Kiyoshi Asai

Publication Activity (10 Years)

Years Active: 1990-2022
Publications (10 Years): 13

Top Topics

Secondary Structure

Prediction Accuracy

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Masaki Tagashira, Kiyoshi Asai
ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures. Bioinform. 38 (3) (2022)
Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinform. 37 (5) (2021)
Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai
RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. BMC Bioinform. 21 (1) (2020)
Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai
Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model. Bioinform. 36 (Supplement-1) (2020)
Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Anish M. S. Shrestha, Naruki Yoshikawa, Kiyoshi Asai
Combining probabilistic alignments with read pair information improves accuracy of split-alignments. Bioinform. 34 (21) (2018)
Hiraku Morita, Nuttapong Attrapadung, Satsuya Ohata, Koji Nuida, Shota Yamada, Kana Shimizu, Goichiro Hanaoka, Kiyoshi Asai
Secure Division Protocol and Applications to Privacy-preserving Chi-squared Tests. ISITA (2018)
Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. BMC Bioinform. (1) (2018)
Goro Terai, Satoshi Kamegai, Akito Taneda, Kiyoshi Asai
Evolutionary design of multiple genes encoding the same protein. Bioinform. 33 (11) (2017)
Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith
Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinform. 33 (6) (2017)
Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai
Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. BMC Genom. 17 (S-1) (2016)
Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai
Rtools: a web server for various secondary structural analyses on single RNA sequences. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Goro Terai, Satoshi Kamegai, Kiyoshi Asai
CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure. Bioinform. 32 (6) (2016)
Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai
Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014). IEEE ACM Trans. Comput. Biol. Bioinform. 12 (4) (2015)
Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
Learning chromatin states with factorized information criteria. Bioinform. 31 (15) (2015)
Takahiro Tsukui, Nozomi Nagano, Myco Umemura, Toshitaka Kumagai, Goro Terai, Masayuki Machida, Kiyoshi Asai
. Bioinform. 31 (7) (2015)
Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
A semi-supervised learning approach for RNA secondary structure prediction. Comput. Biol. Chem. 57 (2015)
Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai
Privacy-preserving search for chemical compound databases. BMC Bioinform. 16 (S18) (2015)
Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai
Editorial. J. Bioinform. Comput. Biol. 12 (6) (2014)
Satoshi Yamasaki, Takatsugu Hirokawa, Kiyoshi Asai, Kazuhiko Fukui
Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method. J. Chem. Inf. Model. 54 (2) (2014)
Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada
Reference-free prediction of rearrangement breakpoint reads. Bioinform. 30 (18) (2014)
Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. Bioinform. 29 (20) (2013)
Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
PBSIM: PacBio reads simulator - toward accurate genome assembly. Bioinform. 29 (1) (2013)
Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai
Generalized Centroid Estimators in Bioinformatics CoRR (2013)
Edward Wijaya, Martin C. Frith, Kiyoshi Asai, Paul Horton
RecountDB: a database of mapped and count corrected transcribed sequences. Nucleic Acids Res. 40 (Database-Issue) (2012)
Michiaki Hamada, Kiyoshi Asai
A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). J. Comput. Biol. 19 (5) (2012)
Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinform. 28 (24) (2012)
Raymond Wan, Vo Ngoc Anh, Kiyoshi Asai
Transformations for the compression of FASTQ quality scores of next-generation sequencing data. Bioinform. 28 (5) (2012)
Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Hisanori Kiryu, Kiyoshi Asai
Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations. Bioinform. 28 (8) (2012)
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res. 39 (2) (2011)
Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai
A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. Bioinform. 27 (13) (2011)
Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Michiaki Hamada, Edward Wijaya, Martin C. Frith, Kiyoshi Asai
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinform. 27 (22) (2011)
Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinform. 27 (13) (2011)
Raymond Wan, Kiyoshi Asai
Sorting next generation sequencing data improves compression effectiveness. BIBM Workshops (2010)
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinform. 11 (2010)
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, Raoul Jean Pierre Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José María Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 1 (2010)
Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama, Kiyoshi Asai
Conic Programming for Multitask Learning. IEEE Trans. Knowl. Data Eng. 22 (7) (2010)
Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinform. 26 (18) (2010)
Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. J. Bioinform. Comput. Biol. 8 (4) (2010)
Edward Wijaya, Jean-François Pessiot, Martin C. Frith, Wataru Fujibuchi, Kiyoshi Asai, Paul Horton
In search of true reads: A classification approach to next generation sequencing data selection. BIBM Workshops (2010)
Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai
