Publications

Preprints


Molecular Atlas Of The Adult Mouse Brain
Ortiz C, Navarro J, Jurek A, Martin A, Lundeberg J, and Meletis K
Available at bioRxiv

An organ-wide gene expression atlas of the developing human heart
Asp M, Giacomello S, Fürth D, Reimegård J, Wärdell E, Custodio J, Salmén F, Sundström E, Åkesson E, Bienko M, Månsson-Broberg A, Ståhl PL, Sylvén C, and Lundeberg J
Available at SSRN

Charting Tissue Expression Anatomy by Spatial Transcriptome Deconvolution
Maaskola J, Bergenstråhle L, Jurek A, Fernández Navarro J, Lagergren J, and Lundeberg J
Available at bioRxiv

Multidimensional transcriptomics provides detailed information about immune cell distribution and identity in HER2+ breast tumors
Salmén F, Vickovic S, Larsson L, Stenbeck L, Vallon-Christersson J, Ehinger A, Häkkinen J, Borg Å, Frisén J, Ståhl PL and Lundeberg J
Available at bioRxiv

2019


A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection
Poux C, Dondalska A, Bergenstråhle J, Pålsson S, Contreras V, Arasa C, Järver P, Albert J, Busse DC, LeGrand R, Lundeberg J, Tregoning JS, Spetz AL
Frontiers in Immunology (2019)

High-density spatial transcriptomics arrays for in situ tissue profiling
Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Äijö T, Bonneau R, Bergenstråhle L, Fernandéz Navarro J, Gould J, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL
Nature Methods (2019)

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
Maniatis S, Äijö T, Vickovic S, Braine C, Kang K, Mollbrink A, Fagegaltier D, Andrusivova Z, Saarenpää S, Saiz-Castro G, Cuevas M, Watters A, Lundeberg J, Bonneau R, Phatnani H
Science (2019)

ST Viewer: A tool for analysis and visualization of Spatial Transcriptomics datasets
Fernández Navarro J, Lundeberg J and Ståhl PL
Bioinformatics (2019)

2018


Barcoded solid phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
Salmén F, Ståhl PL, Mollbrink A, Fernández Navarro J, Vickovic S, Frisén J & Lundeberg J
Nature Protocols (2018)

Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays
Giacomello S and Lundeberg J
Nature Protocols (2018)

Dissecting genetic heterogeneity in Stage III cutaneous malignant melanoma with spatially resolved transcriptomics
Thrane K, Eriksson H, Maaskola J, Hansson J, and Lundeberg J
Cancer Research (2018)

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmeń F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J
Nature Communications (2018)

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics
Lundmark A, Gerasimcik N, Båge T, Jemt A, Mollbrink A, Salmén F, Lundeberg J, Yucel-Lindberg T
Scientific Reports (2018)

ST Spot Detector: a web-based application for automatic spot and tissue detection for Spatial Transcriptomics image data sets
Wong K, Navarro JF, Bergenstråhle L, Ståhl PL, Lundeberg J
Bioinformatics (2018)

2017


Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Asp M, Salmén F, Ståhl PL, Vickovic S, Felldin U, Löfling M, Navarro JF, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J
Scientific Reports (2017)

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts
Navarro J F, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL
Bioinformatics (2017)

Spatially resolved transcriptome profiling in model plant species
Giacomello S, Salmén F, Terebieniec B K, Vickovic S, Navarro J F, Alexeyenko A, Reimegård J, McKee L S, Mannapperuma C, Bulone V, Ståhl P L, Sundström J F, Street N R, Lundeberg J
Nature Plants (2017)

2016


An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Jemt A, Salmén F, Lundmark A, Mollbrink A, Fernández Navarro J, Ståhl PL, Tülay YL, Lundeberg J
Scientific Reports (2016)

Massive and parallel expression profiling using microarrayed single-cell sequencing
Vickovic S, Ståhl PL, Salmén F, Giatrelis S, Westholm JO, Mollbrink A, Fernández Navarro J, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J
Nature Communications (2016)

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
Ståhl PL, Salmén F, Vickovic S, Lundmark A, Fernández Navarro J, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, PI Costea, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J
Science (2016)

2015


Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring
Kvastad L, Werne Solnestam B, Johansson E, Nygren AO, Laddach N, Sahlén P, Vickovic S, Bendigtsen SC, Aaserud M, Floer L, Borgen E, Schwind C, Himmelreich R, Latta D, Lundeberg J
Scientific Reports (2015)

Toward Rare Blood Cell Preservation for RNA Sequencing
Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J
The Journal of Molecular Diagnostics (2015)

2014


Sequencing degraded RNA addressed by 3′ tag counting
Sigurgeirsson B, Emanuelsson O, Lundeberg J
PLoS One (2014)

2013


TagGD: fast and accurate software for DNA Tag generation and demultiplexing
Costea PI, Lundeberg J, Akan P
PLoS One (2013)