Kiyoshi Asai - RankMe

88 papers A 6B 1C 3Misc 1Journal 66Unranked 10

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Deep generative model of RNAs based on variational autoencoder with context-free grammar. Bioinform. Goro Terai, Kiyoshi Asai
2025	J	`jnl`	PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures. PLoS Comput. Biol. Takumi Otagaki, Goro Terai, Kiyoshi Asai, Junichi Iwakiri
2022	J	`jnl`	ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures. Bioinform. Masaki Tagashira, Kiyoshi Asai
2021	J	`jnl`	PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinform. Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
2020	J	`jnl`	Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model. Bioinform. Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai
2020	J	`jnl`	RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. BMC Bioinform. Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai
2019	J	`jnl`	Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data. IEEE ACM Trans. Comput. Biol. Bioinform. Shimpei Nishida, Shun Sakuraba, Kiyoshi Asai, Michiaki Hamada
2019	—	`ch.`	RNA Structure Prediction. Encyclopedia of Bioinformatics and Computational Biology (2) Junichi Iwakiri, Kiyoshi Asai
2018	J	`jnl`	Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. BMC Bioinform. Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai
2018	J	`jnl`	Combining probabilistic alignments with read pair information improves accuracy of split-alignments. Bioinform. Anish Man Singh Shrestha, Naruki Yoshikawa, Kiyoshi Asai
2018	C	`conf`	Secure Division Protocol and Applications to Privacy-preserving Chi-squared Tests. ISITA Hiraku Morita, Nuttapong Attrapadung, Satsuya Ohata, Koji Nuida, Shota Yamada, Kana Shimizu, Goichiro Hanaoka, Kiyoshi Asai
2017	J	`jnl`	Evolutionary design of multiple genes encoding the same protein. Bioinform. Goro Terai, Satoshi Kamegai, Akito Taneda, Kiyoshi Asai
2017	J	`jnl`	Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinform. Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith
2016	J	`jnl`	CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure. Bioinform. Goro Terai, Satoshi Kamegai, Kiyoshi Asai
2016	J	`jnl`	Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. BMC Genom. Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai
2016	J	`jnl`	Rtools: a web server for various secondary structural analyses on single RNA sequences. Nucleic Acids Res. Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai
2015	J	`jnl`	A semi-supervised learning approach for RNA secondary structure prediction. Comput. Biol. Chem. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
2015	J	`jnl`	Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014). IEEE ACM Trans. Comput. Biol. Bioinform. Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai
2015	J	`jnl`	Learning chromatin states with factorized information criteria. Bioinform. Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
2015	J	`jnl`	Privacy-preserving search for chemical compound databases. BMC Bioinform. Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai
2015	J	`jnl`	Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Bioinform. Takahiro Tsukui, Nozomi Nagano, Myco Umemura, Toshitaka Kumagai, Goro Terai, Masayuki Machida, Kiyoshi Asai
2014	J	`jnl`	Editorial. J. Bioinform. Comput. Biol. Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai
2014	J	`jnl`	Reference-free prediction of rearrangement breakpoint reads. Bioinform. Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada
2014	J	`jnl`	Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method. J. Chem. Inf. Model. Satoshi Yamasaki, Takatsugu Hirokawa, Kiyoshi Asai, Kazuhiko Fukui
2013	J	`jnl`	Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. Bioinform. Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
2013	J	`jnl`	Generalized Centroid Estimators in Bioinformatics CoRR Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai
2013	J	`jnl`	PBSIM: PacBio reads simulator - toward accurate genome assembly. Bioinform. Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
2012	J	`jnl`	A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). J. Comput. Biol. Michiaki Hamada, Kiyoshi Asai
2012	J	`jnl`	DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinform. Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara
2012	J	`jnl`	Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations. Bioinform. Hisanori Kiryu, Kiyoshi Asai
2012	J	`jnl`	RecountDB: a database of mapped and count corrected transcribed sequences. Nucleic Acids Res. Edward Wijaya, Martin C. Frith, Kiyoshi Asai, Paul Horton
2012	J	`jnl`	Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res. Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu
2012	J	`jnl`	Transformations for the compression of FASTQ quality scores of next-generation sequencing data. Bioinform. Raymond Wan, Vo Ngoc Anh, Kiyoshi Asai
2011	J	`jnl`	A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. Bioinform. Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai
2011	J	`jnl`	CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res. Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai
2011	J	`jnl`	IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinform. Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai
2011	J	`jnl`	Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res. Michiaki Hamada, Kengo Sato, Kiyoshi Asai
2011	J	`jnl`	Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinform. Michiaki Hamada, Edward Wijaya, Martin C. Frith, Kiyoshi Asai
2010	J	`jnl`	A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures. J. Bioinform. Comput. Biol. Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
2010	J	`jnl`	Conic Programming for Multitask Learning. IEEE Trans. Knowl. Data Eng. Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama, Kiyoshi Asai
