1.J. Usuka, , W. Zhu, and V. Brendel, Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics 16, 203-211, 2000.

2. J. Usuka, and V. Brendel. Gene structure prediction by spliced alignment of genomic DNA with protein sequences: Increased accuracy by differential splice site scoring. J. Mol. Biol. 297, 1075-1085, 2000.

3. V. Brendel., L. Xing, and W. Zhu. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics 20(7), 1157-1169, 2004.

4. V. Brendel, and J. Kleffe, Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA. Nucl. Acids Res. 26, 4748-4757, 1998.

5. V. Brendel, J. Kleffe, J.C. Carle-Urioste, and V Walbot Prediction of splice sites in plant pre-mRNA from sequence properties. J. Mol. Biol. 276, 85-104, 1998.

6. J. Kleffe, K. Hermann, W. Vahrson, B. Wittig and V. Brendel. Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences. Nucl. Acids Res. 24, 4709-4718, 1996

7. M.E. Sparks and V. Brendel. Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants. Bioinformatics. 2 Nov 1;21 Suppl 3:iii20-iii30, 2005.

8. W. Zhu, CR. Buell. Improvement of whole-genome annotation of cereals
through comparative analyses. Genome Res. Mar;17(3):299-310. Epub 2007
Feb 6, 2007.