A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

By M. Sultan, Marcel H. Schulz, Hugues Richard, Alon Magen, A. Klingenhoff, M. Scherf, M. Seifert, T. Borodina, A. Soldatov, D. Parkhomchuk and 6 more. Science, 2008

1,338 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a9c8130cf93080224e960f0dd0c46bd236cc6282

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Citations in the corpus

From RNA-seq reads to differential expression results (2010, methodology): “Longer reads are more likely to cross exon boundaries, thus causing the fraction of junction reads to increase [2].”
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches (2009, background): “, but has also accelerated the process of understanding its regulation in different tissues by examining the expression levels of protein regulators and helping to define cis -regulatory element”
Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, background): “As current second-generation sequencing platforms generate reads whose lengths are shorter than typical read lengths achieved by Sanger sequencing, second-generation sequencing technologies have been primarily applied in contexts that could benefit from such short read lengths (Barski et al. 2007; F”
Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation (2012, background): “Both approaches have proven successful in investigating gene expression and regulation (9–11).”
Modelling and simulating generic RNA-Seq experiments with the flux simulator (2012, background): “Since the first ultra sequencing experiments on cellular transcriptomes (9,10), sample preparations for so-called RNA-Seq have evolved in multiple respects and generated a considerable repertoire of protocols, which however all stem from a common set of elementary components.”
TCC: an R package for comparing tag count data with robust normalization strategies (2013, methodology): “In addition to the RDR6 knockout dataset, we also analyze four other experimental datasets (called “ sultan ” [4], “ gilad ” [22], “ maqc ” [23], and “ katz.mouse ” [24]) obtained from the ReCount database [25].”
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. (2010, methodology): “…have relied on Sanger sequencing of expressed sequence tags (ESTs) and cDNAs, high-density DNA microarrays (for review, see Mockler et al. 2005) and most recently ultrahigh-throughput RNA sequencing (RNA-seq) approaches (Mortazavi et al. 2008; Pan et al. 2008; Sultan et al. 2008; Wang et al. 2008).”
Differential expression in RNA-seq: a matter of depth. (2011, methodology): “Methods traditionally used for microarrays have paved the way to other approaches that take into account the discrete nature of the expression quantification and use different probability distributions to model data (Marioni et al. 2008; Robinson et al. 2010; Anders and Huber 2010; Sultan et al. 200”
Long Noncoding RNAs: Past, Present, and Future (2013, background): “Some high-throughput RNA sequencing (RNA-Seq) analyses suggest that much of pervasive transcription might be explained by alternative splicing and/or extensions of known protein-coding genes (He et al. 2008; Mortazavi et al. 2008; Sultan et al. 2008; van Bakel et al. 2010, 2011).”