| 1. |
|
Doolittle WF: Genes in pieces: were they ever together? Nature 1978, 272:581-582. |
| |
|
|
| |
| 2. |
|
Blake CCF: Do genes in pieces imply proteins in pieces? Nature 1978, 273:267. |
| |
|
|
| |
| 3. |
|
Gilbert W: The exon theory of genes. Cold Spring Harb Symp Quant Biol 1987, 52:901-905. |
| |
|
|
| |
| 4. |
|
Roy SW: Recent evidence for the exon theory of genes. Genetica 2003, 118:251-266. |
| |
|
|
| |
| 5. |
|
Cavalier-Smith T: Intron phylogeny: a new hypothesis. Trends Genet 1991, 7:145-148. |
| |
|
|
| |
| 6. |
|
Palmer JD, Logsdon JM Jr: The recent origins of introns. Curr Opin Genet Dev 1991, 1:470-477. |
| |
|
|
| |
| 7. |
|
Logsdon JM Jr: The recent origins of spliceosomal introns revisited. Curr Opin Genet Dev 1998, 8:637-648. |
| |
|
|
| |
| 8. |
|
Fedorov A, Suboch G, Bujakov M, Fedorova L: Analysis of nonuniformity in intron phase distribution. Nucleic Acids Res 1992, 20:2553-2557. |
| |
|
|
| |
| 9. |
|
Long M, Rosenberg C, Gilbert W: Intron phase correlations and the evolution of the intron/exon structure of genes. Proc Natl Acad Sci USA 1995, 92:12495-12499. |
| |
|
|
| |
| 10. |
|
Long M, de Souza SJ, Rosenberg C, Gilbert W: Relationship between proto-splice sites and intron phases: evidence from dicodon analysis. Proc Natl Acad Sci USA 1998, 95:219-223. |
| |
|
|
| |
| 11. |
|
de Souza SJ, Long M, Klein RJ, Roy SW, Lin S, Gilbert W: Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc Natl Acad Sci USA 1998, 95:5094-5099. |
| |
|
|
| |
| 12. |
|
Dibb NJ, Newman AJ: Evidence that introns arose at proto-splice sites. EMBO J 1989, 8:2015-2021. |
| |
|
|
| |
| 13. |
|
Qiu WG, Schisler N, Stoltzfus A: The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol 2004, 21:1252-1263. |
| |
|
|
| |
| 14. |
|
Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV: Reconstruction of ancestral protosplice sites. Curr Biol 2004, 14:1505-1508. |
| |
|
|
| |
| 15. |
|
Ruvinsky A, Eskesen ST, Eskesen FN, Hurst LD: Can codon usage bias explain intron phase distribution and exon symmetry? J Mol Evol 2005, 60:99-104. |
| |
|
|
| |
| 16. |
|
Meunier J, Duret L: Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol 2004, 21:984-990. |
| |
|
|
| |
| 17. |
|
Roy SW, Lewis BP, Fedorov A, Gilbert W: Footprints of primordial introns on the eukaryotic genome. Trends Genet 2001, 17:496-499. |
| |
|
|
| |
| 18. |
|
Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV: Evidence of splice signal migration from exon to intron during intron evolution. Curr Biol 2003, 13:2170-2174. |
| |
|
|
| |
| 19. |
|
Nakao A, Yoshihama M, Kenmochi N: RPG: the Ribosomal Protein Gene database. Nucleic Acids Res 2004, 32:D168-170. |
| |
|
|
| |
| 20. |
|
Sadusky T, Newman AJ, Dibb NJ: Exon junction sequences as cryptic splice sites: implications for intron origin. Curr Biol 2004, 14:505-509. |
| |
|
|
| |
| 21. |
|
Stoltzfus A: Molecular evolution: introns fall into place. Curr Biol 2004, 14:R351-R352. |
| |
|
|
| |
| 22. |
|
Nguyen HD, Yoshihama M, Kenmochi N: New maximum likelihood estimators for eukaryotic intron evolution. PloS Comput Biol 2005, 1:e79. |
| |
|
|
| |
| 23. |
|
Roy SW, Gilbert W: The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet 2006, 7:211-221. |
| |
|
|
| |
| 24. |
|
Martin W, Koonin EV: Introns and the origin of nucleus-cytosol compartmentalization. Nature 2006, 440:41-45. |
| |
|
|
| |
| 25. |
|
Roy SW, Gilbert W: Rates of intron loss and gain: implications for early eukaryotic evolution. Proc Natl Acad Sci USA 2005, 102:5773-5778. |
| |
|
|
| |
| 26. |
|
Yoshihama M, Nakao A, Nguyen HD, Kenmochi N: Analysis of ribosomal protein gene structures: implications for intron evolution. PloS Genet 2006, 2:e25. |
| |
|
|
| |
| 27. |
|
Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV: Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 2003, 13:1512-1517. |
| |
|
|
| |
| 28. |
|
Csűrös M: Likely Scenarios of intron evolution. In Proceedings of the Comparative Genomics: RECOMB 2005 International Workshop: 18–20 September 2005; Dublin. Volume 3678. Edited by: McLysaght A, Huson D. Springer-Verlag; Lecture Notes in Bioinformatics; 47-60.  |
| |
|
|
| |
| 29. |
|
Csűrös M: On the estimation of intron evolution. PLoS Comput Biol 2006, 2:e84. |
| |
|
|
| |
| 30. |
|
Nguyen HD, Yoshihama M, Kenmochi N: Authors' reply. PLoS Comput Biol 2006, 2:e83. |
| |
|
|
| |
| 31. |
|
NCBI [http://www.ncbi.nlm.nih.gov/]  |
| |
|
|
| |
| 32. |
|
Fungal Genome Initiative [http://www.broad.mit.edu/annotation/fgi/]  |
| |
|
|
| |
| 33. |
|
JGI Eukaryotic Genomics [http://genome.jgi-psf.org/euk_cur1.html]  |
| |
|
|
| |
| 34. |
|
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. |
| |
|
|
| |
| 35. |
|
Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998, 8:967-974. |
| |
|
|
| |
| 36. |
|
Myers EW, Miller W: Optimal alignments in linear space. CABIOS 1988, 4:11-17. |
| |
|
|
| |
| 37. |
|
TIGR Rice Genome Annotation [http://www.tigr.org/tdb/e2k1/osa1/]  |
| |
|
|
| |
| 38. |
|
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. |
| |
|
|
| |
| 39. |
|
Felsenstein J, Churchill GA: A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 1996, 13:93-104. |
| |
|
|
| |
| 40. |
|
Press WH, Teukolsky SA, Vetterling WT, Flannery BP: Minimization or maximization of functions. In Numerical recipes in C: The art of scientific computing. 2nd edition. New York: Cambridge University Press; 1992:394-444.  |
| |
|
|