5 |
0.739 |
|
| 2024 |
Mold JE, Weissman MH, Ratz M, Hagemann-Jensen M, Hård J, Eriksson CJ, Toosi H, Berghenstråhle J, Ziegenhain C, von Berlin L, Martin M, Blom K, Lagergren J, Lundeberg J, Sandberg R, et al. Clonally heritable gene expression imparts a layer of diversity within cell types. Cell Systems. PMID 38340731 DOI: 10.1016/j.cels.2024.01.004 |
0.307 |
|
| 2023 |
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, ... ... Lundeberg J, et al. Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics. Science (New York, N.Y.). 382: eadf8486. PMID 38060664 DOI: 10.1126/science.adf8486 |
0.76 |
|
| 2023 |
Larsson L, Franzén L, Ståhl PL, Lundeberg J. Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization. Bioinformatics (Oxford, England). 39. PMID 37846051 DOI: 10.1093/bioinformatics/btad626 |
0.412 |
|
| 2023 |
Figiel S, Yin W, Doultsinos D, Erickson A, Poulose N, Singh R, Magnussen A, Anbarasan T, Teague R, He M, Lundeberg J, Loda M, Verrill C, Colling R, Gill PS, et al. Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures. Molecular Cancer. 22: 162. PMID 37789377 DOI: 10.1186/s12943-023-01863-2 |
0.343 |
|
| 2023 |
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, et al. Spatial multimodal analysis of transcriptomes and metabolomes in tissues. Nature Biotechnology. PMID 37667091 DOI: 10.1038/s41587-023-01937-y |
0.401 |
|
| 2023 |
Fan Y, Andrusivová Ž, Wu Y, Chai C, Larsson L, He M, Luo L, Lundeberg J, Wang B. Expansion spatial transcriptomics. Nature Methods. PMID 37349575 DOI: 10.1038/s41592-023-01911-1 |
0.473 |
|
| 2023 |
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, ... ... Lundeberg J, et al. Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells. The Journal of Investigative Dermatology. PMID 37142187 DOI: 10.1016/j.jid.2023.02.040 |
0.719 |
|
| 2023 |
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, ... ... Lundeberg J, et al. Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin. Nature Neuroscience. PMID 37095395 DOI: 10.1038/s41593-023-01312-9 |
0.713 |
|
| 2023 |
Lebrigand K, Bergenstråhle J, Thrane K, Mollbrink A, Meletis K, Barbry P, Waldmann R, Lundeberg J. The spatial landscape of gene expression isoforms in tissue sections. Nucleic Acids Research. PMID 36928528 DOI: 10.1093/nar/gkad169 |
0.45 |
|
| 2023 |
Mirzazadeh R, Andrusivova Z, Larsson L, Newton PT, Galicia LA, Abalo XM, Avijgan M, Kvastad L, Denadai-Souza A, Stakenborg N, Firsova AB, Shamikh A, Jurek A, Schultz N, Nistér M, ... ... Lundeberg J, et al. Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples. Nature Communications. 14: 509. PMID 36720873 DOI: 10.1038/s41467-023-36071-5 |
0.332 |
|
| 2023 |
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, ... ... Lundeberg J, et al. A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung. Nature Cell Biology. PMID 36646791 DOI: 10.1038/s41556-022-01064-x |
0.364 |
|
| 2022 |
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, ... ... Lundeberg J, et al. Spatially resolved clonal copy number alterations in benign and malignant tissue. Nature. 608: 360-367. PMID 35948708 DOI: 10.1038/s41586-022-05023-2 |
0.751 |
|
| 2022 |
Larsson L, Bergenstråhle L, He M, Andrusivova Z, Lundeberg J. SnapShot: Spatial transcriptomics. Cell. 185: 2840-2840.e1. PMID 35868280 DOI: 10.1016/j.cell.2022.06.002 |
0.381 |
|
| 2022 |
Ratz M, von Berlin L, Larsson L, Martin M, Westholm JO, La Manno G, Lundeberg J, Frisén J. Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nature Neuroscience. 25: 285-294. PMID 35210624 DOI: 10.1038/s41593-022-01011-x |
0.381 |
|
| 2022 |
