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Items: 22

1.

High-definition spatial transcriptomics for in situ tissue profiling.

Vickovic S, Eraslan G, Salmén F, Klughammer J, Stenbeck L, Schapiro D, Äijö T, Bonneau R, Bergenstråhle L, Navarro JF, Gould J, Griffin GK, Borg Å, Ronaghi M, Frisén J, Lundeberg J, Regev A, Ståhl PL.

Nat Methods. 2019 Oct;16(10):987-990. doi: 10.1038/s41592-019-0548-y. Epub 2019 Sep 9.

PMID:
31501547
2.

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing.

Hård J, Al Hakim E, Kindblom M, Björklund ÅK, Sennblad B, Demirci I, Paterlini M, Reu P, Borgström E, Ståhl PL, Michaelsson J, Mold JE, Frisén J.

Genome Biol. 2019 Apr 1;20(1):68. doi: 10.1186/s13059-019-1673-8.

3.

ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets.

Fernández Navarro J, Lundeberg J, Ståhl PL.

Bioinformatics. 2019 Mar 15;35(6):1058-1060. doi: 10.1093/bioinformatics/bty714.

PMID:
30875427
4.

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.

Salmén F, Ståhl PL, Mollbrink A, Navarro JF, Vickovic S, Frisén J, Lundeberg J.

Nat Protoc. 2018 Nov;13(11):2501-2534. doi: 10.1038/s41596-018-0045-2.

PMID:
30353172
5.

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets.

Wong K, Navarro JF, Bergenstråhle L, Ståhl PL, Lundeberg J.

Bioinformatics. 2018 Jun 1;34(11):1966-1968. doi: 10.1093/bioinformatics/bty030.

PMID:
29360929
6.

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, Fernandez Navarro J, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J.

Sci Rep. 2017 Oct 11;7(1):12941. doi: 10.1038/s41598-017-13462-5.

7.

Spatially resolved transcriptome profiling in model plant species.

Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J.

Nat Plants. 2017 May 8;3:17061. doi: 10.1038/nplants.2017.61.

PMID:
28481330
8.

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts.

Navarro JF, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL.

Bioinformatics. 2017 Aug 15;33(16):2591-2593. doi: 10.1093/bioinformatics/btx211.

PMID:
28398467
9.

Corrigendum: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.

Jemt A, Salmén F, Lundmark A, Mollbrink A, Navarro JF, Ståhl PL, Yucel-Lindberg T, Lundeberg J.

Sci Rep. 2017 Mar 13;7:41109. doi: 10.1038/srep41109. No abstract available.

10.

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, Yucel-Lindberg T, Lundeberg J.

Sci Rep. 2016 Nov 16;6:37137. doi: 10.1038/srep37137. Erratum in: Sci Rep. 2017 Mar 13;7:41109.

11.

Massive and parallel expression profiling using microarrayed single-cell sequencing.

Vickovic S, Ståhl PL, Salmén F, Giatrellis S, Westholm JO, Mollbrink A, Navarro JF, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J.

Nat Commun. 2016 Oct 14;7:13182. doi: 10.1038/ncomms13182.

12.

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J.

Science. 2016 Jul 1;353(6294):78-82. doi: 10.1126/science.aaf2403.

13.

Visual detection of DNA on paper chips.

Song Y, Gyarmati P, Araújo AC, Lundeberg J, Brumer H 3rd, Ståhl PL.

Anal Chem. 2014 Feb 4;86(3):1575-82. doi: 10.1021/ac403196b. Epub 2014 Jan 17.

PMID:
24383957
14.

A novel method for rapid hybridization of DNA to a solid support.

Pettersson E, Ahmadian A, Ståhl PL.

PLoS One. 2013 Aug 12;8(8):e70504. doi: 10.1371/journal.pone.0070504. eCollection 2013.

15.

Toward the single-hour high-quality genome.

Ståhl PL, Lundeberg J.

Annu Rev Biochem. 2012;81:359-78. doi: 10.1146/annurev-biochem-060410-094158. Epub 2012 Mar 20. Review.

PMID:
22443932
16.

Activated paper surfaces for the rapid hybridization of DNA through capillary transport.

Araújo AC, Song Y, Lundeberg J, Ståhl PL, Brumer H 3rd.

Anal Chem. 2012 Apr 3;84(7):3311-7. doi: 10.1021/ac300025v. Epub 2012 Mar 12. Erratum in: Anal Chem. 2013 Dec 3;85(23):11676.

PMID:
22369042
17.

Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.

Ståhl PL, Bjursell MK, Mahdessian H, Hober S, Jirström K, Lundeberg J.

PLoS One. 2011;6(6):e20794. doi: 10.1371/journal.pone.0020794. Epub 2011 Jun 15.

18.

Sun-induced nonsynonymous p53 mutations are extensively accumulated and tolerated in normal appearing human skin.

Ståhl PL, Stranneheim H, Asplund A, Berglund L, Pontén F, Lundeberg J.

J Invest Dermatol. 2011 Feb;131(2):504-8. doi: 10.1038/jid.2010.302. Epub 2010 Oct 14.

19.

Visual DNA as a diagnostic tool.

Pettersson E, Ståhl PL, Mahdessian H, Käller M, Lundeberg J, Ahmadian A.

Electrophoresis. 2009 Nov;30(21):3691-5. doi: 10.1002/elps.200900273.

PMID:
19862744
20.

Flow cytometry for enrichment and titration in massively parallel DNA sequencing.

Sandberg J, Ståhl PL, Ahmadian A, Bjursell MK, Lundeberg J.

Nucleic Acids Res. 2009 May;37(8):e63. doi: 10.1093/nar/gkp188. Epub 2009 Mar 20.

21.

Allelotyping by massively parallel pyrosequencing of SNP-carrying trinucleotide threads.

Pettersson E, Zajac P, Ståhl PL, Jacobsson JA, Fredriksson R, Marcus C, Schiöth HB, Lundeberg J, Ahmadian A.

Hum Mutat. 2008 Feb;29(2):323-9.

PMID:
17994569
22.

Visual DNA -- identification of DNA sequence variations by bead trapping.

Ståhl PL, Gantelius J, Natanaelsson C, Ahmadian A, Andersson-Svahn H, Lundeberg J.

Genomics. 2007 Dec;90(6):741-5. Epub 2007 Oct 24.

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