Sandberg Lab

Ludwig Institute for Cancer Research & Department of Cell and Molecular Biology, Karolinska Institutet


A complete list of publications is available here.

Genomic encoding of transcriptional burst kinetics
Anton JM Larsson, Per Johnsson, Michael Hagemann-Jensen, Leonard Hartmanis, Omid R Faridani, Björn Reinius, Åsa Segerstolpe, Chloe M Rivera, Bing Ren, Rickard Sandberg
Nature (2019) January 10

Computational correction of index switching in multiplexed sequencing libraries
Anton JM Larsson, Geoff Stanley, Rahul Sinha, Irving L Weissman, Rickard Sandberg
Nature Methods (2018) 15, pages 305–307.

Identification of spatial expression trends in single-cell gene expression data
Edsgärd D, Johnsson P, Sandberg R.
Nature Methods (2018). doi:10.1038/nmeth.4634

Single-cell sequencing of the small-RNA transcriptome
Faridani OR1, Abdullayev I1, Hagemann-Jensen M, Schnell JP, Lanner F and Sandberg R
Nature Biotechnology (2016) 34, 1264–1266.

Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq
Björn Reinius*, Jeff E Mold*, Daniel Ramsköld, Qiaolin Deng, Per Johnsson, Jakob Michaelsson, Jonas Frisén & Rickard Sandberg
Nature Genetics (2016) doi:10.1038/ng.3678

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes
Segerstolpe Å*, Palasantza A*, Eliasson P, Andersson E-M, Andréasson A-C, Sun X, Picelli S, Sabirsh A, Clausen M, Bjursell MK, Smith DM, Kasper M, Änmälä C and Sandberg R
Cell Metabolism (2016) 24, 1–15.

scphaser: haplotype inference using single- cell RNA-seq data
Daniel Edsgärd, Björn Reninius and Rickard Sandberg
Bioinformatics. Advance Access

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos
Sophie Petropoulos*, Daniel Edsgärd*, Björn Reinius*, Qiaolin Deng, Sarita Pauliina Panula, Simone Codeluppi, Alvaro Plaza Reyes, Sten Linnarsson, Rickard Sandberg**, Fredrik Lanner**
Cell (2016) 10.1016/j.cell.2016.03.023

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing
Åsa K. Björklund*, Marianne Forkel*, Simone Picelli, Viktoria Konya, Jakob Theorell, Danielle Friberg, Rickard Sandberg**, Jenny Mjösberg**
Nature Immunology (2016) online 15 February, doi:10.1038/ni.3368

Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq
CR Cadwell*, A Palasantza*, X Jiang, P Berens, Q Deng, M Yilmaz, J Reimer, S Shen, M Bethge, KF Tobias, R Sandberg** & AS Tolias**
Nature Biotechnology (2015) Advance Online Publication Dec 21

Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation
Björn Reinius and Rickard Sandberg
Nature Review Genetics (2015) Oct 7. do:10.1038/nrg3888

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.
Pelin Sahlén*, Ilgar Abdullayev*, Daniel Ramsköld, Liudmila Matskova, Nemanja Rilakovic, Britta Lötstedt, Thomas J. Albert, Joakim Lundeberg, Rickard Sandberg
Genome Biology (2015) 16:156, doi:10.1186/s13059-015-0727-9

BMP Signaling and Its pSMAD1/5 Target Genes Differentially Regulate Hair Follicle Stem Cell Lineages
Maria Genander, Peter J Cook, Daniel Ramsköld, Brice E Keyes, Aaron F Mertz, Rickard Sandberg, Elaine Fuchs
Cell Stem Cell (2014), 15 (5), 619-633

Tn5 transposase and tagmentation procedures for massively-scaled sequencing projects
Picelli S, Björklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R.
Genome Res. (2014) Jul 30.

Myelodysplastic Syndromes Are Propagated by Rare and Distinct Human Cancer Stem Cells In Vivo
Petter S. Woll et al.
Cancer Cell (2014) 25, 6: 794–808

Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells
Qiaolin Deng*, Daniel Ramsköld*, Björn Reinius, Rickard Sandberg
Science (2014). Vol. 343 no. 6167 pp. 193-196.

Full-length RNA-seq from single cells using Smart-seq2
Simone Picelli, Omid R Faridani, Åsa K Björklund, Gösta Winberg, Sven Sagasser & Rickard Sandberg
Nature Protocols (2014). 9, 171–181.

Entering the era of single-cell transcriptomics in biology and medicine
Rickard Sandberg
Nature Methods (2014). 11, 22–24.

Smart-seq2 for sensitive full-length transcriptome profiling in single cells
Simone Picelli, Åsa K. Björklund, Omid R. Faridani, Sven Sagasser, Gösta Winberg and Rickard Sandberg
Nature Methods (2013). doi:10.1038/nmeth.2639

A reference transcriptome and inferred proteome for the salamander Notophthalmus viridescens
Ilgar Abdullayev, Matthew Kirkham, Åsa K. Björklund, András Simon, Rickard Sandberg
Exp Cell Res. 2013 Feb 28. doi:pii: S0014-4827(13)00069-4. 10.1016/j.yexcr.2013.02.013.

Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses
Helena Storvall, Daniel Ramsköld, Rickard Sandberg
PLoS ONE. 2013. 8(1): e53822. doi:10.1371/journal.pone.0053822

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
Daniel Ramsköld, Shujun Luo, Yu-Chieh Wang, Robin Li, Qiaolin Deng, Omid R Faridani, Gregory A Daniels, Irina Khrebtukova, Jeanne F Loring, Louise C Laurent, Gary P Schroth & Rickard Sandberg
Nature Biotechnology 2012. 30, 777–782

How to analyze gene expression using RNA-Sequencing data
*Ramskold D, *Kavak E and Sandberg R
Meth Mol Biol 2012. Volume 802, Part 4, 259-274. (NOTE: written and submitted Aug 2010)

Sequentially Acting Sox Transcription Factors in Neural Lineage Development
*Bergsland M., *Ramskold D., Zaouter C., Klum S., **Sandberg R., **Muhr J
Genes & Development 2011. 25: 453-464 (Dec 1st)

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
Sanjeev Shukla, Ersen Kavak, Melissa Gregory, Masahiko Imashimizu, Bojan Shutinoski, Mikhail Kashlev, Philipp Oberdoerffer, Rickard Sandberg & Shalini Oberdoerffer
Nature 2011. 479, 74–79 (03 November)

Notch signaling: simplicity in design - versatility in function
Emma Andersson, Rickard Sandberg, and Urban Lendahl
Development 2011. September 1, 138, 3593-3612.

Transcription Factor-Induced Lineage Selection of Stem-Cell-Derived Neural Progenitor Cells
Lia Panman, Elisabet Andersson, Zhanna Alekseenko, Eva Hedlund, Nigel Kee, Jamie Mong, Christopher W. Uhde, Qiaolin Deng, Rickard Sandberg, Lawrence W. Stanton, Johan Ericson, Thomas Perlmann
Cell Stem Cell 2011. Volume 8, Issue 6, 663-675

Heterogeneity in mammalian RNA 3′ end formation
Joel R. Neilson and Rickard Sandberg
Exp Cell Res 2010. doi:10.1016/j.yexcr.2010.02.040

An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
Ramskold D, Wang ET, **Burge CB, **Sandberg R
PLoS Comput Biol 2009. 5(12): e1000598. doi:10.1371/journal.pcbi.1000598

Alternative Isoform Regulation in Human Tissue Transcriptomes
*Wang ET, *Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB.
Nature 2008. 27 Nov. 456, 470-476

Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites
*Sandberg R, *Neilson JR, Sarma, Sharp PA and Burge CB
Science. 2008. 320, 5883, 1643-7

Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
CB Nielsen, N Shomron, R Sandberg, E Hornstein, J Kitzman and CB Burge
RNA. 2007. Nov;13(11):1894-910.

Improved precision and accuracy for microarrays using updated probe set definitions
Rickard Sandberg and Ola Larsson
BMC Bioinformatics. 2007. 8, 48

Lack of correct data format and comparability limits future integrative microarray research
Ola Larsson and Rickard Sandberg
Nat Biotechnol. 2006. 24, 11, 1322-3

Comparative microarray analysis
Ola Larsson, Kristian Wennmalm and Rickard Sandberg
Omics. 2006. 10, 3, 381-97

Gene expression perturbation in vitro- a growing case for three-dimensional (3D) culture systems
Anna Birgersdotter, Rickard Sandberg and Ingemar Ernberg
Semin Cancer Biol. 2005. 15, 5, 405-12

The molecular portrait of in vitro growth by meta-analysis of gene-expression profiles
Rickard Sandberg and Ingemar Ernberg
Genome Biol. 2005. 6, 8, R65

Assessment of tumor characteristic gene expression in cell lines using a tissue similarity index (TSI)
Rickard Sandberg and Ingemar Ernberg
Proc Natl Acad Sci USA. 2005. 102, 6, 2052--7

Systems biology is taking off
Måns Ehrenberg, Johan Elf, Erik Aurell,Rickard Sandberg and Jesper Tegner
Genome Res. 2003. 13, 11, 2377--80

Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content
Rickard Sandber, Carl-Ivar Branden, Ingemar Ernberg and Joakim Coster
Gene. 2003. 311, 35-42

Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier
Rickard Sandberg and G Winberg, Carl-Ivar Branden, A Kaske, I Ernberg and J Coster
Genome Res. 2001. 11, 8, 1404--9

Regional and strain-specific gene expression mapping in the adult mouse brain
*Sandberg R, *Yasuda R, Pankratz DG, Carter TA, Del Rio JA, Wodicka L, Mayford M, Lockhart DJ and Barlow C
Proc Natl Acad Sci USA. 2000. 97, 20, 11038--43

Antisense PNA effects in Escherichia coli are limited by the outer-membrane LPS layer
L Good, R Sandberg, O Larsson, P E Nielsen and C Wahlestedt
Microbiology (Reading, Engl). 2000. 146 ( Pt 10), 2665--70

* co-first authors, ** co-corresponding authors

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