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, et al. The spatial transcriptomic landscape of the healing mouse intestine following damage. Nature Communications. 13: 828. PMID 35149721 DOI: 10.1038/s41467-022-28497-0 |
0.359 |
|
| 2021 |
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, ... ... Lundeberg J, et al. Genome-wide spatial expression profiling in formalin-fixed tissues. Cell Genomics. 1: 100065. PMID 36776149 DOI: 10.1016/j.xgen.2021.100065 |
0.762 |
|
| 2021 |
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. Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver. Nature Communications. 12: 7046. PMID 34857782 DOI: 10.1038/s41467-021-27354-w |
0.751 |
|
| 2021 |
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. Super-resolved spatial transcriptomics by deep data fusion. Nature Biotechnology. PMID 34845373 DOI: 10.1038/s41587-021-01075-3 |
0.769 |
|
| 2021 |
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. Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. Nature Communications. 12: 6012. PMID 34650042 DOI: 10.1038/s41467-021-26271-2 |
0.757 |
|
| 2021 |
Chelebian E, Avenel C, Kartasalo K, Marklund M, Tanoglidi A, Mirtti T, Colling R, Erickson A, Lamb AD, Lundeberg J, Wählby C. Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer. Cancers. 13. PMID 34638322 DOI: 10.3390/cancers13194837 |
0.325 |
|
| 2021 |
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, ... ... Lundeberg J, et al. A single-cell and spatially resolved atlas of human breast cancers. Nature Genetics. 53: 1334-1347. PMID 34493872 DOI: 10.1038/s41588-021-00911-1 |
0.736 |
|
| 2021 |
Anderson A, Lundeberg J. sepal: Identifying Transcript Profiles with Spatial Patterns by Diffusion-based Modeling. Bioinformatics (Oxford, England). PMID 33704427 DOI: 10.1093/bioinformatics/btab164 |
0.394 |
|
| 2021 |
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, ... ... Lundeberg J, et al. The spatial RNA integrity number assay for in situ evaluation of transcriptome quality. Communications Biology. 4: 57. PMID 33420318 DOI: 10.1038/s42003-020-01573-1 |
0.366 |
|
| 2021 |
Larsson L, Frisén J, Lundeberg J. Spatially resolved transcriptomics adds a new dimension to genomics. Nature Methods. 18: 15-18. PMID 33408402 DOI: 10.1038/s41592-020-01038-7 |
0.318 |
|
| 2020 |
Andersson A, Bergenstråhle J, Asp M, Bergenstråhle L, Jurek A, Fernández Navarro J, Lundeberg J. Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography. Communications Biology. 3: 565. PMID 33037292 DOI: 10.1038/s42003-020-01247-y |
0.774 |
|
| 2020 |
Bergenstråhle J, Larsson L, Lundeberg J. Seamless integration of image and molecular analysis for spatial transcriptomics workflows. Bmc Genomics. 21: 482. PMID 32664861 DOI: 10.1186/s12864-020-06832-3 |
0.352 |
|
| 2020 |
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, ... ... Lundeberg J, et al. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma. Cell. PMID 32579974 DOI: 10.1016/J.Cell.2020.05.039 |
0.385 |
|
| 2020 |
Saiselet M, Rodrigues-Vitória J, Tourneur A, Craciun L, Spinette A, Larsimont D, Andry G, Lundeberg J, Maenhaut C, Detours V. Transcriptional output, cell-type densities, and normalization in spatial transcriptomics. Journal of Molecular Cell Biology. 12: 906-908. PMID 32573704 DOI: 10.1093/jmcb/mjaa028 |
0.329 |
|
| 2020 |
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. Nature Biomedical Engineering. PMID 32572199 DOI: 10.1038/S41551-020-0578-X |
0.76 |
|
| 2020 |
Asp M, Bergenstråhle J, Lundeberg J. Spatially Resolved Transcriptomes-Next Generation Tools for Tissue Exploration. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 42: e1900221. PMID 32363691 DOI: 10.1002/bies.201900221 |
0.399 |
|
| 2020 |
