Nilsson M

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Family name Nilsson
Given name Mats
Initials M
ORCID

ORCID 0000-0001-9985-0387
Affiliations Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.

46 publications

DOI Crossref
High-parametric protein maps reveal the spatial organization in early-developing human lung
Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B
- - (-) - [2024-01-25; online 2024-01-25]
Spatial Proteomics [Service]
DOI Crossref
BirthSeq, a new method to isolate and analyze dated cells from any tissue in vertebrates
Rueda-Alaña E, Grillo M, Vazquez E, ..., Nilsson M, García-Moreno F
- - (-) - [2023-10-10; online 2023-10-10]
In Situ Sequencing (ISS) [Service]
PubMed DOI Crossref
Spatial multimodal analysis of transcriptomes and metabolomes in tissues.
Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J
Nat. Biotechnol. - (-) - [2023-09-04; online 2023-09-04]
In Situ Sequencing (ISS) [Collaborative] Spatial Mass Spectrometry [Collaborative]
DOI Crossref
Single cell-resolutionin situsequencing elucidates spatial dynamics of multiple sclerosis lesion and disease evolution
Langseth CM, Kukanja P, Rubio Rodríguez-Kirby LA, ..., Nilsson M, Castelo-Branco G
- - (-) - [2023-06-30; online 2023-06-30]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Service]
PubMed DOI Crossref
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.
Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E
Nat. Neurosci. 26 (5) 891-901 [2023-05-00; online 2023-04-24]
BioImage Informatics [Collaborative] Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Optimizing Xenium In Situ data utility by quality assessment and best practice analysis workflows
Salas SM, Czarnewski P, Kuemmerle LB, ..., Ishaque N, Nilsson M
- - (-) - [2023-02-14; online 2023-02-14]
In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]
BioImage Informatics [Collaborative] In Situ Sequencing (ISS) [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.
Liu I, Jiang L, Samuelsson ER, ..., Nilsson M, Filbin MG
Nat. Genet. 54 (12) 1881-1894 [2022-12-00; online 2022-12-05]
In Situ Sequencing (ISS) [Collaborative]
PubMed DOI Crossref
Spatial genomics maps the structure, nature and evolution of cancer clones.
Lomakin A, Svedlund J, Strell C, ..., Nilsson M, Yates LR
Nature 611 (7936) 594-602 [2022-11-00; online 2022-11-09]
In Situ Sequencing (ISS) [Service]
PubMed DOI Crossref
De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks.
Marco Salas S, Yuan X, Sylven C, ..., Wählby C, Partel G
PLoS Comput. Biol. 18 (8) e1010366 [2022-08-00; online 2022-08-12]
BioImage Informatics [Service] In Situ Sequencing (ISS) [Collaborative]
DOI Crossref
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
Wernersson E, Gelali E, Girelli G, ..., Crosetto N, Bienko M
- - (-) - [2022-02-02; online 2022-02-02]
Spatial Proteomics [Service]
PubMed DOI Crossref
A roadmap for the Human Developmental Cell Atlas.
Haniffa M, Taylor D, Linnarsson S, ..., Webb S, Human Cell Atlas Developmental Biological Network
Nature 597 (7875) 196-205 [2021-09-00; online 2021-09-08]
In Situ Sequencing (ISS) [Collaborative] Spatial Proteomics
PubMed DOI Crossref
Comprehensive in situ mapping of human cortical transcriptomic cell types.
Langseth CM, Gyllborg D, Miller JA, ..., Hilscher MM, Nilsson M
Commun Biol 4 (1) 998 [2021-08-24; online 2021-08-24]
In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
Molecular architecture of the developing mouse brain.
La Manno G, Siletti K, Furlan A, ..., Lönnerberg P, Linnarsson S
Nature 596 (7870) 92-96 [2021-08-00; online 2021-07-28]
In Situ Sequencing (ISS) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps.
