[2012]

N. Ichinose, T. Yada, and O. Gotoh, "Large-scale motif discovery using DNA Gray code and equiprobable oligomers", Bioinformatics, 28(1):25-31, 2012

[2011]

T. Irie, S.J. Park, R. Yamashita, M. Seki, T. Yada, S. Sugano, K. Nakai, and Y. Suzuki, "Predicting promoter activities of primary human DNA sequences", Nucl. Acids Res., 39, e75, 2011

H. Iwata and O. Gotoh, "Comparative analysis of information contents relevant to recognition of introns in many species", BMC Genomics, 12, 45, 2011

[2010]

R. Nakato and O. Gotoh, "Cgaln: fast and space-efficient whole-genome alignment", BMC Bioinformatics, 11, 224, 2010

X.S. Wang and O. Gotoh, "Inference of cancer-specific gene regulatory networks using soft computing rules", Gene Reg. Sys. Biol., 4, 19-34, 2010

X.S. Wang and O. Gotoh, "A Robust Gene Selection Method for Microarray-based Cancer Classification", Cancer Informatics, 9, 15-30, 2010

[2009]

X.S. Wang and O. Gotoh, "Accurate Molecular Classification of Cancer Using Simple Rules", BMC Medical Genomics, 2, 64, 2009

X.S. Wang and O. Gotoh, "Microarray-Based Cancer Prediction Using Soft Computing Approach", Cancer Informatics, 7, 123-139, 2009

[2008]

N. Ichinose, T. Yada, O. Gotoh, and K. Aihara, "Reconstruction of transcription-translation dynamics with a model of gene networks", Journal of Theoretical Biology, 255, 4, 378-386, 2008

O. Gotoh, "Direct mapping and alignment of protein sequences onto genomic sequence", Bioinformatics, 24(21):2438-2444, 2008

O. Gotoh, "A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence", Nucl. Acids Res., 36, 2630-2638, 2008

S. Yamada, O. Gotoh, O., and H. Yamana, "Improvement in speed and accuracy of multiple sequence alignment program PRIME", IPSJ Transactions on Bioinformatics, 1, 2-12, 2008

[2006]

S. Yamada, O. Gotoh, and H. Yamana, "Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost", BMC Bioinformatics, 7:524, 2006

H. Nagasaki, M. Arita, T. Nishizawa, M. Suwa, and O. Gotoh, "Automated classification of alternative splicing and transcriptional initiation and construction of a visual database of the classified patterns", Bioinformatics, 22, 1211-1216, 2006

[2005]

M. Machida, , K. Asai, M. Sano, et al., "Genome sequencing and analysis of Aspergillus oryzae", Nature 438, 1157-1161, 2005

H. Nagasaki, M. Arita, T. Nishizawa, M. Suwa, and O. Gotoh, "Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes", Gene, 364, 53-62, 2005

[2004]

T. Ota, Y. Suzuki, T. Nishikawa, et al., "Complete sequencing and characterization of 21,243 full-length human cDNAs", Nat. Genet., 36, 40-45, 2004

[2003]

K. Ohshima, M. Hattori, T. Yada, T. Gojobori, Y. Sakaki, and N. Okada, "Wholegenome screening indicates a possible burst of formation of processed pseudogenes and alu repeats by particular L1 subfamilies in ancestral primates", Genome Biol., 4, R74, 2003

[2002]

Y. Watanabe, A. Fujiyama, Y. Ichiba, M. Hattori, T. Yada, Y. Sakaki, and T. Ikemura, "Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timingswitch regions", Human Molecular Genetics, 11, 13-21, 2002

[2001]

T. Yada, Y. Totoki, T. Takagi, and K. Nakai, "A novel bacterial gene-finding system with improved accuracy in locating start codons", DNA Res., 8, 97-106, 2001

F. Miura, T. Yada, K. Nakai, Y. Sakaki, and T. Ito, "Differential display analysis of mutants for the transcription factor pdr1p regulating multidrug resistance in the budding yeast", FEBS Letters, 505, 103-108, 2001

International Human Genome Sequencing Consortium, "Initial sequencing and analysis of the human genome", Nature, 409, 860-921, 2001

The International Human Genome Mapping Consortium, "A physical map of the human genome", Nature, 409, 934-941, 2001

Natsuhiro Ichinose and Kazuyuki Aihara, "Detection of Mutual Determinisim between a Pair of Spike Trains", Biological Cybernetics, 85, 5, 327-333, 2001

[2000]

O. Gotoh, "Homology-based gene structure prediction: simplified matching algorithm using a translated colon (ton) and improved accuracy by allowing for long gaps", Bioinformatics, 16, 190-202, 2000

Aoyama, Y., Kudo, M., Asai, K., Okonogi, K., Horiuchi, T., Gotoh, O., Yoshida, Y., "Emergence of fluconazole-resistant sterol 14-demethylase P450 (CYP51) in Candida albicans is a model demonstrating the diversification mechanism of P450", Arch. Biochem. Biophys., 379, 170-171, 2000

Yoshida, Y., Aoyama, Y., Noshiro, M., and Gotoh, O., "Sterol 14-Demethylase P450 (CYP51) provides a breakthrough for the discussion on the evolution of cytochrome P450 gene superfamily", Biochem. Biophys. Res. Commun. 273, 799-804, 2000

Kimura, R., Yoshii, H., Nomura, M., Kotomura, N., Mukai, T., Ishihara, S., Ohba, K., Yanase, T., Gotoh, O., Nawata, H., Morohashi, K., "Identification of novel first exons in Ad4BP/SF-1 (NR5A1) gene and their tissue- and species-specific usage", Biochem Biophys Res Commun. 278, 63-71, 2000

Teramoto, M., Nakamatsu, K., Noshiro, M., Matsuda, Y., Gotoh, O., Shen, M., Tsutsumi, S., Kawamoto, T., Iwamoto, Y., Kato, Y., "Gene structure and chromosomal location of a human bHLH transcriptional factor DEC1-Stra13-SHARP-2/BHLHB2", J. Biochem. 129, 391-396, 2000

The Chromosome 21 Mapping and Sequencing Consortium, "The DNA sequence of human chromosome 21", Nature, 405, 311-319, 2000