A genomic view of alternative splicing

By Barmak Modrek, Christopher J. Lee. Nature Genetics, 2002

1,396 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b742e1b5f7b913512e8862cc79286203f6a9091f

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Citations in the corpus

GMAP: a genomic mapping and alignment program for mRNA and EST sequence (2005, background): “The seed-and-extend strategy is found in a variety of programs, including those for genome–genome alignment (Chainet al., 2003; Morgenstern, 1999; Batzoglouet al., 2000; Kent and Zahler, 2000; Schwartzet al., 2000; Maet al., 2002; Brudnoet al., 2003a,b; Bray et al., 2003; Kalafuset al., 2004), and…”
Reconstruction of cellular signalling networks and analysis of their properties (2005, background): “At present, estimates indicate that 40–60% of the genes in the human genome are subject to alternative-splicing event”
Alternative splicing and evolution: diversification, exon definition and function (2010, background): “The inclusion of different exons in mRNA — alternative splicing (AS) — results in the generation of different isoforms from a single gene and is the basis for the discrepancy between the estimated 24,000 protein-coding genes in the human genome and the 100,000 different proteins that are postulated ”
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data (2012, methodology): “Direct sequencing of full-length mRNAs and mRNA fragments has been a popular and effective approach for discovery and quantification of alternative splicing events (3,4,9).”
Current methods of gene prediction, their strengths and weaknesses. (2002, background): “A recent review on this topic (128) reports an estimated 35±59% of human genes showing evidence for at least one alternative splice site form.”
Splicing in disease: disruption of the splicing code and the decoding machinery (2007, background): “About 80% of this variability falls within ORFs, greatly expanding the human proteom”
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 (2003, background): “Up to 60% of human genes have alternatively spliced isoforms (7,8), with an estimated average of 2.”
Towards a unified science of cultural evolution. (2006, background): “Alternative splicing is not a rare or occasional event and it seems to occur in approximately half of all human genes (Modrek & Lee 2002).”
Opportunities and challenges Genome-wide analyses of alternative splicing in plants: (2008, neutral): “The observation that upward of 80% of human genes have been demonstrated to undergo AS supports its use as a mechanism for resolving this discrepancy (Modrek and Lee 2002; Leipzig et al. 2004).”
Comparing the human and chimpanzee genomes: Searching for needles in a haystack (2005, background): “For example, microarrays based on human oligonucleotide sequences may not accurately detect levels of expression in nonhuman primates nor detect significant alternative splicing of mRNAs (Modrek and Lee 2002; Hsieh et al. 2003; Preuss et al. 2004; Steinmetz and Davis 2004).”
Function of alternative splicing. (2005, neutral): “Furthermore, alternative splicing is abundantly used in the brain (Lander et al., 2001; Modrek and Lee, 2002).”
Listening to silence and understanding nonsense: exonic mutations that affect splicing (2002, background): “Recent analysis of reconstructed mRNAs that are derived from chromosome 22 indicates that ∼60% of genes are represented by two or more transcript”
Understanding alternative splicing: towards a cellular code (2005, background): “Analyses of expressed sequence tag (EST) and cDNA datasets conservatively estimated that ∼40–60% of human genes are alternatively spliced (reviewed in Ref”