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Research: Evidence for widespread subfunctionalization of splice forms in vertebrate genomes
- Matthew J. Lambert,
- Wayne O. Cochran,
- Brandon M. Wilde,
- Kyle G. Olsen,
- and Cynthia D. Cooper
Genome Res. May 2015 25: 624-632; Published in Advance March 19, 2015, doi:10.1101/gr.184473.114
...easy. BMC Genomics 10: 22. Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R. 2004. A nonEST based method for exon-skipping prediction. Genome Res 14: 1617–1623. Subfunctionalization of splice forms Genome Research 631 www..org Studer RA, Robinson-RechaviM. 2009. How confident canwe...
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Research: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons
- Sahar Gelfman,
- David Burstein,
- Osnat Penn,
- Anna Savchenko,
- Maayan Amit,
- Schraga Schwartz,
- Tal Pupko,
- and Gil Ast
Genome Res. January 2012 22: 35-50; Published in Advance October 5, 2011, doi:10.1101/gr.119834.110
...a novel evolutionary theory for the formation of alternative cassette exons (exon skipping) through a transition from constitutive exons, during the evolution of vertebrates. In addition, by analyzing evolutionary rate shifts,we identify cis-acting regulatory sequences and prove their functionality...
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Research: Genome-wide evidence for selection acting on single amino acid repeats
- Wilfried Haerty and
- G. Brian Golding
Genome Res. June 2010 20: 755-760; Published in Advance January 7, 2010, doi:10.1101/gr.101246.109
..., Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R. 2004. A nonEST-based method for exon-skipping prediction. Genome Res 14: 1617– 1623. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, et al. 2007. Discovery of functional elements in 12 Drosophila...
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LETTER: Alternative approach to a heavy weight problem
- Amir Goren,
- Eddo Kim,
- Maayan Amit,
- Ron Bochner,
- Galit Lev-Maor,
- Nadav Ahituv,
- and Gil Ast
Genome Res. February 2008 18: 214-220; Published in Advance December 20, 2007, doi:10.1101/gr.6661308
.... Nucleic Acids Res. 29 : 308 – 311 . ↵ Sorek, R. , Shemesh, R. , Cohen, Y. , Basechess, O. , Ast, G. , Shamir, R. ( 2004 ) A non-EST–based method for exon-skipping prediction . Genome Res. 14 : 1617 – 1623 . ↵ Steiner, B. , Truninger, K. , Sanz, J. , Schaller, A. , Gallati, S. ( 2004 ) The role of common...
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Methods: Conserved introns reveal novel transcripts in Drosophila melanogaster
- Michael Hiller,
- Sven Findeiß,
- Sandro Lein,
- Manja Marz,
- Claudia Nickel,
- Dominic Rose,
- Christine Schulz,
- Rolf Backofen,
- Sonja J. Prohaska,
- Gunter Reuter,
- and Peter F. Stadler
Genome Res. July 2009 19: 1289-1300; Published in Advance May 20, 2009, doi:10.1101/gr.090050.108
...even in well-studied organisms, and so far, no computational methods exist to predict such RNAs from genomic sequences only. The subclass of these transcripts that is evolutionarily conserved usually has conserved intron positions. We demonstrate here that a genome-wide comparative genomics approach...
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LETTER: Transcription-mediated gene fusion in the human genome
- Pinchas Akiva,
- Amir Toporik,
- Sarit Edelheit,
- Yifat Peretz,
- Alex Diber,
- Ronen Shemesh,
- Amit Novik,
- and Rotem Sorek
Genome Res. January 2006 16: 30-36; Published in Advance December 12, 2005, doi:10.1101/gr.4137606
.... ↵ Sorek, R., Ast, G., and Graur, D. 2002 . Alu -containing exons are alternatively spliced. Genome Res. 12 : 1060 -1067. ↵ Sorek, R., Shemesh, R., Cohen, Y., Basechess, O., Ast, G., and Shamir, R. 2004 . A non-EST-based method for exon-skipping prediction. Genome Res. 14 : 1617 -1623. ↵ Thomson, T...
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Letter: Complex selection on 5′ splice sites in intron-rich organisms
- Manuel Irimia,
- Scott William Roy,
- Daniel E. Neafsey,
- Josep F. Abril,
- Jordi Garcia-Fernandez,
- and Eugene V. Koonin
Genome Res. November 2009 19: 2021-2027; Published in Advance September 10, 2009, doi:10.1101/gr.089276.108
..., Shamir R. 2004. A non-EST-based method for exon-skipping prediction. Genome Res 14: 1617–1623. Staley JP, Guthrie C. 1999. An RNA switch at the 59 splice site requires ATP and the DEAD box protein Prp28p. Mol Cell 3: 55–64. Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI...
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