``On negative selection against ATG triplets near start codons
in eucaryotic and procaryotic genomes''
Saito, R. and Tomita, M.;
Journal of Molecular Evolution
, Volume 48, Number 2, 213-217, 1999.
``Analysis of completed genomes suggests that many
procaryotes do not rely on hairpins for transcription termination''
Washio, T., Sasayama, J. and Tomita, M.;
Nucleic Acids Research,
Volume 26, Number 23, 5237-5535, 1998.
``CpG distribution patterns in methylated and nonmethylated species''
Tom Shimizu, Kouichi Takahashi and Masaru Tomita;
Gene,
Volume 205, Number 1-2, 103-107, 1997.
``Inferring duplication history of junk DNA using subclassified Alu
elements'' Yoshimi Toda and Masaru Tomita;
Gene,
Volume 205 Number l-2, 173-176, 1997.
``Introns and Reading Frames: Correlation Between Splicing
Sites and Their Codon Positions'' Masaru Tomita, Nobuyoshi Shimizu and
Douglas L. Brutlag;
Molecular Biology and Evolution
, Volume 13, Number 9, 1219-1223, 1996.
Papers in submission
``Computer analysis of base pairing free-energy between
Shine-Dalgarno sequence and 16SrRNA in various procaryotes''
Osada, Y., Saito, R. and Tomita, M.;
Bioinformatics(accepted).
``Comparative study of overlapping genes in the genomes
of Mycoplasma genitalium and Mycoplasma pneumoniae'' Fukuda, Y.,
Washio, T. and Tomita, M.;
Nucleic Acids Research(accepted).
``ApA dinucleotide periodicity in procaryote, eucaryote and organelle
genomes'' Wada, M., Kawashima, Y. and Tomita, M.;
``On leaky scanning of AUG triplets in 5'UTR of vertebrate mRNAs''
Saito, R., Sasaki, H. and Tomita, M.;
``On low frequency of CpG dinucleotides in bacterial genomes''
Goto, M., Washio, T. and Tomita, M.;
``The expression frequency of the human immunoglobulin lambda
light chain genes and the roles of their recombination signal
sequences'' Okada, T., Tomita, M., Kawasaki, K., Minoshima, S. and
Shimizu, N.;
``Comprehensive sequence analysis in 5'flunking region of primate Alu
elements'' Toda, Y., Saito, R. and Tomita, M.;