Simon Anders

Summary

Publications

  1. pmc Detecting differential usage of exons from RNA-seq data
    Simon Anders
    European Molecular Biology Laboratory, 69111 Heidelberg, Germany
    Genome Res 22:2008-17. 2012
  2. pmc Visualization of genomic data with the Hilbert curve
    Simon Anders
    European Bioinformatics Institute EMBL EBI, Hinxton, CB10 1SD, UK
    Bioinformatics 25:1231-5. 2009
  3. pmc Differential expression analysis for sequence count data
    Simon Anders
    European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany
    Genome Biol 11:R106. 2010
  4. pmc Drift and conservation of differential exon usage across tissues in primate species
    Alejandro Reyes
    Genome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 110:15377-82. 2013
  5. doi request reprint Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
    Simon Anders
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Protoc 8:1765-86. 2013
  6. pmc An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae
    Stefan Wilkening
    European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
    Genetics 196:853-65. 2014
  7. pmc An efficient method for genome-wide polyadenylation site mapping and RNA quantification
    Stefan Wilkening
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 41:e65. 2013
  8. pmc Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements
    Kathi Zarnack
    European Molecular Biology Laboratory EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Cell 152:453-66. 2013

Collaborators

Detail Information

Publications8

  1. pmc Detecting differential usage of exons from RNA-seq data
    Simon Anders
    European Molecular Biology Laboratory, 69111 Heidelberg, Germany
    Genome Res 22:2008-17. 2012
    ..The method facilitates the study of regulation and function of alternative exon usage on a genome-wide scale. An implementation of DEXSeq is available as an R/Bioconductor package...
  2. pmc Visualization of genomic data with the Hilbert curve
    Simon Anders
    European Bioinformatics Institute EMBL EBI, Hinxton, CB10 1SD, UK
    Bioinformatics 25:1231-5. 2009
    ..This is demonstrated with examples from different use cases. An open-source application, called HilbertVis, is presented that allows the user to produce and interactively explore such plots...
  3. pmc Differential expression analysis for sequence count data
    Simon Anders
    European Molecular Biology Laboratory, Mayerhofstraße 1, 69117 Heidelberg, Germany
    Genome Biol 11:R106. 2010
    ..We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package...
  4. pmc Drift and conservation of differential exon usage across tissues in primate species
    Alejandro Reyes
    Genome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 110:15377-82. 2013
    ..Our findings support the theory that isoform regulation is an important target of evolution in primates, and our method provides a powerful tool for discovering potentially functional tissue-dependent isoforms. ..
  5. doi request reprint Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
    Simon Anders
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Protoc 8:1765-86. 2013
    ..Hands-on time for typical small experiments (e.g., 4-10 samples) can be <1 h, with computation time <1 d using a standard desktop PC. ..
  6. pmc An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae
    Stefan Wilkening
    European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
    Genetics 196:853-65. 2014
    ..We also reveal confounding factors like mutations and aneuploidy in pooled approaches, providing valuable lessons for future designs of complex trait mapping studies. ..
  7. pmc An efficient method for genome-wide polyadenylation site mapping and RNA quantification
    Stefan Wilkening
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 41:e65. 2013
    ..Finally, we observe that overlap of convergent 3'-UTRs is frequent but sharply limited by coding regions, suggesting factors that restrict compression of the yeast genome...
  8. pmc Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements
    Kathi Zarnack
    European Molecular Biology Laboratory EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Cell 152:453-66. 2013
    ..Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease...