Global Identification of Human Transcribed Sequences with Genome Tiling Arrays

By Paul Bertone, V. Štolc, Thomas E. Royce, Joel S. Rozowsky, Alexander E. Urban, Xiaowei Zhu, Johannes Rinn, W. Tongprasit, M. Samanta, S. Weissman and 2 more. Science, 2004

1,120 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/47580ffa5eb01c55f0d79bb98744ea5721d09f9a

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Citations in the corpus

Long Noncoding RNAs: Past, Present, and Future (2013, background): “Although lncRNAs are found across many taxa, and many crucial discoveries have been made in plants, fungi, and invertebrates (Gelbart and Kuroda 2009; Au et al. 2011), we largely limit our discussion to mammalian examples, with occasional reference to lncRNAs of other taxa.”
Long non-coding RNAs with enhancer-like function in human (2010, background): “These experiments indicate that a major portion of the genome is being transcribed and that protein-coding sequences only account for a minority of cellular transcriptional output (Bertone et al., 2004; Birney et al., 2007; Cheng et al., 2005; Kapranov et al., 2007).”
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. (2011, methodology): “2006) using data collected with tiling microarrays (Bertone et al. 2004; Kapranov et al. 2007), shotgun sequencing of expressed sequence tags (ESTs) and cloned cDNA (Carninci et al.”
Radiogenomics and Radiotherapy Response Modeling (2017, background): “They are defined as transcripts of 200 up to 100,000 bp lacking an open reading frame (Bertone et al., 2004).”
AlleleSeq: analysis of allele-specific expression and binding in a network framework (2011, background): “…of genes as well as novel transcribedregions,thatis,noveltranscriptionallyactiveregions (TARs) or transfrags (Kapranov et al , 2002; Rinn et al , 2003; Bertone et al , 2004), are coordinated with ASB of transcription factors and other DNA binding proteins located adjacent to the transcribed region.”
What is a gene, post-ENCODE? History and updated definition. (2007, background): “Different statistical models (Karplus et al. 1999; Bertone et al. 2004; Schadt et al. 2004; Gibbons et al. 2005; Ji and Wong 2005; Li et al. 2005; Du et al. 2006; Marioni et al. 2006) have been proposed to explain the generation of the tiling array data.”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, neutral): “These observations are consistent with the well-known discrepancy between the levels of observable mRNAs and large structural RNAs compared with the total RNA in a cell, suggesting that there are numerous RNA species yet to be classified 13–15 .”
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals (2009, background): “Thus, to expand our understanding of functional lincRNAs, we are faced with two important challenges: (1) identifying lincRNAs that are most likely to be functional; and (2) inferring putative functions for these lincRNAs that can be tested in hypothesis-driven experiments.”
Long noncoding RNAs: functional surprises from the RNA world. (2009, background): “…to protein-coding regions, but is instead pervasive throughout the mammalian genome as demonstrated by large-scale cDNA cloning projects (Carninci et al. 2005; Katayama et al. 2005) and genomic tiling arrays (Bertone et al. 2004; Cheng et al. 2005; Birney et al. 2007; Kapranov et al. 2007a).”