Padlock Probe-Based Targeted In Situ Sequencing: Overview of Methods and Applications.

Anastasia Magoulopoulou, Sergio Marco Salas, Katarína Tiklová, Erik R Samuelsson, Markus M. Hilscher, M. Nilsson

Annual review of genomics and human genetics (Print), 2023

Fourth Generation of Next‐Generation Sequencing Technologies: Promise and Consequences

Rongqin Ke, Marco Mignardi, T. Hauling, M. Nilsson

Human Mutation, 2016

Next-generation pathology--surveillance of tumor microecology.

B. Koos, M. Kamali-Moghaddam, L. David, M. Sobrinho-Simões, A. Dimberg, M. Nilsson, Carolina Wählby, O. Söderberg

Journal of Molecular Biology, 2015

Fourth-generation sequencing in the cell and the clinic

Marco Mignardi, M. Nilsson

Genome Medicine, 2014

Spatial Multimodal Analysis of Transcriptomes and Metabolomes in Tissues

Marco Vicari, R. Mirzazadeh, A. Nilsson, Reza Shariatgorji, Patrik Bjärterot, L. Larsson, Hower Lee, M. Nilsson, Julia Foyer, Markus Ekvall, Paulo Czarnewski, Xiaoqun Zhang, P. Svenningsson, P. Andrén, J. Lundeberg

bioRxiv, 2023

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

Sergio Marco Salas, Paulo Czarnewski, L. B. Kuemmerle, Saga Helgadottir, Christoffer Matsson-Langseth, Sebastian Tismeyer, Christophe Avenel, Habib Rehman, Katarina Tiklova, Axel Andersson, Maria Chatzinikolaou, F. Theis, Malte D. Luecken, C. Wählby, Naveed Ishaque, M. Nilsson

bioRxiv, 2023

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

Erik L. G. Wernersson, Eleni Gelali, Gabriele Girelli, Su Wang, David Castillo, C. Langseth, Huy Nguyen, Shyamtanu Chattoraj, Anna Martinez Casals, E. Lundberg, M. Nilsson, M. Martí-Renom, Chao-ting Wu, N. Crosetto, M. Bienko

2022

Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue

Hower Lee, Sergio Marco Salas, Daniel Gyllborg, M. Nilsson

Scientific Reports, 2022

De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks

Sergio Marco Salas, Xiao Yuan, Christer Sylven, M. Nilsson, C. Wählby, Gabriele Partel

PLoS Comput. Biol., 2022

PoSTcode: Probabilistic image-based spatial transcriptomics decoder

M. Gataric, Jun Sung Park, Tong Li, Vasyl Vaskivskyi, J. Svedlund, C. Strell, Kenny Roberts, M. Nilsson, L. Yates, O. Bayraktar, M. Gerstung

bioRxiv, 2021

Matisse: a MATLAB-based analysis toolbox for in situ sequencing expression maps

Sergio Marco Salas, Daniel Gyllborg, C. Langseth, M. Nilsson

BMC Bioinformatics, 2021

Automated identification of the mouse brain’s spatial compartments from in situ sequencing data

Gabriele Partel, Markus M. Hilscher, G. Milli, L. Solorzano, Anna H. Klemm, M. Nilsson, Carolina Wählby

BMC Biology, 2020

Single cell RNA expression analysis using flow cytometry based on specific probe ligation and rolling circle amplification.

Yansong Zhao, Chen Lin, Pengcheng Wu, Xiaoyuan Chen, Yuancun Zhao, Yupeng Li, Lu Chen, M. Nilsson, Rongqin Ke

ACS Sensors, 2020

Probabilistic cell typing enables fine mapping of closely related cell types in situ

Xiaoyan Qian, K. Harris, T. Hauling, Dimitris Nicoloutsopoulos, A. B. Muñoz-Manchado, N. Skene, J. Hjerling-Leffler, M. Nilsson

Nature Methods, 2019

RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples

Chenglin Wu, Michele Simonetti, Carla Rossell, Marco Mignardi, R. Mirzazadeh, L. Annaratone, C. Marchiò, A. Sapino, M. Bienko, N. Crosetto, M. Nilsson

Communications Biology, 2018

Emerging fluorescence technology to study the spatial and temporal dynamics of organelles within cells

L. Solorzano, Maxime Bombrun, P. Ranefall, Joakim Lindblad, Amin Allalou, Gabriele, Partel, Xiaoyan Qian, M. Nilsson, Carolina Wählby, Hui Gao, N. Mejhert, Peter Arne

