Genome-wide detection of alternative splicing in expressed sequences of human genes

By Barmak Modrek, Alissa M. Resch, Catherine S. Grasso, Christopher J. Lee. Nucleic Acids Res., 2001

704 citations recorded by the source corpus.

Subfields: Immunology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cfe0a8e400894ca3a33730569c30bf2f54bff054

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Citations in the corpus

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. (2003, background): “Unlike the human genome, where millions of EST alignments indicate that approximately half of the genes are alternatively spliced (5,34,35), the study of alternative splicing in Arabidopsis has been mostly limited to the study of individual genes (36±39).”
Function of alternative splicing. (2005, neutral): “…is also supported by ESTbased database analysis, indicating that 35–60% of all human gene products are alternatively spliced (Mironov et al., 1999; Brett et al., 2000; Kan et al., 2001; Modrek et al., 2001), suggesting that alternative splicing of human genes is the rule and not the exception.”
Current methods of gene prediction, their strengths and weaknesses. (2002, methodology): “(b) Alternative splicing: EST-based methods are widely used to identify more systematically such events and to understand their roles (126,127).”
Alternative splicing: new insights from global analyses. (2006, background): “Initial analyses of the resulting data sets are revealing important global regulatory features of AS.”
A hitchhiker's guide to expressed sequence tag (EST) analysis (2006, methodology): “With the exponential rise in genomic data from global sequencing projects, EST databases are used for gene structure prediction [20, 76], to investigate alternative splicing [77–80], to discriminate between genes exhibiting tissue or disease-specific expression [81] and for the discovery and charact”
Reconstruction of cellular signalling networks and analysis of their properties (2005, background): “Initial estimates indicate that genes corresponding to proteins with signalling functions comprise more than 75% of all alternatively spliced gene”
Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments (2006, methodology): “Alternatively spliced sites (positive set) were extracted from HASDB (Modrek, et al., 2001) as 20 nt-long sequences around 5 0 splice sites, centered around a GT dinucleotide, which had more than one competing 3 0 site.”
A genomic view of alternative splicing (2002, neutral): “Modrek et al. (2001)18 Used UNIGENE.”
Reliability and reproducibility issues in DNA microarray measurements. (2006, background): “It is estimated that at least half of the human genes are alternatively spliced, and might have many potential splice variants [ 53 ].”
Variation in alternative splicing across human tissues (2004, background): “Pairs of inferred A3Es or A5Es differing by fewer than six nucleotides were excluded from further analysis, as in [8], because of the possibility that such small differences might sometimes result from EST sequencing or alignment errors.”
Multiple sequence alignment using partial order graphs (2002, methodology): “This alignment was produced by POA as part of our genome-wide study of alternative splicing in human EST sequences (Modrek et al., 2001).”