Peer-reviewed Articles
Kiryu, H., Ichikawa, Y. & Kojima, Y. "TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column." Algorithms Mol Biol 14, 23 (2019) doi:10.1186/s13015-019-0158-3
Yasuhiro Kojima, Hirotaka Matsumoto, and Hisanori Kiryu. "Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations" Bioinformatics; btz498 doi: 10.1093/bioinformatics/btz498 (2019)
R. Kawaguchi, H. Kiryu, J. Iwakiri and J. Sese. "reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction" BMC Bioinformatics 20 (Suppl 3) :130 (2019).
Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S. H. Ko, Shigeru B. H. Ko, Norio Gouda, Tetsutaro Hayashi, Itoshi Nikaido, SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation., Bioinformatics; btx194 doi: 10.1093/bioinformatics/btx194 (2017)
Hirotaka Matsumoto and Hisanori Kiryu, SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation, BMC Bioinformatics 17:232 (2016)
Risa Kawaguchi and Hisanori Kiryu, Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome, BMC Bioinformatics 17:203 doi:10.1186/s12859-016-1067-9 (2016)
Hisanori Kiryu, and Kiyoshi Asai, Rchange: Algorithms for computing the energy changes of RNA secondary structures in response to base mutations, Bioinformatics 28(8) 1093-1101 doi: 10.1093/bioinformatics/bts097 (2012)
[PubMed]
Hisanori Kiryu, Sufficient statistics and expectation maximization algorithms in phylogenetic tree models, Bioinformatics 27(17), 2346-2353 doi:10.1093/bioinformatics/btr420 (2011)
[PubMed]
Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, and Kiyoshi Asai, Generalized Centroid Estimators in Bioinformatics, PLoS ONE 6(2): e16450, doi:10.1371/journal.pone.0016450. (2011)
Hamada M, Sato K, Kiryu H, Mituyama T, and Asai K, CentroidAlign: Fast and Accurate Aligner for Structured RNAs by Maximizing Expected Sum-of-pairs Score, Bioinformatics 25(24): 3236-3243 doi: 10.1093/bioinformatics/btp580 (2009)
[PubMed]
Hamada M, Sato K, Kiryu H, Mituyama T, and Asai K, Predictions of RNA secondary structure by combining homologous sequence information, Bioinformatics 25: i330-i338; doi:10.1093/bioinformatics/btp228 (2009)
[PubMed]
Hamada M, Kiryu H, Sato K, Mituyama T, and Asai K, Prediction of RNA secondary structure using generalized centroid estimators, Bioinformatics. 25:465-73. doi: 10.1093/bioinformatics/btn601(2009)
[PubMed]
Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai, Robust prediction of consensus secondary structures using averaged base pairing probability matrices, Bioinformatics 23: 434-441. doi: 10.1093/bioinformatics/btl636 (2007)
[PubMed]
Berezhnoy Andrey Yu, Shckorbatov Yuriy G., and Hisanori Kiryu, Regularities in the E. coli promoters composition in connection with the DNA strands interaction and promoter activity, Journal of Zhejiang Univ. Science B 7 (12) 969-973 doi: 10.1631/jzus.2006.B0969 (2006)
H. Kiryu, Transcription rate of RNA polymerase under rotary torque, Physical Review E 69, 041902 doi:10.1103/PhysRevE.69.041902 (2004)
H. Kiryu, Oscillations of persistent edge currents in the parafermion quantum Hall states, Physical Review B 65, 113407, doi:10.1103/PhysRevB.65.113407 (2001)