2017

Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ

Marco Mignardi, A. Mezger, Xiaoyan Qian, L. La Fleur, J. Botling, Chatarina Larsson, M. Nilsson

Nucleic Acids Research, 2015

Image based in situ sequencing for RNA analysis in tissue

A. Pacureanu, Rongqin Ke, Marco Mignardi, M. Nilsson, Carolina Wählby

IEEE International Symposium on Biomedical Imaging, 2014

In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay

I. Weibrecht, Elin Lundin, Sara Kiflemariam, Marco Mignardi, I. Grundberg, Chatarina Larsson, B. Koos, M. Nilsson, O. Söderberg

Nature Protocols, 2013

In situ sequencing for RNA analysis in preserved tissue and cells

Rongqin Ke, Marco Mignardi, A. Pacureanu, J. Svedlund, J. Botling, Carolina Wählby, M. Nilsson

Nature Methods, 2013

Simultaneous Visualization of Both Signaling Cascade Activity and End-Point Gene Expression in Single Cells

I. Weibrecht, I. Grundberg, M. Nilsson, O. Söderberg

PLoS ONE, 2011

Study of gene-specific DNA repair in the comet assay with padlock probes and rolling circle amplification.

S. Henriksson, S. Shaposhnikov, M. Nilsson, A. Collins

Toxicology Letters, 2011

In situ detection and genotyping of individual mRNA molecules

Chatarina Larsson, I. Grundberg, O. Söderberg, M. Nilsson

Nature Methods, 2010

Detection of Alu sequences and mtDNA in comets using padlock probes.

S. Shaposhnikov, Chatarina Larsson, S. Henriksson, A. Collins, M. Nilsson

Mutagenesis, 2006

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

A. Lomakin, J. Svedlund, C. Strell, M. Gataric, Artem Shmatko, Gleb D. Rukhovich, Jun Sung Park, Y. Ju, S. Dentro, Vitalii Kleshchevnikov, Vasyl Vaskivskyi, Tong Li, O. Bayraktar, Sarah Pinder, A. Richardson, S. Santagata, P. Campbell, H. Russnes, M. Gerstung, M. Nilsson, L. Yates

Nature, 2022

Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma

C. Ruiz-Moreno, Sergio Marco Salas, Erik R Samuelsson, S. Brandner, M. Kranendonk, M. Nilsson, H. Stunnenberg

bioRxiv, 2022

EPCO-21. THE SPATIAL ORGANIZATION OF H3-K27M MUTANT DIFFUSE MIDLINE GLIOMA

Ilon Liu, Jiang Li, Erik R Samuelsson, Sergio Marco Salas, A. Beck, Olivia A Hack, Daeun Jeong, McKenzie L Shaw, B. Englinger, Jenna LaBelle, Hafsa M Mire, S. Madlener, Lisa Mayr, Michael A Quezada, Maria C Trissal, E. Panditharatna, K. Ernst, Taylor A. Gatesman, Matthew J Halbert, Hana Pálová, P. Pokorná, J. Štěrba, O. Slabý, R. Geyeregger, A. Diaz, A. Resnick, M. Suvà, David Jones, S. Agnihotri, Jessica Ostlin, C. Koschmann, C. Haberler, T. Czech, I. Slavc, J. Cotter, K. Ligon, S. Alexandrescu, W. Yung, I. Arrillaga-Romany, J. Gojo, M. Monje, M. Nilsson, Mariella G. Filbin

Neuro-Oncology, 2022

The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location

Ilon Liu, Li Jiang, Erik R Samuelsson, Sergio Marco Salas, A. Beck, Olivia A Hack, Daeun Jeong, McKenzie L Shaw, B. Englinger, Jenna LaBelle, Hafsa M Mire, S. Madlener, Lisa Mayr, Michael A Quezada, Maria C Trissal, E. Panditharatna, K. Ernst, Jayne Vogelzang, Taylor A. Gatesman, Matthew E. Halbert, Hana Pálová, P. Pokorná, J. Štěrba, O. Slabý, R. Geyeregger, A. Diaz, Izac J. Findlay, M. Dun, A. Resnick, M. Suvà, David C. Jones, S. Agnihotri, J. Svedlund, C. Koschmann, C. Haberler, T. Czech, I. Slavc, J. Cotter, K. Ligon, S. Alexandrescu, W. Yung, I. Arrillaga-Romany, J. Gojo, M. Monje, M. Nilsson, Mariella G. Filbin

Nature Genetics, 2022

In situ sequencing identifies TMPRSS2–ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers

Sara Kiflemariam, Marco Mignardi, Muhammad Akhtar Ali, A. Bergh, M. Nilsson, T. Sjöblom

Journal of Pathology, 2014

Regeneration-associated WNT signaling is activated in long-term reconstituting AC133bright acute myeloid leukemia cells.

