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 data. Bioinformatics 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 experiments. Nature 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 species. PNAS 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 Bioconductor. Nature 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 elements. Cell 152: 453-466. [Link]
S Anders*, A Reyes*, W Huber (2012): Detecting differential usage of exons from RNA-seq data. Genome 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 curve. Bioinformatics 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 entanglement. Physical 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]
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.
GraphSim: Python/C library for circuit simulation in quantum information theory.