********** July 18, 2001, M.K.
362.pdf
Interpolated Markov chains for eukaryotic promoter recognition
Bioinformatics, 15(5), 362--369, 1999
Uwe Ohler, et al.

********** July 16, 2001, M.K.
1453.pdf
The complete genome sequence of Escherichia coli K-12
Science, 27(5), 1453--1462, September, 1997
Blattner et al.

********** July 16, 2001, M.K.
391.pdf
Prediction of transcriptional regulatory sites in the complete genome
sequence of Escherichia coli K-12
Bioinformatics, 14(5), 391--400, 1998
Denis Thieffry, Heladia Salgado, Araceli M. Huerta and Julio
Collado-Vides

********** April 11, 2001, M.K.
ismb2000.pdf
Regulatory Element Detection Using A Probabilistic Segmentation Model
ISMB 8, 67-74 (2000).
H. J. Bussemaker, H. Li, and E. D. Siggia

********** March 5, 2001, M.K.
C-1998-9.ps.gz
Discovering Frequent Patterns from Strings
Jaak Vilo

**********
Ecoli directory has been made on 2-27-2001. Information related with Ecoli 
should be put in there.	-Qing

**********
Promoter Prediction Papers
Thu Feb 15 2001
1202.pdf
Predicting Gene Regulatory Elements in Silico on a Genomic Scale
Brazma, Janassen, Vilo and Ukkonen

180265397v1.pdf
Building a dictionary for genomes: Identification of presumptive
regulatory sites by statistical analysis
Bussemaker, Li and Siggia

1947a.pdf
Extracting Regulatory Sites from the Upstream Region of Yeast Genes by
Computational Analysis of Oligonucleotide Frequencies
Helden, Andre and Vides

695.pdf
Prediction of transcription regulatory sites in Archaea by a
comparative genomic approach
Gelfand, Koonin and Mironov

861.pdf
Eukaryotic Promoter Recognition
Fickett and Hatzigeorgiou

ISMB-97.pdf
Data Mining for Regulatory Elements in Yeast Genome
Brazma, Vilo, Ukkonen and Valtonen

bergeron.pdf
COMBINATORIAL TOOLS FOR THE ANALYSIS OF TRANSCRIPTIONAL REGULATION
Bergeron, Gaul and Bergeron

gen-network-arc.pdf
Systematic determination of genetic network architecture
Tavazoie, Hughes, Campbell, Cho and Church

motif.pdf
Automatic extraction of motifs represented in the hidden Markov model
from a number of DNA sequences
Yada, Totoki, Ishikawa, Asai and Nakai

regulatory-element.pdf
Regulatory element detection using correlation with expression
Bussemaker, Li and Siggia

regulatory.pdf
Discovery and modeling of transcriptional regulatory regions
Fickett and Wasserman

x1065.pdf
An Expert Network for DNA Sequence Analysis
Fu