A. Beghini, F. Corlazzoli, L. Del Giacco, M. Ré, F. Lazzaroni, Matteo Brioschi, G. Valentini, F. Ferrazzi, A. Ghilardi, M. Righi, M. Turrini, Marco Mignardi, C. Cesana, V. Bronte, M. Nilsson, E. Morra, R. Cairoli

Neoplasia, 2012

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung

A. Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, J. Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, A. Liontos, X. Abalo, Žaneta Andrusivová, R. Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, B. Ayoglu, A. Firsova, J. Michaëlsson, E. Lundberg, C. Wählby, E. Sundström, S. Linnarsson, J. Lundeberg, M. Nilsson, C. Samakovlis

Nature Cell Biology, 2023

Spatial Resolution of Mycobacterium tuberculosis Bacteria and Their Surrounding Immune Environments Based on Selected Key Transcripts in Mouse Lungs

Anastasia Magoulopoulou, Xiaoyan Qian, Todia Pediatama Setiabudiawan, Sergio Marco Salas, C. Yokota, M. Rottenberg, M. Nilsson, B. Carow

Frontiers in Immunology, 2022

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma

B. Carow, T. Hauling, Xiaoyan Qian, I. Kramnik, M. Nilsson, M. Rottenberg

bioRxiv, 2019

Non-Random mtDNA Segregation Patterns Indicate a Metastable Heteroplasmic Segregation Unit in m.3243A>G Cybrid Cells

A. Raap, Roshan S Jahangir Tafrechi, F. M. van de Rijke, A. Pyle, Carolina Wählby, K. Szuhai, R. Ravelli, R. de Coo, H. Rajasimha, M. Nilsson, P. Chinnery, D. Samuels, G. Janssen

PLoS ONE, 2012

OPENchip: an on-chip in situ molecular profiling platform for gene expression analysis and oncogenic mutation detection in single circulating tumour cells.

A. C. Lee, J. Svedlund, E. Darai, Yongju Lee, Daewon Lee, Han-Byoel Lee, Sung-Min Kim, Okju Kim, H. Bae, Ahyoun Choi, Sumin Lee, Yunjin Jeong, S. Song, Yeongjae Choi, Huiran Yeom, Caleb S. Lee, W. Han, D. S. Lee, Jin-Young Jang, N. Madaboosi, M. Nilsson, Sunghoon Kwon

Lab on a Chip, 2020

A microfluidic platform towards automated multiplexed in situ sequencing

N. Maïno, T. Hauling, G. Cappi, N. Madaboosi, D. Dupouy, M. Nilsson

Scientific Reports, 2019

Title Analysis of IAV Replication and Co-infection Dynamics bya Versatile RNA Viral Genome Labeling Method

D. Dou, I. Hernández-Neuta, Hao Wang, Henrik Östbye, Xiaoyan Qian, Swantje Thiele, Patricia Resa-Infante, Nancy Mounogou Kouassi, V. Sender, K. Hentrich, P. Mellroth, B. Henriques-Normark, ulsah Gabriel, M. Nilsson, R. Daniels

2018

Analysis of IAV Replication and Co-infection Dynamics by a Versatile RNA Viral Genome Labeling Method.

D. Dou, I. Hernández-Neuta, Hao Wang, Henrik Östbye, Xiaoyan Qian, Swantje Thiele, Patricia Resa-Infante, Nancy Mounogou Kouassi, V. Sender, K. Hentrich, P. Mellroth, B. Henriques-Normark, G. Gabriel, M. Nilsson, R. Daniels

Cell Reports, 2017

In situ rolling circle amplification detection of Crimean Congo hemorrhagic fever virus (CCHFV) complementary and viral RNA.

C. Andersson, S. Henriksson, K. Magnusson, M. Nilsson, A. Mirazimi

Virology, 2012

Methods for analysis of the cancer microenvironment and their potential for disease prediction, monitoring and personalized treatments

C. Clausson, I. Grundberg, I. Weibrecht, M. Nilsson, O. Söderberg

The EPMA Journal, 2012

Padlock probes and rolling circle amplification for detection of repeats and single-copy genes in the single-cell comet assay.

