Mapping and quantifying mammalian transcriptomes by RNA-Seq

By Ali Mortazavi, B. Williams, Kenneth McCue, Lorian Schaeffer, Barbara J. Wold. Nature Methods, 2008

13,613 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ef117c95b92b68b751143155022a5c1a600afe5c

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Citations in the corpus

Differential expression analysis for sequence count data (2010, background): “An important summary statistic is the number of reads in a class; for RNA-Seq, this read count has been found to be (to good approximation) linearly related to the abundance of the target transcript [2].”
Type 1 diabetes (2002, positive): “For these expanded studies, we used RNA sequencing (RNA-seq) technology, which is rapidly supplanting microarray analysis as the method of choice for transcriptomic analysis ( 18 ).”
Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43 (2011, background): “However, recent advances in DNA sequencing technology have provided powerful tools for exploring transcriptomes at remarkable resolutio”
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, neutral): “31 (29) and calculated RPKM values (Reads Per Kilobase of exon model per Million mapped reads) (30).”
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data (2009, methodology): “Gene expression was initially estimated by calculating read density as ‘reads per kilobase of exon model per million mapped reads’ (RPKM) [13].”
TopHat: discovering splice junctions with RNA-Seq (2009, neutral): “Availability: TopHat is free, open-source software available from http://tophat.cbcb.umd.edu Contact: cole@cs.umd.edu Supplementary information: Supplementary data are available at Bioinformatics online.”
Under pressure: investigating the biology of plant infection by Magnaporthe oryzae (2009, background): “oryzae will most likely be achieved by comparative and evolutionary genomics approaches, coupled with transcriptional profiling of infected plant tissues using next-generation sequencing method”
Integrative analysis of 111 reference human epigenomes (2015, background): “Extended data (1-12), supplementary figures (S1-S13), supplementary tables (S1-S6) are available in the online version of the paper.”
Measuring reproducibility of high-throughput experiments (2011, neutral): “On the other hand, for the peak callers (Erange, Cisgenome, Quest and SISSRS) whose peaks ﬁt the one-component model, the motif occurrence still shows an increasing trend at default thresholds.”
FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations (2014, methodology): “RNA-Seq coverage datasets are displayed in GBrowse and are used to calculate RPKM gene expression values (20).”
Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage (2011, neutral): “This method is also used by Mortazavi et al. 50 .”