Marco Salas S, Gyllborg D, Mattsson Langseth C, Nilsson M
BMC Bioinformatics 22 (1) 391 [2021-07-31; online 2021-07-31]
In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury
Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G
Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.
Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M
Nucleic Acids Res. 48 (19) e112 [2020-11-04; online 2020-09-30]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
Automated identification of the mouse brain's spatial compartments from in situ sequencing data.
Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C
BMC Biol. 18 (1) 144 [2020-10-19; online 2020-10-19]
BioImage Informatics [Collaborative] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Probabilistic cell typing enables fine mapping of closely related cell types in situ.
Qian X, Harris KD, Hauling T, ..., Hjerling-Leffler J, Nilsson M
Nat. Methods 17 (1) 101-106 [2020-01-00; online 2019-11-18]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Service]
PubMed DOI Crossref
In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections
Hilscher MM, Gyllborg D, Yokota C, Nilsson M
Methods Mol. Biol. 2148 (-) 313-329 [2020-00-00; online 2020-05-12]
Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Collaborative]
PubMed DOI Crossref
Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer.
Svedlund J, Strell C, Qian X, ..., Sieuwerts AM, Nilsson M
EBioMedicine 48 (-) 212-223 [2019-10-00; online 2019-09-13]
In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
Profiling surface proteins on individual exosomes using a proximity barcoding assay.
Wu D, Yan J, Shen X, ..., Landegren U, Kamali-Moghaddam M
Nat Commun 10 (1) 3854 [2019-08-26; online 2019-08-26]
Affinity Proteomics Uppsala [Technology development] Bioinformatics Support for Computational Resources [Service] PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
Spatiotemporal structure of cell fate decisions in murine neural crest
Soldatov R, Kaucka M, Kastriti ME, ..., Kharchenko PV, Adameyko I
Science 364 (6444) eaas9536 [2019-06-07; online 2019-06-07]
Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma.
Carow B, Hauling T, Qian X, ..., Nilsson M, Rottenberg ME
Nat Commun 10 (1) 1823 [2019-04-23; online 2019-04-23]
In Situ Sequencing (ISS) [Collaborative]
PubMed DOI Crossref
Placing RNA in context and space - methods for spatially resolved transcriptomics.
Strell C, Hilscher MM, Laxman N, ..., Yokota C, Nilsson M
FEBS J. 286 (8) 1468-1481 [2019-04-00; online 2018-03-31]
In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11.
La Fleur L, Falk-Sörqvist E, Smeds P, ..., Moens L, Botling J
Lung Cancer 130 (-) 50-58 [2019-04-00; online 2019-01-09]
Bioinformatics Support for Computational Resources [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A microfluidic platform towards automated multiplexed in situ sequencing.
Maïno N, Hauling T, Cappi G, ..., Dupouy DG, Nilsson M
Sci Rep 9 (1) 3542 [2019-03-05; online 2019-03-05]
In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development
Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T
Nat Commun 10 (1) 581 [2019-02-04; online 2019-02-04]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Collaborative]
PubMed DOI Crossref
RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples.
Wu C, Simonetti M, Rossell C, ..., Crosetto N, Nilsson M
Commun Biol 1 (-) 209 [2018-11-28; online 2018-11-28]
Advanced FISH Technologies [Technology development] In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
Expression profiling and in situ screening of circular RNAs in human tissues.
Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L
Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer.
Mathot L, Kundu S, Ljungström V, ..., Nilsson M, Sjöblom T
Cancer Res. 77 (7) 1730-1740 [2017-04-01; online 2017-01-20]
Clinical Genomics Uppsala [Collaborative]
DOI Crossref
P1.02-063 Mutation Profiling by Targeted Next-Generation Sequencing of an Unselected NSCLC Cohort
La Fleur L, Falk-Sorqvist E, Smeds P, ..., Moens L, Botling J
Journal of Thoracic Oncology 12 (1) S526-S527 [2017-01-00; online 2017-01-00]
Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Decoding Gene Expression in 2D and 3D
Bombrun M, Ranefall P, Lindblad J, ..., Nilsson M, Wählby C
Scandinavian Conference on Image Analysis 2017 - (-) 257-268 [2017-00-00; online 2017-05-19]
BioImage Informatics [Collaborative]
PubMed DOI Crossref
Single-Nucleotide Polymorphisms and Cancer Risk, Tumor Recurrence, or Survival of Head and Neck Cancer Patients.
