Nilsson M

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 Box 1031 Se-171 21 Solna Sweden

50 publications

PubMed DOI Crossref

Spatial single-cell atlas reveals regional variations in healthy and diseased human lung.

Firsova AB, Marco Salas S, Kuemmerle LB, ..., Nawijn MC, Samakovlis C

Nat Commun 16 (1) 9745 [2025-11-05; online 2025-11-05]

PubMed DOI Crossref

Spatiotemporal gene expression and cellular dynamics of the developing human heart.

Lázár E, Mauron R, Andrusivová Ž, ..., Adameyko I, Lundeberg J

Nat. Genet. 57 (11) 2756-2771 [2025-11-00; online 2025-10-29]

DOI Crossref

A dual genetic constraint underlies the conservation of early brains in vertebrates

Senovilla-Ganzo R, Bekiari C, Rueda-Alaña E, ..., Kaessmann H, García-Moreno F

- - (-) - [2025-10-29; online 2025-10-29]

PubMed DOI Crossref

Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap.

Ruiz-Moreno C, Salas SM, Samuelsson E, ..., Nilsson M, Stunnenberg HG

Neuro-oncology 27 (9) 2281-2295 [2025-10-14; online 2025-05-02]

PubMed DOI Crossref

Pooled optical screening in bacteria using chromosomally expressed barcodes.

Soares RRG, García-Soriano DA, Larsson J, ..., Nilsson M, Elf J

Commun Biol 8 (1) 851 [2025-06-03; online 2025-06-03]

PubMed DOI Crossref

Spatial miRNomics: towards the integration of microRNAs in spatial biology.

Robles-Remacho A, Nilsson M

Nat. Rev. Genet. 26 (5) 291-292 [2025-05-00; online 2025-02-07]

PubMed DOI Crossref

Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.

Marco Salas S, Kuemmerle LB, Mattsson-Langseth C, ..., Ishaque N, Nilsson M

Nat. Methods 22 (4) 813-823 [2025-04-00; online 2025-03-13]

DOI Crossref

Oligodendroglia vulnerability in the human dorsal striatum in Parkinson’s disease

Barba-Reyes JM, Harder L, Salas SM, ..., Serrano-Pozo A, Muñoz-Manchado AB

- - (-) - [2025-01-20; online 2025-01-20]

PubMed DOI Crossref

Evolutionary convergence of sensory circuits in the pallium of amniotes.

Rueda-Alaña E, Senovilla-Ganzo R, Grillo M, ..., De Pittà M, García-Moreno F

Science (New York, N.Y.) 387 (6735) eadp3411 [2025-01-02; online 2025-02-14]

PubMed 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

Nat Commun 15 (1) 9381 [2024-10-30; online 2024-10-30]

DOI Crossref

A topographic lung cell atlas reveals regional variation in cell-type specific gene programs and identifies healthy and diseased cellular neighborhoods

Samakovlis C, Firsova A, Salas SM, ..., Nilsson M, Nawijn M

- - (-) - [2024-10-07; online 2024-10-07]

PubMed DOI Crossref

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.

Andersson A, Escriva Conde M, Surova O, ..., Nilsson M, Nyström H

Clin. Cancer Res. 30 (19) 4517-4529 [2024-10-01; online 2024-07-26]

PubMed DOI Crossref

Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.

Lee H, Langseth CM, Salas SM, ..., Grillo M, Nilsson M

Development 151 (16) - [2024-08-15; online 2024-08-29]

PubMed DOI Crossref

Interneuron diversity in the human dorsal striatum.

Garma LD, Harder L, Barba-Reyes JM, ..., Hyman BT, Muñoz-Manchado AB

Nat Commun 15 (1) 6164 [2024-07-22; online 2024-07-22]

PubMed DOI Crossref

BirthSeq, a new method to isolate and analyze dated cells in different vertebrates.

Rueda-Alaña E, Grillo M, Vázquez E, ..., Nilsson M, García-Moreno F

Development 151 (13) - [2024-07-01; online 2024-07-10]

PubMed DOI Crossref

A community effort to track commercial single-cell and spatial 'omic technologies and business trends.

De Jonghe J, Opzoomer JW, Vilas-Zornoza A, ..., Cribbs AP, Taylor-King JP

Nat. Biotechnol. 42 (7) 1017-1023 [2024-07-00; online 2024-07-18]

PubMed DOI Crossref

Spatial multimodal analysis of transcriptomes and metabolomes in tissues.

Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J

Nat. Biotechnol. 42 (7) 1046-1050 [2024-07-00; online 2023-09-04]

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 21 (7) 1245-1256 [2024-07-00; online 2024-06-06]

Magda Bienko SciLifeLab Fellow

DOI Crossref

Evolutionary convergence of sensory circuits in the pallium of amniotes

Rueda-Alaña E, Senovilla-Ganzo R, Grillo M, ..., De Pitta M, García-Moreno F

- - (-) - [2024-05-02; online 2024-05-02]

DOI Crossref

Spatial Dynamics of the Developing Human Heart

Lázár E, Mauron R, Andrusivová Ž, ..., Adameyko I, Lundeberg J

- - (-) - [2024-03-14; online 2024-03-14]

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]

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]

DOI Crossref

Single cell-resolution in situ sequencing 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]

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]

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]

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]

DOI Crossref

Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues

Vicari M, Mirzazadeh R, Nilsson A, ..., Andrén PE, Lundeberg J

- - (-) - [2023-01-27; online 2023-01-27]

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]

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]

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]

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]

Magda Bienko SciLifeLab Fellow

DOI Crossref

Developmental origins of cell heterogeneity in the human lung

Sountoulidis A, Salas SM, Braun E, ..., Nilsson M, Samakovlis C

- - (-) - [2022-01-12; online 2022-01-12]

PubMed DOI Crossref

Rolling Circle Amplification in Integrated Microsystems: An Uncut Gem toward Massively Multiplexed Pathogen Diagnostics and Genotyping.

Soares RRG, Madaboosi N, Nilsson M

Acc. Chem. Res. 54 (21) 3979-3990 [2021-11-02; online 2021-10-12]

PubMed DOI Crossref

Correction to '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. 49 (15) 9002 [2021-09-07; online 2021-08-01]

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]

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]

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]

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]

DOI Crossref

Developmental landscape of human forebrain at a single-cell level unveils early waves of oligodendrogenesis

van Bruggen D, Pohl F, Langseth CM, ..., Sundström E, Castelo-Branco G

- - (-) - [2021-07-22; online 2021-07-22]

DOI Crossref

De novo spatiotemporal modelling of cell-type signatures identifies novel cell populations in the developmental human heart

Salas SM, Yuan X, Sylven C, ..., Wählby C, Partel G

- - (-) - [2021-07-11; online 2021-07-11]

DOI Crossref

Spatial genomics maps the structure, character and evolution of cancer clones

Lomakin A, Svedlund J, Strell C, ..., Nilsson M, Yates LR

- - (-) - [2021-04-16; online 2021-04-16]

DOI Crossref

Comprehensive in situ mapping of human cortical transcriptomic cell types

Langseth CM, Gyllborg D, Miller JA, ..., Hilscher MM, Nilsson M

- - (-) - [2021-01-28; online 2021-01-28]

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]

DOI Crossref

Human Developmental Cell Atlas: milestones achieved and the roadmap ahead

Haniffa M, Taylor D, Linnarsson S, ..., Vento-Tormo R, Webb S

- - (-) - [2020-10-12; online 2020-10-12]

DOI Crossref

Real‐time analysis of switchable nanocomposites of magnesium pyrophosphates and rolling circle amplification products

Minero GAS, Fock J, Tian B, ..., Nilsson M, Fougt Hansen M

ChemNanoMat 6 (8) 1276-1282 [2020-08-00; online 2020-04-21]

DOI Crossref

Molecular architecture of the developing mouse brain

La Manno G, Siletti K, Furlan A, ..., Lönnerberg P, Linnarsson S

- - (-) - [2020-07-03; online 2020-07-03]

DOI Crossref

SCRINSHOT, a spatial method for single-cell resolution mapping of cell states in tissue sections

Sountoulidis A, Liontos A, Nguyen HP, ..., Nilsson M, Samakovlis C

- - (-) - [2020-02-07; online 2020-02-07]

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]

DOI Crossref

Identification of spatial compartments in tissue from in situ sequencing data

Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C

- - (-) - [2019-09-18; online 2019-09-18]

PubMed DOI Crossref

Smartphone-based clinical diagnostics: towards democratization of evidence-based health care.

Hernández-Neuta I, Neumann F, Brightmeyer J, ..., Ozcan A, Nilsson M

J. Intern. Med. 285 (1) 19-39 [2019-01-00; online 2018-09-12]