These papers provide background information for the study of promoters. Many of them may not be accessed without a subscription to their hosting Web sites. However, all of these papers are accessible from within Virginia Tech. If you have a Virginia Tech PID and would like to access these papers from off campus, use the library proxy server.
Muse SV.
Estimating synonymous and nonsynonymous substitution rates.
Mol Biol Evol. 1996 Jan;13(1):105-14.
Format: PDFMuse SV.
Examining rates and patterns of nucleotide substitution in plants.
Plant Mol Biol. 2000 Jan;42(1):25-43.
Format: PDFHuelsenbeck JP, Crandall KA.
Phylogeny estimation and hypothesis testing using maximum likelihood.
Annu Rev Ecol Syst. 1997 Nov;28(1):437-466.
Formats: HTML, PDFCoward E.
Shufflet: shuffling sequences while conserving the k-let counts.
Bioinformatics. 2003 15: 1058-1059.
Format: PDFRombauts S, Florquin K, Lescot M, Marchal K, Rouze P, Van De Peer Y.
Computational Approaches to Identify Promoters and cis-Regulatory Elements in Plant Genomes.
Plant Physiol. 2003 Jul;132(3):1162-76.
Formats: HTML, PDFHelden JV, Andre B, Collado-Vides J.
Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies.
J Mol Biol. 1998 Sep 4;281(5):827-42.
Formats: HTML, PDFFickett JW, Hatzigeorgiou AG.
Eukaryotic Promoter Recognition.
Genome Research. 1997; 7: 861-878.
Formats: HTML, PDFZhang MQ.
Identification of Human Gene Core Promoters in Silico.
Genome Research. 1998; 8: 319-328.
Formats: HTML, PDFPedersen AG, Baldi P, Chauvin Y, Brunak S.
The Biology of Eukaryotic Promoter Prediction: A Review.
Computers and Chemistry. 1999; 23: 191-207.
Formats: HTML, PDFReichmann JL.
Transcriptional Regulation: a genomic overview
The Arabidopsis Book, 2002, American Society of Plant Biologists
Format: PDFEskin E, Pevzner PA.
Finding Composite Regulatory Patterns in DNA Sequences.
Bioinformatics. 2002; Jul; 18 Suppl 1: S354-63.
Format: PDFUwe Ohler.
Computational promotyer recognition in Eukaryotic Genomic DNA.
PhD thesis, Nov 2001.
Format: PDF
Additional References
Dr. Heath has compiled a list (in plain-text) of about 46 papers that might be of interest.