Publications

Select recent publications – click here for a complete list.

Fredriksson NJ, Elliott K, Filges S, Van den Eynden J, Ståhlberg A, Larsson E. Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature.
PLoS Genet. 2017 May 10;13(5):e1006773.

Van den Eynden J, Basu S, Larsson E. Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution.
PLoS Genet. 2016 Dec 27;12(12):e1006506.

Alaei-Mahabadi B, Bhaduryb J, Karlsson JW, Nilsson JA, Larsson E. Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers.
Proc Natl Acad Sci U S A. 2016 Nov.

Ashouri A, Sayin VI, Van den Eynden J, Singh SX, Papagiannakopoulos T, Larsson E. Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events.
Nature Communications. 2016 Oct.

FocalScan: Scanning for altered genes in cancer based on coordinated DNA and RNA change. Karlsson J, Larsson E.
Nucleic Acids Res. 2016 Jul 29.

The gut microbiota modulates host amino acid and glutathione metabolism in mice. Mardinoglu A, Shoaie S, Bergentall M, Ghaffari P, Zhang C, Larsson E, Bäckhed F, Nielsen J.
Mol Syst Biol. 2015 Oct 16;11(10):834.

Stewart JB, Alaei-Mahabadi B, Sabarinathan R, Samuelsson T, Gorodkin J, Gustafsson CM, Larsson E. Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers.
PLoS Genetics 2015 Jun 30;

Duggimpudi S, Larsson E, Nabhani S, Borkhardt A, Hoell JI. The cell cycle regulator CCDC6 is a key target of RNA-binding protein EWS.
PLoS One. 2015 Mar 9;10(3)

Tang KW, Hellstrand K, Larsson E. Absence of cytomegalovirus in high-coverage DNA sequencing of human glioblastoma multiforme.
Int J Cancer. 2015 Feb 15;136(4):977-81.

Fredriksson NJ, Ny L, Nilsson JA, Larsson E. Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.
Nature Genetics. 2014 Dec;46(12):1258-63.

Pandey GK, Mitra S, Subhash S, Hertwig F, Kanduri M, Mishra K, Fransson S, Ganeshram A, Mondal T, Bandaru S, Ostensson M, Akyürek LM, Abrahamsson J, Pfeifer S, Larsson E, Shi L, Peng Z, Fischer M, Martinsson T, Hedborg F, Kogner P, Kanduri C. The Risk-Associated Long Noncoding RNA NBAT-1 Controls Neuroblastoma Progression by Regulating Cell Proliferation and Neuronal Differentiation.
Cancer Cell. 2014 Nov 10;26(5):722-37

Meryet-Figuiere M, Alaei-Mahabadi B, Ali MM, Mitra S, Subhash S, Pandey GK, Larsson E, Kanduri C. Temporal separation of replication and transcription during S-phase progression.
Cell Cycle. 2014 Oct 15;13(20):3241-8.

Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T. Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets.
RNA. 2014 Jul;20(7):1090-102.

Sayin VI, Ibrahim MX, Larsson E, Nilsson JA, Lindahl P, Bergo MO. Antioxidants accelerate lung cancer progression in mice.
Science Transl Med. 2014 Jan 29;6(221).

Akrami R, Jacobsen A, Hoell J, Schultz N, Sander C, Larsson E. Comprehensive Analysis of Long Non-Coding RNAs in Ovarian Cancer Reveals Global Patterns and Targeted DNA Amplification.
PLoS One. 2013 Nov 12;8(11):e80306.

Tang K, Alaei-Mahabadi B, Samuelsson T, Lindh M, Larsson E. The landscape of viral expression and host gene fusion and adaptation in human cancer.
Nature Communications. 2013 Oct 1;4:2513.

Alaei-Mahabadi B, Larsson E. Limited evidence for evolutionarily conserved targeting of long non-coding RNAs by microRNAs.
Silence. 2013 Aug 20;4(1):4.

Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N. Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal.
Science Signal. 2013 Apr 2;6(269).

Shahrouki P, Larsson E. The non-coding oncogene: a case of missing DNA evidence?
Front Genet. 2012;3:170.

Ashwini J, Marks DS, Larsson E. miRcode: a map of putative microRNA target sites in the long non-coding transcriptome.
Bioinformatics. 2012 Aug 1;28(15):2062-3.

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
Cancer Discov. 2012 May;2(5):401-4.

Creighton CJ, Hernandez-Herrera A, Jacobsen A, Levine DA, Mankoo P, Schultz N, Ghosh-Choudhury T, Du Y, Zhang Y, Larsson E, Sheridan R, Xiao W, Spellman PT, Getz G, Anderson ML, Wheeler DA, Perou CM, Gibbs RA, Sander C, Hayes DN, Gunaratne PH, and The Cancer Genome Atlas Research Network. Integrated analyses of microRNAs uncover tumor suppressor candidates in high-grade serous ovarian carcinoma.
Plos One. 2012;7(3):e34546.

Hoell JI*, Larsson E*, Runge S, Nusbaum JD, Duggimpudi S, Farazi TA, Hafner M, Borkhardt A, Sander C, Tuschl T. RNA targets of wild-type and mutant FET family proteins.
Nature Struct Mol Biol. 2011 Nov 13;18(12):1428-31.

Larsson E, Tremaroli V, Lee YS, Koren O, Nookaew I, Fricker A, Nielsen J, Ley RE, Backhed F. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through Myd88.
Gut. 2011 Nov 23. (Highlighted in Nature Rev. Gastroent. Hepat. 2012 vol. 9)

Somwar R, Erdjument-Broomage H, Larsson E, Shum D, Lockwood WW, Yang G, Sander C, Ouerfelli O, Djaballah H, Tempst PJ, Varmus HE. SOD1 is a Target for a Small Molecule Identified in a Screen for Inhibitors of the Growth of Lung Adenocarcinoma Cell Lines.
Proc Natl Acad Sci U S A. 2011 Sep 27;108(39):16375-80

Larsson E, Sander C, Marks DS. mRNA turnover rate limits siRNA and microRNA efficacy.
Mol Syst Biol. 2010 Nov 16;6:433. (Highlighted in Nature Rev. Genet. 2011 Jan vol. 12.)

Hagberg CE, Falkevall A, Wang X, Larsson E, Huusko J, Nilsson I, van Meeteren LA, Samen E, Lu L, Vanwildemeersch M, Klar J, Genove G, Pietras K, Stone-Elander S, Claesson-Welsh L, Yla-Herttuala S, Lindahl P, Eriksson U. Vascular endothelial growth factor B controls endothelial fatty acid uptake.
Nature. 2010 Apr 8;464(7290):917-21.

Arvey A, Larsson E, Sander C, Leslie CS, Marks DS. Target mRNA abundance dilutes microRNA and siRNA activity.
Mol Syst Biol. 2010 Apr 20;6:363.

Larsson E, Fredlund Fuchs P, Heldin J, Barkefors I, Bondjers C, Genové G, Arrondel C, Gerwins P, Kurschat C, Schermer B, Benzing T, Harvey SJ, Kreuger J, Lindahl P. Discovery of microvascular miRNAs using public gene expression data: miR-145 is expressed in pericytes and is a regulator of Fli1.
Genome Med. 2009 Nov 16;1(11):108.