Computational Genomics Journal Club

S. Batzoglou, L. Pachter, J. Mesirov, B. Berger, and E. Lander. Human and mouse gene structure: comparative analysis and application to exon prediction. (Postscript)

The following paper describes (among other things) the directionality effect on splice sites as described in the focus paper and discussed during the meeting:

L. Pachter, S. Batzoglou, V.I. Spitkovsky, E. Banks, E. Langer, D.J. Kleitman, and B. Berger. A dictionary based approach for gene annotation (Postscript)

Gene Finding:

C. Burge and S. Karlin (1997) Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology. 268:78-94 (PDF)

M. Burset and R. Guico (1996) Evaluation of gene structure prediction programs. Genomics. 34(3): 353-367 (PDF)

Human and Mouse Comparative Genomics:

W. Makalowski and M.S. Bugoski(1998) Evolutionary parameters of the transcribed mammalian genome - an analysis of 2,820 orthologous rodent and human sequences. Proc. Natl. Acad. Sciences. 95(16): 9407-9412 (PDF)

W. Jang, A. Hua, SV Spilson, W. Miller, B.A. Roe, and M. H. Meisler (1999) Comparative sequence of human and mouse BAC clones from the mnd2 region of chromosome 2p13. Genome Research. 9:53-61 (PDF)

W. Makalowski, J. Zhang, and M.S. Boguski (1996) Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. Genome Research. 6:846-857