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Staff at EMBL

Simon Anders

Research Scientist
Huber Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Tel: +49 6221 387-8632
Fax: +49 6221 387-8166
E-mail: send a mail


HTSeq - A Python framework to work with high-throughput sequencing data. Anders, S., Pyl, P.T. & Huber, W. Bioinformatics. 2014 Sep 25. pii: btu638. Europe PMC

An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae. Wilkening, S., Lin, G., Fritsch, E.S., Tekkedil, M.M., Anders, S., Kuehn, R., Nguyen, M., Aiyar, R.S., Proctor, M., Sakhanenko, N.A., Galas, D.J., Gagneur, J., Deutschbauer, A. & Steinmetz, L.M. Genetics. 2013 Dec 27. Europe PMC

Accounting for technical noise in single-cell RNA-seq experiments. Brennecke, P., Anders, S., Kim, J.K., Kolodziejczyk, A.A., Zhang, X., Proserpio, V., Baying, B., Benes, V., Teichmann, S.A., Marioni, J.C. & Heisler, M.G. Nat Methods. 2013 Nov;10(11):1093-5. doi: 10.1038/nmeth.2645. Epub 2013 Sep 22. Europe PMC

Drift and conservation of differential exon usage across tissues in primate species. Reyes, A., Anders, S., Weatheritt, R.J., Gibson, T.J., Steinmetz, L.M. & Huber, W. Proc Natl Acad Sci U S A. 2013 Sep 17;110(38):15377-82. doi:10.1073/pnas.1307202110. Epub 2013 Sep 3. Europe PMC

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Anders, S., McCarthy, D.J., Chen, Y., Okoniewski, M., Smyth, G.K., Huber, W. & Robinson, M.D. Nat Protoc. 2013 Sep;8(9):1765-86. doi: 10.1038/nprot.2013.099. Epub 2013 Aug 22. Europe PMC

An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Wilkening, S., Pelechano, V., Jarvelin, A.I., Tekkedil, M.M., Anders, S., Benes, V. & Steinmetz, L.M. Nucleic Acids Res. 2013 Mar 1;41(5):e65. doi: 10.1093/nar/gks1249. Epub 2013 Jan7. Europe PMC

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements. Zarnack, K., Konig, J., Tajnik, M., Martincorena, I., Eustermann, S., Stevant, I., Reyes, A., Anders, S., Luscombe, N.M. & Ule, J. Cell. 2013 Jan 31;152(3):453-66. doi: 10.1016/j.cell.2012.12.023. Europe PMC

Detecting differential usage of exons from RNA-seq data. Anders, S., Reyes, A. & Huber, W. Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111. Epub 2012 Jun21. Europe PMC

Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Schlattl, A., Anders, S., Waszak, S.M., Huber, W. & Korbel, J.O. Genome Res. 2011 Dec;21(12):2004-13. doi: 10.1101/gr.122614.111. Epub 2011 Aug23. Europe PMC

Differential expression analysis for sequence count data. Anders, S. & Huber, W. Genome Biol. 2010 Oct 27;11(10):R106. Europe PMC

Genome-wide analysis of mRNA decay patterns during early Drosophila development. Thomsen, S., Anders, S., Janga, S.C., Huber, W. & Alonso, C.R. Genome Biol. 2010;11(9):R93. Epub 2010 Sep 21. Europe PMC

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Morgan, M., Anders, S., Lawrence, M., Aboyoun, P., Pages, H. & Gentleman, R. Bioinformatics. 2009 Oct 1;25(19):2607-8. Epub 2009 Aug 3. Europe PMC

Visualization of genomic data with the Hilbert curve. Anders, S. Bioinformatics. 2009 May 15;25(10):1231-5. Epub 2009 Mar 17. Europe PMC

A variational method based on weighted graph states. Anders, S., Briegel, H.J. & Dür, W. New Journal of Physics. 2007;9(10):361-361 Link

Classical simulation of quantum systems. Anders, S. PhD Thesis. University of Innsbruck. 2007 Link

Ground-state approximation for strongly interacting spin systems in arbitrary spatial dimension. Anders, S., Plenio, M.B., Dur, W., Verstraete, F. & Briegel, H.J. Phys Rev Lett. 2006 Sep 8;97(10):107206. Epub 2006 Sep 8. Europe PMC

Quantum communication cost of preparing multipartite entanglement. Kruszynska, C., Anders, S., Dür, W. & Briegel, H. Physical Review A. 2006;73(6) Link

Fast simulation of stabilizer circuits using a graph-state representation Anders, S. & Briegel, H. Physical Review A. 2006;73(2) Link