Additional information about the method:
- Karlin S, Mrázek J. (2000) Predicted highly expressed genes of diverse prokaryotic genomes. J Bacteriol. 182:5238-50.
- Karlin S, Mrázek J, Campbell A, Kaiser D. (2001) Characterizations of highly expressed genes of four fast-growing bacteria. J Bacteriol. 183:5025-40.
- Karlin S, Mrázek J. (2001) Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage. Proc Natl Acad Sci U S A. 98:5240-5.
- Mrázek J, Bhaya D, Grossman AR, Karlin S. (2001) Highly expressed and alien genes of the Synechocystis genome. Nucleic Acids Res. 29:1590-601.
- Karlin S, Barnett MJ, Campbell AM, Fisher RF, Mrázek J. (2003) Predicting gene expression levels from codon biases in alpha-proteobacterial genomes. Proc Natl Acad Sci U S A. 100:7313-8.
- Karlin S, Theriot J, Mrázek J. (2004) Comparative analysis of gene expression among low G+C gram-positive genomes. Proc Natl Acad Sci U S A. 1016182-7.
- Karlin S, Mrázek J, Ma J, Brocchieri L. (2005) Predicted highly expressed genes in archaeal genomes. Proc Natl Acad Sci U S A. 102:7303-8.
- Mrázek J, Spormann AM, Karlin S. (2006) Genomic comparisons among gamma-proteobacteria. Environ Microbiol. 8:273-88.
- Mrázek J, Karlin S. (1999) Detecting alien genes in bacterial genomes. Ann N Y Acad Sci. 870:314-29.
Some other relevant papers:
- Jansen R, Bussemaker HJ, Gerstein M. (2003) Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res. 31:2242-51.
- Lawrence JG, Ochman H. (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A. 95:9413-7.
- Azad RK, Lawrence JG. (2005) Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection. PLoS Comput Biol. 1:e56