Ruprecht-Karls-Universit├Ąt Heidelberg

Anders Group: Publications

Publications by S. Anders:

S Söderholm, Y Fu, L Gaelings, …, S Anders, …, D Kainov (2016): Multi-omics studies towards novel modulators of influenza A virus-host interaction. Viruses 8:269.  [Link]

Y Fu, L Gaelings, S Söderholm, S Belanov, J Nandania, T A Nyman, S Matikainen, S Anders, V Velagapudi, D E Kainov (2016): JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses. Antiviral Research 133:23.  [Link]

W Huber, V Carey, R Gentleman, S Anders, M Carlson, …, M Morgan (2015):  Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods 12:115.    [Link]

M Love, S Anders, V Kim, W Huber (2015):  RNA-Seq workflow: gene-level exploratory analysis and differential expression [version 1; referees: 1 approved]. F1000 Research 4:1070.   [Link]

L Velten, S Anders, A Pękowska, A I Järvelin, W Huber, V J Pelechano, L M Steinmetz (2015):  Single-cell polyadenylation-site mapping reveals variability in 3’ isoform choice. Molecular Systems Biology, 11:812.   [Link]

C Hauer, T Curk, S Anders, Th Schwarzl, …, M W Hentze, A E Kulozik (2015):  Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP. Nature Communications 6:7921.   [Link]

F A Klein, S Anders, T Pakozdi, Y Ghavi-Helm, E E M Furlong, W Huber (2015):  FourCSeq: Analysis of 4C sequencing data. Bioinformatics 31: 3085–3091.  [Link]

S Anders, P T Pyl, W Huber (2015):  HTSeq – A Python framework to work with high-throughput sequencing dataBioinformatics 31:166-169.   [Link]

M I Love, W Huber, S Anders (2014):  Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2.  Genome Biology 15:550.   [Link]

P Brennecke*, S Anders*, J K Kim*, A A Kołodziejczyk, X Zhang, V Proserpio, B Baying, V Benes, S A Teichmann, J C Marioni, M G Heisler (2013):  Accounting for technical noise in single-cell RNA-seq experimentsNature Methods 10: 1093.   [Link]

S Wilkening*, G Lin*, E S Fritsch*, M M Tekkedil, S Anders, R Kuehn, ..., L M Steinmetz (2014):  An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae.  Genetics 196: 853.    [Link]

A Reyes*, S Anders*, R J Weatheritt, T J Gibson, L M Steinmetz, W Huber (2013):  Drift and conservation of differential exon usage across tissues in primate speciesPNAS 110: 15377.   [Link]

S Anders, D J McCarthy, Y Chen, M Okoniewski, G K Smyth, W Huber, M D Robinson (2013):  Count-based differential expression analysis of RNA sequencing data using R and Bio­con­ductorNature Protocols 8: 1765.   [Link]

S Wilkening, V Pelechano, A I Järvelin, M M Tekkedil, S Anders, V Benes, L M Steinmetz (2013):  An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Research 41: e65.   [Link]

K Zarnack, J König, M Tajnik, I Martincorena, S Eustermann, I Stévant, A Reyes, S Anders, N M Luscombe, J Ule (2013):  Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of alu elementsCell 152: 453-466.   [Link]

S Anders*, A Reyes*, W Huber (2012):  Detecting differential usage of exons from RNA-seq dataGenome Research 22: 2008-2017.   [Link]

A Schlattl, S Anders, S M Waszak, W Huber, JO Korbel (2011):  Relating CNVs to transcrip­tome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions.  Genome Research 21: 2004-2013.   [Link]

S Anders, W Huber (2010):  Differential expression analysis for sequence count data.  Genome Biology 11: R106.   [Link]

S Thomsen, S Anders, S C Janga, W Huber, C R Alonso (2010):  Genome-wide analysis of mRNA decay patterns during early Drosophila development.  Genome Biology 11: R93.   [Link]

M Morgan, S Anders, M Lawrence, P Aboyoun, H Pagès, R Gentleman (2009):  ShortRead: a Bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics 25: 2607.  [Link]

S Anders (2009):  Visualization of genomic data with the Hilbert curveBioinformatics 25: 1231-1235.   [Link]

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

C Kruszynska, S Anders, W Dür, H J Briegel (2006):  Quantum communication cost of preparing multipartite entanglementPhysical Review A 73: 062328.   [Link]

S Anders, M B Plenio, W Dür, F Verstraete, H J Briegel (2006):  Ground-state approximation for strongly interacting spin systems in arbitrary spatial dimension.  Physical Review Letters 97: 107206.   [Link]

S Anders, H J Briegel (2006):  Fast simulation of stabilizer circuits using a graph-state represen­tation.  Physical Review A 73: 022334.   [Link]

 

Software

DESeq2:  R/Bioconductor package for comparative analysis of sequencing count data, successor to DESeq.   

DEXSeq:  R/Bioconductor package for comparative analysis of exon usage in RNA-Seq data.

DESeq:  R/Bioconductor package for comparative analysis of sequencing count data. 

HTSeq:  Python package, programming framework to process high-throughput sequencing data. 

HilbertVis:  R/Bioconductor package for visualization of long genomic data sequences. 

GraphSimPython/C library for circuit simulation in quantum information theory.