Voiced-unvoiced classification using weighted distance measures. - Kiyoshi Asai; Shigeru Chiba (ICSLP, 1990)

A new method of consonant detection and classification using neural networks. - Shigeru Chiba; Kiyoshi Asai (ICSLP, 1990)

Dividing the distributions of HMM and linear interpolation in speech recognition. - Kiyoshi Asai; Satoru Hayamizu; Ken'ichi Handa (ICASSP, 1992)

A Multi-Level Description Scheme of Protein Conformation. - Kentaro Onizuka; Stephen T. C. Wong; Masato Ishikawa; Kiyoshi Asai (ISMB, 1993)

Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. - Hidetoshi Tanaka; Masato Ishikawa; Kiyoshi Asai; Akihiko Konagaya (ISMB, 1993)

Prediction of protein secondary structure by the hidden Markov model. - Kiyoshi Asai; Satoru Hayamizu; Ken'ichi Handa (Comput. Appl. Biosci., 1993)

A Three-Dimensional Animation System for Protein Folding Simulation. - Masayuki Akahoshi; Kentaro Onizuka; Masato Ishikawa; Kiyoshi Asai (HICSS (5), 1994)

Protein Structure Prediction Based on Multi-Level Description. - Kentaro Onizuka; Hiroshi Tsuda; Masato Ishikawa; Akira Aiba; Kiyoshi Asai; Katunobu Ito (HICSS (5), 1994)

The Multi-Scale 3D-1D Compatibility Scoring for Inverse Protein Folding Protein. - Kentaro Onizuka; Masayuki Akahoshi; Masato Ishikawa; Kiyoshi Asai (ISMB, 1994)

A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser. - Yutaka Ueno; Kiyoshi Asai (ISMB, 1997)

Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. - Tetsushi Yada; Yasushi Totoki; Masato Ishikawa; Kiyoshi Asai; Kenta Nakai (Bioinform., 1998)

Reconstructing Metabolic Pathways with New Enzyme Classification. - Masanori Arita; Kiyoshi Asai; Takaaki Nishioka (German Conference on Bioinformatics, 2000)

Modeling splicing sites with pairwise correlations. - Masanori Arita; Koji Tsuda; Kiyoshi Asai (ECCB, 2002)

Marginalized kernels for biological sequences. - Koji Tsuda; Taishin Kin; Kiyoshi Asai (ISMB, 2002)

Approximating Incomplete Kernel Matrices by the em Algorithm - Koji Tsuda; Shotaro Akaho; Kiyoshi Asai (CoRR, 2002)

GA-Based Inference of Euler Angles for Single Particle Analysis. - Shusuke Saeki; Kiyoshi Asai; Katsutoshi Takahashi; Yutaka Ueno; Katsunori Isono; Hitoshi Iba (GECCO, 2003)

The em Algorithm for Kernel Matrix Completion with Auxiliary Data. - Koji Tsuda; Shotaro Akaho; Kiyoshi Asai (J. Mach. Learn. Res., 2003)

A New Variational Framework for Rigid-Body Alignment. - Tsuyoshi Kato; Koji Tsuda; Kentaro Tomii; Kiyoshi Asai (SSPR/SPR, 2004)

Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data. - Koji Tsuda; Shinsuke Uda; Taishin Kin; Kiyoshi Asai (Neural Process. Lett., 2004)

Selective integration of multiple biological data for supervised network inference. - Tsuyoshi Kato; Koji Tsuda; Kiyoshi Asai (Bioinform., 2005)

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

Accurate extraction of functional associations between proteins based on common interaction partners and common domains. - Kinya Okada; Shigehiko Kanaya; Kiyoshi Asai (Bioinform., 2005)

Mining frequent stem patterns from unaligned RNA sequences. - Michiaki Hamada; Koji Tsuda; Taku Kudo; Taishin Kin; Kiyoshi Asai (Bioinform., 2006)

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. - Yasuo Tabei; Koji Tsuda; Taishin Kin; Kiyoshi Asai (Bioinform., 2006)

