Extracting relations between promoter sequences and their strengths from microarray data. - Hisanori Kiryu; Taku Oshima; Kiyoshi Asai (Bioinform., 2005)

Robust prediction of consensus secondary structures using averaged base pairing probability matrices. - Hisanori Kiryu; Taishin Kin; Kiyoshi Asai (Bioinform., 2007)

Murlet: a practical multiple alignment tool for structural RNA sequences. - Hisanori Kiryu; Yasuo Tabei; Taishin Kin; Kiyoshi Asai (Bioinform., 2007)

Rfold: an exact algorithm for computing local base pairing probabilities. - Hisanori Kiryu; Taishin Kin; Kiyoshi Asai (Bioinform., 2008)

A fast structural multiple alignment method for long RNA sequences. - Yasuo Tabei; Hisanori Kiryu; Taishin Kin; Kiyoshi Asai (BMC Bioinform., 2008)

Software.ncrna.org: web servers for analyses of RNA sequences. - Kiyoshi Asai; Hisanori Kiryu; Michiaki Hamada; Yasuo Tabei; Kengo Sato; Hiroshi Matsui; Yasubumi Sakakibara; Goro Terai; Toutai Mituyama (Nucleic Acids Res., 2008)

Prediction of RNA secondary structure using generalized centroid estimators. - Michiaki Hamada; Hisanori Kiryu; Kengo Sato; Toutai Mituyama; Kiyoshi Asai (Bioinform., 2009)

Predictions of RNA secondary structure by combining homologous sequence information. - Michiaki Hamada; Kengo Sato; Hisanori Kiryu; Toutai Mituyama; Kiyoshi Asai (Bioinform., 2009)

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. - Michiaki Hamada; Kengo Sato; Hisanori Kiryu; Toutai Mituyama; Kiyoshi Asai (Bioinform., 2009)

Sufficient statistics and expectation maximization algorithms in phylogenetic tree models. - Hisanori Kiryu (Bioinform., 2011)

A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. - Hisanori Kiryu; Goro Terai; Osamu Imamura; Hiroyuki Yoneyama; Kenji Suzuki; Kiyoshi Asai (Bioinform., 2011)

Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations. - Hisanori Kiryu; Kiyoshi Asai (Bioinform., 2012)

Generalized Centroid Estimators in Bioinformatics - Michiaki Hamada; Hisanori Kiryu; Wataru Iwasaki 001; Kiyoshi Asai (CoRR, 2013)

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. - Risa Kawaguchi; Hisanori Kiryu (BMC Bioinform., 2016)

SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation. - Hirotaka Matsumoto; Hisanori Kiryu (BMC Bioinform., 2016)

Rtools: a web server for various secondary structural analyses on single RNA sequences. - Michiaki Hamada; Yukiteru Ono; Hisanori Kiryu; Kengo Sato; Yuki Kato; Tsukasa Fukunaga; Ryota Mori; Kiyoshi Asai (Nucleic Acids Res., 2016)

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. - Hirotaka Matsumoto; Hisanori Kiryu; Chikara Furusawa; Minoru S. H. Ko; Shigeru B. H. Ko; Norio Gouda; Tetsutaro Hayashi; Itoshi Nikaido (Bioinform., 2017)

TMRS: an algorithm for computing the time to the most recent substitution event from a multiple alignment column. - Hisanori Kiryu; Yuto Ichikawa; Yasuhiro Kojima (Algorithms Mol. Biol., 2019)

reactIDR: evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction. - Risa Kawaguchi; Hisanori Kiryu; Junichi Iwakiri; Jun Sese (BMC Bioinform., 2019)

Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations. - Yasuhiro Kojima; Hirotaka Matsumoto; Hisanori Kiryu (Bioinform., 2020)

MODEC: an unsupervised clustering method integrating omics data for identifying cancer subtypes. - Yanting Zhang; Hisanori Kiryu (Briefings Bioinform., 2022)