Berglund E, Saarenpää S, Jemt A, Gruselius J, Larsson L, Bergenstråhle L, Lundeberg J, Giacomello S. Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues. Bmc Genomics. 21: 298. PMID 32293264 DOI: 10.1186/s12864-020-6631-z |
0.451 |
|
| 2019 |
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, ... ... Lundeberg J, et al. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell. 179: 1647-1660.e19. PMID 31835037 DOI: 10.1016/j.cell.2019.11.025 |
0.397 |
|
| 2019 |
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, et al. High-definition spatial transcriptomics for in situ tissue profiling. Nature Methods. PMID 31501547 DOI: 10.1038/S41592-019-0548-Y |
0.489 |
|
| 2019 |
Fernández Navarro J, Lundeberg J, Ståhl PL. ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets. Bioinformatics (Oxford, England). 35: 1058-1060. PMID 30875427 DOI: 10.1093/bioinformatics/bty714 |
0.344 |
|
| 2018 |
Giacomello S, Lundeberg J. Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays. Nature Protocols. 13: 2425-2446. PMID 30353173 DOI: 10.1038/s41596-018-0046-1 |
0.318 |
|
| 2018 |
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. Nature Protocols. 13: 2501-2534. PMID 30353172 DOI: 10.1038/S41596-018-0045-2 |
0.42 |
|
| 2018 |
Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J. Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma. Cancer Research. 78: 5970-5979. PMID 30154148 DOI: 10.1158/0008-5472.CAN-18-0747 |
0.361 |
|
| 2018 |
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, ... ... Lundeberg J, et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. Nature Communications. 9: 2419. PMID 29925878 DOI: 10.1038/S41467-018-04724-5 |
0.323 |
|
| 2018 |
Lundmark A, Gerasimcik N, Båge T, Jemt A, Mollbrink A, Salmén F, Lundeberg J, Yucel-Lindberg T. Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics. Scientific Reports. 8: 9370. PMID 29921943 DOI: 10.1038/s41598-018-27627-3 |
0.343 |
|
| 2018 |
Wong K, Fernández Navarro J, Bergenstråhle L, Ståhl PL, Lundeberg J. ST Spot Detector: a web-based application for automatic spot and tissue detection for Spatial Transcriptomics image data sets. Bioinformatics (Oxford, England). PMID 29360929 DOI: 10.1093/bioinformatics/bty030 |
0.353 |
|
| 2017 |
Asp M, Salmén F, Ståhl PL, Vickovic S, Felldin U, Löfling M, Fernandez Navarro J, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J. Spatial detection of fetal marker genes expressed at low level in adult human heart tissue. Scientific Reports. 7: 12941. PMID 29021611 DOI: 10.1038/s41598-017-13462-5 |
0.328 |
|
| 2017 |
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. Nature Plants. 3: 17061. PMID 28481330 DOI: 10.1038/nplants.2017.61 |
0.418 |
|
| 2017 |
Navarro JF, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL. ST Pipeline: an automated pipeline for spatial mapping of unique transcripts. Bioinformatics (Oxford, England). 33: 2591-2593. PMID 28398467 DOI: 10.1093/bioinformatics/btx211 |
0.369 |
|
| 2016 |
Jemt A, Salmén F, Lundmark A, Mollbrink A, Fernández Navarro J, Ståhl PL, Yucel-Lindberg T, Lundeberg J. An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries. Scientific Reports. 6: 37137. PMID 27849009 DOI: 10.1038/srep37137 |
0.353 |
|
| 2016 |
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. Nature Communications. 7: 13182. PMID 27739429 DOI: 10.1038/Ncomms13182 |
0.323 |
|
| 2016 |
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, ... ... Lundeberg J, et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science (New York, N.Y.). 353: 78-82. PMID 27365449 DOI: 10.1126/Science.Aaf2403 |
0.411 |
|
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