S. Henriksson, M. Nilsson

Methods in molecular biology, 2012

Different localization of CCHFV vRNA compared cRNA during infection as determined by in situ padlock probe detection

C. Andersson, S. Henriksson, M. Nilsson, A. Mirazimi

2010

Spatial and temporal heterogeneity in the lineage progression of fine oligodendrocyte subtypes

Markus M. Hilscher, C. Langseth, Petra Kukanja, C. Yokota, M. Nilsson, G. Castelo-Branco

BMC Biology, 2022

Spatial cell type mapping of the oligodendrocyte lineage in the mouse juvenile and adult CNS with in situ sequencing

Markus M. Hilscher, C. Langseth, Petra Kukanja, C. Yokota, M. Nilsson, G. Castelo-Branco

bioRxiv, 2021

A spatial atlas of inhibitory cell types in mouse hippocampus

Xiaoyan Qian, K. Harris, T. Hauling, Dimitris Nicoloutsopoulos, A. B. Muñoz-Manchado, N. Skene, J. Hjerling-Leffler, M. Nilsson

bioRxiv, 2018

Developmental origins of cell heterogeneity in the human lung

A. Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, J. Bergenstråhle, Marco Vicari, Paulo Czarnewski, Jonas Theelke, A. Liontos, X. Abalo, Žaneta Andrusivová, Michaela Asp, Xiaofei Li, L. Hu, Sanem Sariyar, Anna Martinez Casals, B. Ayoglu, A. Firsova, J. Michaëlsson, E. Lundberg, C. Wählby, E. Sundström, S. Linnarsson, J. Lundeberg, M. Nilsson, C. Samakovlis

bioRxiv, 2022

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

David van Bruggen, Fabio Pohl, C. Langseth, Petra Kukanja, Hower Lee, Alejandro Mossi Albiach, Mukund Kabbe, M. Meijer, S. Linnarsson, Markus M. Hilscher, M. Nilsson, E. Sundström, G. Castelo-Branco

Developmental Cell, 2022

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin

Xiaofei Li, Žaneta Andrusivová, Paulo Czarnewski, C. Langseth, Alma Andersson, Y. Liu, Daniel Gyllborg, Emelie Braun, L. Larsson, Lijuan Hu, Zhanna Alekseenko, Hower Lee, Christophe Avenel, H. Kallner, E. Åkesson, I. Adameyko, M. Nilsson, S. Linnarsson, J. Lundeberg, E. Sundström

bioRxiv, 2022

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

David van Bruggen, Fabio Pohl, C. Langseth, Petra Kukanja, Hower Lee, Mukund Kabbe, M. Meijer, Markus M. Hilscher, M. Nilsson, E. Sundström, G. Castelo-Branco

bioRxiv, 2021

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

Sergio Marco Salas, Xiao-ying Yuan, C. Sylvén, M. Nilsson, Carolina Wählby, Gabriele Partel

bioRxiv, 2021

Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development

Katarina Tiklova, Åsa K. Björklund, L. Lahti, A. Fiorenzano, Sara Nolbrant, L. Gillberg, N. Volakakis, C. Yokota, Markus M. Hilscher, T. Hauling, Fredrik Holmström, E. Joodmardi, M. Nilsson, M. Parmar, T. Perlmann

Nature Communications, 2019

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

Michaela Asp, S. Giacomello, L. Larsson, Chenglin Wu, Daniel Fürth, Xiaoyan Qian, E. Wärdell, Joaquín Custodio, Johan Reimegård, Fredrik Salmén, C. Österholm, Patrik L. Ståhl, E. Sundström, E. Åkesson, O. Bergmann, M. Bienko, A. Månsson-Broberg, M. Nilsson, C. Sylvén, J. Lundeberg

Cell, 2019

Spatiotemporal structure of cell fate decisions in murine neural crest

R. Soldatov, M. Kaucká, M. Kastriti, Julian Petersen, T. Chontorotzea, Lukas Englmaier, N. Akkuratova, Yunshi Yang, M. Häring, V. Dyachuk, C. Bock, M. Farlik, Michael L. Piacentino, F. Boismoreau, Markus M. Hilscher, C. Yokota, Xiaoyan Qian, M. Nilsson, M. Bronner, L. Croci, W. Hsiao, D. Guertin, J. Brunet, G. Consalez, P. Ernfors, K. Fried, P. Kharchenko, I. Adameyko

Science, 2019

Alternative Splicing of the Chromodomain Protein Morf4l1 Pre-mRNA Has Implications on Cell Differentiation in the Developing Chicken Retina

H. Boije, H. Ring, S. Shirazi Fard, I. Grundberg, M. Nilsson, F. Hallböök

Journal of Molecular Neuroscience, 2013

Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet.

J. Salamon, Xiaoyan Qian, M. Nilsson, D. Lynn

Cell Systems, 2018