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Genomics and bioinformatics

Massively parallel sequencing and other high-throughput methodologies enable detailed mapping of the genomic and transcriptomic changes that underlie the development of cancer and other diseases. Rapid accumulation of genetic information makes it increasingly feasible to test biological hypotheses using computational methods and available data.

We are tackling challenges in human genomics, with emphasis on cancer and non-coding RNAs. Using bioinformatics we aim to gain insights into the evolution and function of regulatory RNAs (microRNAs and long non-coding RNAs), in both healthy and malignant cells. We regularly collaborate with experimental groups, locally and elsewhere. Current areas of research also include the development of bioinformatical tools to facilitate analysis of large-scale genomics data.


Selected recent publications

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;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;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;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 S, Tuschl T. RNA targets of wild-type and mutant FET family proteins.
Nature Struct Mol Biol. 2011;18(12):1428-31. (*Equal contribution)

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;108(39):16375-80

Larsson E, Sander C, Marks DS. mRNA turnover rate limits siRNA and microRNA efficacy.
Mol Syst Biol. 2010;6:433.

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;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;6:363.

Sidansvarig: Dan Baeckström|Sidan uppdaterades: 2013-07-29

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