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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
PubMed
DOI
Crossref
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.
Wernersson E, Gelali E,
Girelli G
, ...,
Crosetto N
,
Bienko M
Nat. Methods
-
(-) - [2024-06-06; online 2024-06-06]
Integrated Microscopy Technologies Stockholm [Collaborative]
Spatial Proteomics [Service]
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]
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