[AH10]Simon Anders and Wolfgang Huber. Differential expression analysis for sequence count data. Genome Biol, 11(10):R106, 2010. URL:
[AMC+13]Simon Anders, Davis J McCarthy, Yunshun Chen, Michal Okoniewski, Gordon K Smyth, Wolfgang Huber, and Mark D Robinson. Count-based differential expression analysis of rna sequencing data using r and bioconductor. Nat Protoc, 8(9):1765–86, Sep 2013. URL:
[BH95]Yoav Benjamini and Yosef Hochberg. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological), 57(1):289–300, 1995.
[DFB+13]Joshua G Dunn, Catherine K Foo, Nicolette G Belletier, Elizabeth R Gavis, and Jonathan S Weissman. Ribosome profiling reveals pervasive and regulated stop codon readthrough in drosophila melanogaster. Elife, 2(0):e01179, 2013. URL:, doi:10.7554/elife.01179.
[FRJ+15]Alexander P. Fields, Edwin H. Rodriguez, Marko Jovanovic, Noam Stern-Ginossar, Brian J. Haas, Philipp Mertins, Raktima Raychowdhury, Nir Hacohen, Steven A. Carr, Nicholas T. Ingolia, Aviv Regev, and Jonathan S. Weissman. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Molecular Cell, 60(5):816–827, Mar 2015. URL:, doi:10.1016/j.molcel.2015.11.013.
[IGNW09]Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, and Jonathan S Weissman. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324(5924):218–23, Apr 2009. URL:, doi:10.1126/science.1168978.
[ILW11]Nicholas T Ingolia, Liana F Lareau, and Jonathan S Weissman. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 147(4):789–802, Nov 2011. URL:, doi:10.1016/j.cell.2011.10.002.
[LHA14]Michael I Love, Wolfgang Huber, and Simon Anders. Moderated estimation of fold change and dispersion for rna-seq data with deseq2. Genome Biol, 15(12):550, 2014. URL:, doi:10.1186/s13059-014-0550-8.
[OBS+11]Eugene Oh, Annemarie H Becker, Arzu Sandikci, Damon Huber, Rachna Chaba, Felix Gloge, Robert J Nichols, Athanasios Typas, Carol A Gross, Günter Kramer, Jonathan S Weissman, and Bernd Bukau. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell, 147(6):1295–308, Dec 2011. URL:, doi:10.1016/j.cell.2011.10.044.
[RME+13]Jose Manuel Rodriguez, Paolo Maietta, Iakes Ezkurdia, Alessandro Pietrelli, Jan-Jaap Wesselink, Gonzalo Lopez, Alfonso Valencia, and Michael L. Tress. Appris: annotation of principal and alternative splice isoforms. Nucleic Acids Research, 41(D1):D110–D117, 2013. URL:, arXiv:, doi:10.1093/nar/gks1058.
[RZW+14]Silvi Rouskin, Meghan Zubradt, Stefan Washietl, Manolis Kellis, and Jonathan S Weissman. Genome-wide probing of rna structure reveals active unfolding of mrna structures in vivo. Nature, 505(7485):701–5, Jan 2014. URL:, doi:10.1038/nature12894.
[SGWM+12]Noam Stern-Ginossar, Ben Weisburd, Annette Michalski, Vu Thuy Khanh Le, Marco Y Hein, Sheng-Xiong Huang, Ming Ma, Ben Shen, Shu-Bing Qian, Hartmut Hengel, Matthias Mann, Nicholas T Ingolia, and Jonathan S Weissman. Decoding human cytomegalovirus. Science, 338(6110):1088–93, 2012. doi:10.1126/science.1227919.