Network-based de-noising improves prediction from microarray data. - Tsuyoshi Kato; Yukio Murata; Koh Miura; Kiyoshi Asai; Paul Horton; Koji Tsuda; Wataru Fujibuchi (BMC Bioinform., 2006)

Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions. - Kinya Okada; Kiyoshi Asai; Masanori Arita (APBC, 2007)

Stem Kernels for RNA Sequence Analyses. - Yasubumi Sakakibara; Kiyoshi Asai; Kengo Sato (BIRD, 2007)

Multi-Task Learning via Conic Programming. - Tsuyoshi Kato; Hisashi Kashima; Masashi Sugiyama; Kiyoshi Asai (NIPS, 2007)

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)

Stem Kernels for RNA Sequence Analyses. - Yasubumi Sakakibara; Kris Popendorf; Nana Ogawa; Kiyoshi Asai; Kengo Sato (J. Bioinform. Comput. Biol., 2007)

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. - Taishin Kin; Kouichirou Yamada; Goro Terai; Hiroaki Okida; Yasuhiko Yoshinari; Yukiteru Ono; Aya Kojima; Yuki Kimura; Takashi Komori; Kiyoshi Asai (Nucleic Acids Res., 2007)

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

Directed acyclic graph kernels for structural RNA analysis. - Kengo Sato; Toutai Mituyama; Kiyoshi Asai; Yasubumi Sakakibara (BMC 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)

A local multiple alignment method for detection of non-coding RNA sequences. - Yasuo Tabei; Kiyoshi Asai (Bioinform., 2009)

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. - Toutai Mituyama; Kouichirou Yamada; Emi Hattori; Hiroaki Okida; Yukiteru Ono; Goro Terai; Aya Yoshizawa; Takashi Komori; Kiyoshi Asai (Nucleic Acids Res., 2009)

CENTROIDFOLD: a web server for RNA secondary structure prediction. - Kengo Sato; Michiaki Hamada; Kiyoshi Asai; Toutai Mituyama (Nucleic Acids Res., 2009)

Sorting next generation sequencing data improves compression effectiveness. - Raymond Wan 001; Kiyoshi Asai (BIBM Workshops, 2010)

In search of true reads: A classification approach to next generation sequencing data selection. - Edward Wijaya; Jean-François Pessiot; Martin C. Frith; Wataru Fujibuchi; Kiyoshi Asai; Paul Horton (BIBM Workshops, 2010)

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. - Yuki Kato; Kengo Sato; Michiaki Hamada; Yoshihide Watanabe; Kiyoshi Asai; Tatsuya Akutsu (Bioinform., 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F. Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord H. Barboza; et al. (J. Biomed. Semant., 2010)

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. - Michiaki Hamada; Kengo Sato; Kiyoshi Asai (BMC Bioinform., 2010)

A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. - Kengo Sato; Michiaki Hamada; Toutai Mituyama; Kiyoshi Asai; Yasubumi Sakakibara (J. Bioinform. Comput. Biol., 2010)

Conic Programming for Multitask Learning. - Tsuyoshi Kato; Hisashi Kashima; Masashi Sugiyama; Kiyoshi Asai (IEEE Trans. Knowl. Data Eng., 2010)

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. - Michiaki Hamada; Edward Wijaya; Martin C. Frith; Kiyoshi Asai (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)

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. - Kengo Sato; Yuki Kato; Michiaki Hamada; Tatsuya Akutsu; Kiyoshi Asai (Bioinform., 2011)

Improving the accuracy of predicting secondary structure for aligned RNA sequences. - Michiaki Hamada; Kengo Sato; Kiyoshi Asai (Nucleic Acids Res., 2011)

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. - Michiaki Hamada; Koichiro Yamada; Kengo Sato; Martin C. Frith; Kiyoshi Asai (Nucleic Acids Res., 2011)

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

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. - Kengo Sato; Yuki Kato; Tatsuya Akutsu; Kiyoshi Asai; Yasubumi Sakakibara (Bioinform., 2012)

Transformations for the compression of FASTQ quality scores of next-generation sequencing data. - Raymond Wan 001; Vo Ngoc Anh; Kiyoshi Asai (Bioinform., 2012)

