Publications

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Van den Eynden J, Jiménez-Sánchez A, Miller ML, Larsson E. Lack of detectable neoantigen depletion signals in the untreated cancer genome.
Nat Genet. 2019 Nov 25.

Lindberg M, Boström M, Elliott K, Larsson E. Intragenomic variability and extended sequence patterns in the mutational signature of ultraviolet light.
Proc Natl Acad Sci U S A. 2019 Sep 23.

Persson Ö, Muthukumar Y, Basu S, Jenninger L, Uhler JP, Berglund AK, McFarland R, Taylor RW, Gustafsson CM, Larsson E*, Falkenberg M*. Copy-choice recombination during mitochondrial L-strand synthesis causes DNA deletions.
Nat Commun. 2019 Feb 15;10(1):759.

Elliott K, Boström M, Filges S, Lindberg M, Van den Eynden J, Ståhlberg A, Clausen AR, Larsson E. Elevated pyrimidine dimer formation at distinct genomic bases underlies promoter mutation hotspots in UV-exposed cancers.
PLoS Genet. 2018 Dec 26;14(12).

DNA polymerase η contributes to genome-wide lagging strand synthesis. Kreisel K, Engqvist MKM, Kalm J, Thompson LJ, Boström M, Navarrete C, McDonald JP, Larsson E, Woodgate R, Clausen AR.
Nucleic Acids Res. 2018 Dec 28

Van den Eynden J, Umapathy G, Ashouri A, Cervantes-Madrid D, Szydzik J, Ruuth K, Koster J, Larsson E, Guan J, Palmer RH, Hallberg B. Phosphoproteome and gene expression profiling of ALK inhibition in neuroblastoma cell lines reveals conserved oncogenic pathways.
Sci Signal. 2018 Nov 20;11(557).

Nicholls TJ, Nadalutti CA, Motori E, Sommerville EW, Gorman GS, Basu S, Hoberg E, Turnbull DM, Chinnery PF, Larsson NG, Larsson E, Falkenberg M, Taylor RW, Griffith JD, Gustafsson CM. Topoisomerase 3α Is Required for Decatenation and Segregation of Human mtDNA.
Mol Cell. 2018 Jan 4;69(1):9-23.e6.

Karlsson J, Kroneis T, Jonasson E, Larsson E*, Ståhlberg A*. Transcriptomic Characterization of the Human Cell Cycle in Individual Unsynchronized Cells.
J Mol Biol. 2017 Dec 8;429(24):3909-3924.

Tang KW, Larsson E. Tumour virology in the era of high-throughput genomics.
Philos Trans R Soc Lond B Biol Sci. 2017 Oct 19;372(1732).

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.
Nat Commun. 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;

Fredriksson NJ, Ny L, Nilsson JA, Larsson E. Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types.
Nat Genet. 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

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.
Sci Transl Med. 2014 Jan 29;6(221).

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.
Nat Commun. 2013 Oct 1;4:2513.

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.
Sci Signal. 2013 Apr 2;6(269).

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.

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