Prediction of RNA secondary structure using generalized centroid estimators. Bioinform. 25 (4) (2009)
Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI (2009)
Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, Kiyoshi Asai
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res. 37 (Database-Issue) (2009)
Yasuo Tabei, Kiyoshi Asai
A local multiple alignment method for detection of non-coding RNA sequences. Bioinform. 25 (12) (2009)
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
Predictions of RNA secondary structure by combining homologous sequence information. Bioinform. 25 (12) (2009)
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinform. 25 (24) (2009)
Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama
CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
Directed acyclic graph kernels for structural RNA analysis. BMC Bioinform. 9 (2008)
Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama
Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res. 36 (Web-Server-Issue) (2008)
Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
Rfold: an exact algorithm for computing local base pairing probabilities. Bioinform. 24 (3) (2008)
Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
A fast structural multiple alignment method for long RNA sequences. BMC Bioinform. 9 (2008)
Kinya Okada, Kiyoshi Asai, Masanori Arita
Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions. APBC (2007)
Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato
Stem Kernels for RNA Sequence Analyses. J. Bioinform. Comput. Biol. 5 (5) (2007)
Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato
Stem Kernels for RNA Sequence Analyses. BIRD (2007)
Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama, Kiyoshi Asai
Multi-Task Learning via Conic Programming. NIPS (2007)
Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinform. 23 (4) (2007)
Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res. 35 (Database-Issue) (2007)
Hisanori Kiryu, Yasuo Tabei, Taishin Kin, Kiyoshi Asai
Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinform. 23 (13) (2007)
Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinform. 22 (14) (2006)
Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul Horton, Koji Tsuda, Wataru Fujibuchi
Network-based de-noising improves prediction from microarray data. BMC Bioinform. 7 (S-1) (2006)
Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai
Mining frequent stem patterns from unaligned RNA sequences. Bioinform. 22 (20) (2006)
Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai
Accurate extraction of functional associations between proteins based on common interaction partners and common domains. Bioinform. 21 (9) (2005)
Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
Selective integration of multiple biological data for supervised network inference. Bioinform. 21 (10) (2005)
Hisanori Kiryu, Taku Oshima, Kiyoshi Asai
Extracting relations between promoter sequences and their strengths from microarray data. Bioinform. 21 (7) (2005)
Koji Tsuda, Shinsuke Uda, Taishin Kin, Kiyoshi Asai
Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data. Neural Process. Lett. 19 (1) (2004)
Tsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai
A New Variational Framework for Rigid-Body Alignment. SSPR/SPR (2004)
Shusuke Saeki, Kiyoshi Asai, Katsutoshi Takahashi, Yutaka Ueno, Katsunori Isono, Hitoshi Iba
GA-Based Inference of Euler Angles for Single Particle Analysis. GECCO (2003)
Koji Tsuda, Shotaro Akaho, Kiyoshi Asai
The em Algorithm for Kernel Matrix Completion with Auxiliary Data. J. Mach. Learn. Res. 4 (2003)
Masanori Arita, Koji Tsuda, Kiyoshi Asai
Modeling splicing sites with pairwise correlations. ECCB (2002)
Koji Tsuda, Taishin Kin, Kiyoshi Asai
Marginalized kernels for biological sequences. ISMB (2002)
Koji Tsuda, Shotaro Akaho, Kiyoshi Asai
Approximating Incomplete Kernel Matrices by the em Algorithm CoRR (2002)
Masanori Arita, Kiyoshi Asai, Takaaki Nishioka
Reconstructing Metabolic Pathways with New Enzyme Classification. German Conference on Bioinformatics (2000)
Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai, Kenta Nakai
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinform. 14 (4) (1998)
Yutaka Ueno, Kiyoshi Asai
A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser. ISMB (1997)
Kentaro Onizuka, Masayuki Akahoshi, Masato Ishikawa, Kiyoshi Asai
The Multi-Scale 3D-1D Compatibility Scoring for Inverse Protein Folding Protein. ISMB (1994)
Masayuki Akahoshi, Kentaro Onizuka, Masato Ishikawa, Kiyoshi Asai
A Three-Dimensional Animation System for Protein Folding Simulation. HICSS (5) (1994)
Kentaro Onizuka, Hiroshi Tsuda, Masato Ishikawa, Akira Aiba, Kiyoshi Asai, Katunobu Ito
Protein Structure Prediction Based on Multi-Level Description. HICSS (5) (1994)
Kiyoshi Asai, Satoru Hayamizu, Ken'ichi Handa
Prediction of protein secondary structure by the hidden Markov model. Comput. Appl. Biosci. 9 (2) (1993)
Kentaro Onizuka, Stephen T. C. Wong, Masato Ishikawa, Kiyoshi Asai
A Multi-Level Description Scheme of Protein Conformation. ISMB (1993)
Hidetoshi Tanaka, Masato Ishikawa, Kiyoshi Asai, Akihiko Konagaya
Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. ISMB (1993)
Kiyoshi Asai, Satoru Hayamizu, Ken'ichi Handa
Dividing the distributions of HMM and linear interpolation in speech recognition. ICASSP (1992)
Shigeru Chiba, Kiyoshi Asai
A new method of consonant detection and classification using neural networks. ICSLP (1990)
Kiyoshi Asai, Shigeru Chiba
Voiced-unvoiced classification using weighted distance measures. ICSLP (1990)