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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

Publications

Total: 15 publication(s)

2014

Anders S, Pyl PT, Huber W. (2014)
HTSeq - A Python framework to work with high-throughput sequencing data
Bioinformatics doi:10.1093/bioinformatics/btu638
Europe PMC | doi

Wilkening S, Lin G, Fritsch ES, Tekkedil MM, Anders S, Kuehn R, Nguyen M, Aiyar RS, Proctor M, Sakhanenko NA, Galas DJ, Gagneur J, Deutschbauer A, Steinmetz LM. (2014)
An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae
Genetics 196(3):853-865. doi:10.1534/genetics.113.160291
Europe PMC | doi


2013

Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. (2013)
Accounting for technical noise in single-cell RNA-seq experiments
Nat. Methods 10(11):1093-1095. doi:10.1038/nmeth.2645
Europe PMC | doi

Anders S, McCarthy DJ, Chen Y, Okoniewski M, Smyth GK, Huber W, Robinson MD. (2013)
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
Nat Protoc 8(9):1765-1786. doi:10.1038/nprot.2013.099
Europe PMC | doi

Reyes A, Anders S, Weatheritt RJ, Gibson TJ, Steinmetz LM, Huber W. (2013)
Drift and conservation of differential exon usage across tissues in primate species
Proc. Natl. Acad. Sci. U.S.A. 110(38):15377-15382. doi:10.1073/pnas.1307202110
Europe PMC | doi

Wilkening S, Pelechano V, Jarvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM. (2013)
An efficient method for genome-wide polyadenylation site mapping and RNA quantification (vol 41, pg e65, 2013)
Nucleic Acids Res 41(12):6370. doi:10.1093/nar/gkt364
doi

Wilkening S, Pelechano V, Järvelin AI, Tekkedil MM, Anders S, Benes V, Steinmetz LM. (2013)
An efficient method for genome-wide polyadenylation site mapping and RNA quantification
Nucleic Acids Res. 41(12):6370. doi:10.1093/nar/gks1249
Europe PMC | doi

Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J. (2013)
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements
Cell 152(3):453-466. doi:10.1016/j.cell.2012.12.023
Europe PMC | doi


2012

Anders S, Reyes A, Huber W. (2012)
Detecting differential usage of exons from RNA-seq data
Genome Res. 22(10):2008-2017. doi:10.1101/gr.133744.111
Europe PMC | doi


2011

Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO. (2011)
Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions
Genome Res. 21(12):2004-2013. doi:10.1101/gr.122614.111
Europe PMC | doi


2010

Anders S, Huber W. (2010)
Differential expression analysis for sequence count data
Genome Biol. 11(10):R106. doi:10.1186/gb-2010-11-10-r106
Europe PMC | doi

Thomsen S, Anders S, Janga SC, Huber W, Alonso CR. (2010)
Genome-wide analysis of mRNA decay patterns during early Drosophila development
Genome Biol. 11(9):R93. doi:10.1186/gb-2010-11-9-r93
Europe PMC | doi


2009

Morgan M, Anders S, Lawrence M, Aboyoun P, Pagès H, Gentleman R. (2009)
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
Bioinformatics 25(19):2607-2608. doi:10.1093/bioinformatics/btp450
Europe PMC | doi

Anders S. (2009)
Visualization of genomic data with the Hilbert curve
Bioinformatics 25(10):1231-1235. doi:10.1093/bioinformatics/btp152
Europe PMC | doi


2006

Anders S, Plenio MB, Dür W, Verstraete F, Briegel HJ. (2006)
Ground-state approximation for strongly interacting spin systems in arbitrary spatial dimension
Phys. Rev. Lett. 97(10):107206. doi:10.1103/physrevlett.97.107206
Europe PMC | doi