Laytragoon-Lewin N, Cederblad L, Andersson BÅ, ..., Löfgren S, Lewin F
Oncology 92 (3) 161-169 [2016-12-21; online 2016-12-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
New technologies for DNA analysis--a review of the READNA Project.
McGinn S, Bauer D, Brefort T, ..., Willcocks JP, Gut IG
N Biotechnol 33 (3) 311-330 [2016-05-25; online 2015-10-26]
Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
Multiplexed protein profiling by sequential affinity capture.
Ayoglu B, Birgersson E, Mezger A, ..., Nilsson P, Schwenk JM
Proteomics 16 (8) 1251-1256 [2016-04-00; online 2016-03-31]
Affinity Proteomics Stockholm [Technology development]
PubMed DOI Crossref
Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development.
Johansson MM, Lundin E, Qian X, ..., Nilsson M, Jazin E
Biol Sex Differ 7 (-) 5 [2016-01-12; online 2016-01-12]
Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Susceptibility to infections, without concomitant hyper-IgE, reported in 1976, is caused by hypomorphic mutation in the phosphoglucomutase 3 (PGM3) gene.
Lundin KE, Hamasy A, Backe PH, ..., Stenmark S, Smith CI
Clin. Immunol. 161 (2) 366-372 [2015-12-00; online 2015-10-19]
Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.
Moens LN, Falk-Sörqvist E, Ljungström V, ..., Nilsson M, Botling J
J Mol Diagn 17 (6) 729-739 [2015-11-00; online 2015-09-03]
Clinical Genomics Uppsala NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio.
Clausson C, Arngården L, Ishaq O, ..., Wählby C, Söderberg O
Sci Rep 5 (-) 12317 [2015-07-23; online 2015-07-23]
BioImage Informatics [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]
PubMed DOI Crossref
Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia.
Mansouri L, Sutton LA, Ljungström V, ..., Nilsson M, Rosenquist R
J. Exp. Med. 212 (6) 833-843 [2015-06-01; online 2015-05-18]
Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
In situ sequencing identifies TMPRSS2-ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers.
Kiflemariam S, Mignardi M, Ali MA, ..., Nilsson M, Sjöblom T
J. Pathol. 234 (2) 253-261 [2014-10-00; online 2014-08-04]
Tissue Profiling
PubMed DOI Crossref
Feasibility of targeted next-generation sequencing of the TP53 and ATM genes in chronic lymphocytic leukemia.
Mansouri L, Sutton LA, Ljungström V, ..., Nilsson M, Rosenquist R
Leukemia 28 (3) 694-696 [2014-03-00; online 2013-10-31]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Molecular tools for companion diagnostics.
Zieba A, Grannas K, Söderberg O, ..., Nilsson M, Landegren U
N Biotechnol 29 (6) 634-640 [2012-09-15; online 2012-05-24]
Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics
PubMed DOI Crossref
Targeted enrichment of genomic DNA regions for next-generation sequencing.
Mertes F, Elsharawy A, Sauer S, ..., Lehrach H, Brookes AJ
Brief Funct Genomics 10 (6) 374-386 [2011-11-00; online 2011-11-26]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Targeted resequencing of candidate genes using selector probes.
Johansson H, Isaksson M, Sörqvist EF, ..., Ericsson O, Nilsson M
Nucleic Acids Res. 39 (2) e8 [2011-01-00; online 2010-11-08]
Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure
SciLifeLab Data Centre
Publications 9.5.0