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). - Michiaki Hamada; Kiyoshi Asai (J. Comput. Biol., 2012)

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. - Yuki Kato; Kengo Sato; Kiyoshi Asai; Tatsuya Akutsu (Nucleic Acids Res., 2012)

RecountDB: a database of mapped and count corrected transcribed sequences. - Edward Wijaya; Martin C. Frith; Kiyoshi Asai; Paul Horton (Nucleic Acids Res., 2012)

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. - Junichi Iwakiri; Tomoshi Kameda; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2013)

PBSIM: PacBio reads simulator - toward accurate genome assembly. - Yukiteru Ono; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2013)

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

Reference-free prediction of rearrangement breakpoint reads. - Edward Wijaya; Kana Shimizu; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2014)

Editorial. - Tetsuo Shibuya; Chuan Yi Tang; Paul Horton; Kiyoshi Asai (J. Bioinform. Comput. Biol., 2014)

Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method. - Satoshi Yamasaki; Takatsugu Hirokawa; Kiyoshi Asai; Kazuhiko Fukui (J. Chem. Inf. Model., 2014)

Learning chromatin states with factorized information criteria. - Michiaki Hamada; Yukiteru Ono; Ryohei Fujimaki; Kiyoshi Asai (Bioinform., 2015)

Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens. - Takahiro Tsukui; Nozomi Nagano; Myco Umemura; Toshitaka Kumagai; Goro Terai; Masayuki Machida; Kiyoshi Asai (Bioinform., 2015)

A semi-supervised learning approach for RNA secondary structure prediction. - Haruka Yonemoto; Kiyoshi Asai; Michiaki Hamada (Comput. Biol. Chem., 2015)

Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014). - Tetsuo Shibuya; Chuan Yi Tang; Paul Horton; Kiyoshi Asai (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Privacy-preserving search for chemical compound databases. - Kana Shimizu; Koji Nuida; Hiromi Arai; Shigeo Mitsunari; Nuttapong Attrapadung; Michiaki Hamada; Koji Tsuda; Takatsugu Hirokawa; Jun Sakuma; Goichiro Hanaoka; Kiyoshi Asai (BMC Bioinform., 2015)

CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure. - Goro Terai; Satoshi Kamegai; Kiyoshi Asai (Bioinform., 2016)

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. - Goro Terai; Junichi Iwakiri; Tomoshi Kameda; Michiaki Hamada; Kiyoshi Asai (BMC Genom., 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)

Training alignment parameters for arbitrary sequencers with LAST-TRAIN. - Michiaki Hamada; Yukiteru Ono; Kiyoshi Asai; Martin C. Frith (Bioinform., 2017)

Evolutionary design of multiple genes encoding the same protein. - Goro Terai; Satoshi Kamegai; Akito Taneda; Kiyoshi Asai (Bioinform., 2017)

Secure Division Protocol and Applications to Privacy-preserving Chi-squared Tests. - Hiraku Morita; Nuttapong Attrapadung; Satsuya Ohata; Koji Nuida; Shota Yamada 001; Kana Shimizu; Goichiro Hanaoka; Kiyoshi Asai (ISITA, 2018)

Combining probabilistic alignments with read pair information improves accuracy of split-alignments. - Anish Man Singh Shrestha; Naruki Yoshikawa; Kiyoshi Asai (Bioinform., 2018)

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. - Taichi Hagio; Shun Sakuraba; Junichi Iwakiri; Ryota Mori; Kiyoshi Asai (BMC Bioinform., 2018)

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. - Shimpei Nishida; Shun Sakuraba; Kiyoshi Asai; Michiaki Hamada (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

RNA Structure Prediction. - Junichi Iwakiri; Kiyoshi Asai (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model. - Hiroki Takizawa; Junichi Iwakiri; Goro Terai; Kiyoshi Asai (Bioinform., 2020)

RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. - Hiroki Takizawa; Junichi Iwakiri; Kiyoshi Asai (BMC Bioinform., 2020)

PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. - Yukiteru Ono; Kiyoshi Asai; Michiaki Hamada (Bioinform., 2021)

ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures. - Masaki Tagashira; Kiyoshi Asai (Bioinform., 2022)