Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

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JBrowse: a next-generation genome browser. (2009, background): “Several recently developed genome browsers, the NCBI Sequence Viewer (http://www.ncbi.nlm.nih.gov/projects/sviewer), Anno-J (Lister et al. 2008), and version 2 of GBrowse, avoid the costs of pre-rendering in different ways.”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, background): “…that could benefit from such short read lengths (Barski et al. 2007; Fahlgren et al. 2007; Johnson et al. 2007; Kasschau et al. 2007; Cokus et al. 2008; Lister et al. 2008; Lu et al. 2008; Mortazavi et al. 2008; Nobuta et al. 2008; Sultan et al. 2008; Sunkar et al. 2008; Wilhelm et al. 2008).”
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome (2016, background): “…RNA-seq datasets generated from root (Hsieh et al. 2009; Breakfield et al. 2012), leaf (Yu et al. 2013), aerial part (Fahlgren et al. 2010), flower (Lister et al. 2008; Cuperus et al. 2010; Law et al. 2013), embryo (Lu et al. 2012), and silique (Hardcastle et al. 2012) (Supplemental Table S2).”
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie, and Ballgown (2016, background): “Using high-throughput sequencing machines, a single experiment can capture the expression levels of thousands of genes at once with high accuracy 1–3 .”