Nilsson M

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]

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]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service] In Situ Sequencing (ISS) [Service]

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]

Bioinformatics Support for Computational Resources [Service]

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]

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]

In Situ Sequencing (ISS) [Collaborative]

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 [Technology development] Spatial Proteomics [Service]

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]

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]

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]

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]

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]

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 (NBIS) [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]

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]

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] Bioinformatics (NBIS) [Collaborative] In Situ Sequencing (ISS) [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

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] Bioinformatics (NBIS) [Service] In Situ Sequencing (ISS) [Collaborative]

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]

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

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]

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]

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]

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]

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]

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 (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]

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]

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]

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]

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]

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]

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]

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]

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 [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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 (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Collaborative]

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]

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 (NBIS) [Collaborative] 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]

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 [Collaborative] Clinical Genomics Uppsala [Collaborative]

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]

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] Bioinformatics (NBIS) [Collaborative]

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]

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 [Collaborative] Clinical Genomics Uppsala [Collaborative]

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]

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]

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 [Collaborative] Clinical Genomics Uppsala [Collaborative]

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 Clinical Genomics Uppsala NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

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] Bioinformatics (NBIS) [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]

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

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

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

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

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