2010	—	`conf`	In search of true reads: A classification approach to next generation sequencing data selection. BIBM Workshops Edward Wijaya, Jean-François Pessiot, Martin C. Frith, Wataru Fujibuchi, Kiyoshi Asai, Paul Horton
2010	J	`jnl`	Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinform. Michiaki Hamada, Kengo Sato, Kiyoshi Asai
2010	J	`jnl`	RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinform. Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu
2010	—	`conf`	Sorting next generation sequencing data improves compression effectiveness. BIBM Workshops Raymond Wan, Kiyoshi Asai
2010	J	`jnl`	The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomed. Semant. 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
2009	C	`conf`	A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
2009	J	`jnl`	A local multiple alignment method for detection of non-coding RNA sequences. Bioinform. Yasuo Tabei, Kiyoshi Asai
2009	J	`jnl`	CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama
2009	J	`jnl`	CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinform. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
2009	J	`jnl`	Prediction of RNA secondary structure using generalized centroid estimators. Bioinform. Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai
2009	J	`jnl`	Predictions of RNA secondary structure by combining homologous sequence information. Bioinform. Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
2009	J	`jnl`	The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res. Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, Kiyoshi Asai
2008	J	`jnl`	A fast structural multiple alignment method for long RNA sequences. BMC Bioinform. Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
2008	J	`jnl`	Directed acyclic graph kernels for structural RNA analysis. BMC Bioinform. Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara
2008	J	`jnl`	Rfold: an exact algorithm for computing local base pairing probabilities. Bioinform. Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
2008	J	`jnl`	Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res. Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama
2007	B	`conf`	Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions. APBC Kinya Okada, Kiyoshi Asai, Masanori Arita
2007	—	`conf`	Multi-Task Learning via Conic Programming. NIPS Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama, Kiyoshi Asai
2007	J	`jnl`	Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinform. Hisanori Kiryu, Yasuo Tabei, Taishin Kin, Kiyoshi Asai
2007	J	`jnl`	Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinform. Hisanori Kiryu, Taishin Kin, Kiyoshi Asai
2007	—	`conf`	Stem Kernels for RNA Sequence Analyses. BIRD Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato
2007	J	`jnl`	Stem Kernels for RNA Sequence Analyses. J. Bioinform. Comput. Biol. Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato
2007	J	`jnl`	fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res. Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai
2006	J	`jnl`	Mining frequent stem patterns from unaligned RNA sequences. Bioinform. Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai
2006	J	`jnl`	Network-based de-noising improves prediction from microarray data. BMC Bioinform. Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul Horton, Koji Tsuda, Wataru Fujibuchi
2006	J	`jnl`	SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinform. Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai
2005	J	`jnl`	Accurate extraction of functional associations between proteins based on common interaction partners and common domains. Bioinform. Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai
2005	J	`jnl`	Extracting relations between promoter sequences and their strengths from microarray data. Bioinform. Hisanori Kiryu, Taku Oshima, Kiyoshi Asai
2005	J	`jnl`	Selective integration of multiple biological data for supervised network inference. Bioinform. Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai
2004	—	`conf`	A New Variational Framework for Rigid-Body Alignment. SSPR/SPR Tsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai
2004	J	`jnl`	Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data. Neural Process. Lett. Koji Tsuda, Shinsuke Uda, Taishin Kin, Kiyoshi Asai
2003	A	`conf`	GA-Based Inference of Euler Angles for Single Particle Analysis. GECCO Shusuke Saeki, Kiyoshi Asai, Katsutoshi Takahashi, Yutaka Ueno, Katsunori Isono, Hitoshi Iba
2003	J	`jnl`	The em Algorithm for Kernel Matrix Completion with Auxiliary Data. J. Mach. Learn. Res. Koji Tsuda, Shotaro Akaho, Kiyoshi Asai
2002	J	`jnl`	Approximating Incomplete Kernel Matrices by the em Algorithm CoRR Koji Tsuda, Shotaro Akaho, Kiyoshi Asai
2002	A	`conf`	Marginalized kernels for biological sequences. ISMB Koji Tsuda, Taishin Kin, Kiyoshi Asai
2002	C	`conf`	Modeling splicing sites with pairwise correlations. ECCB Masanori Arita, Koji Tsuda, Kiyoshi Asai
2000	—	`conf`	Reconstructing Metabolic Pathways with New Enzyme Classification. German Conference on Bioinformatics Masanori Arita, Kiyoshi Asai, Takaaki Nishioka
1998	J	`jnl`	Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences. Bioinform. Tetsushi Yada, Yasushi Totoki, Masato Ishikawa, Kiyoshi Asai, Kenta Nakai
1997	A	`conf`	A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser. ISMB Yutaka Ueno, Kiyoshi Asai
1994	—	`conf`	A Three-Dimensional Animation System for Protein Folding Simulation. HICSS (5) Masayuki Akahoshi, Kentaro Onizuka, Masato Ishikawa, Kiyoshi Asai
1994	—	`conf`	Protein Structure Prediction Based on Multi-Level Description. HICSS (5) Kentaro Onizuka, Hiroshi Tsuda, Masato Ishikawa, Akira Aiba, Kiyoshi Asai, Katunobu Ito
1994	A	`conf`	The Multi-Scale 3D-1D Compatibility Scoring for Inverse Protein Folding Protein. ISMB Kentaro Onizuka, Masayuki Akahoshi, Masato Ishikawa, Kiyoshi Asai
1993	A	`conf`	A Multi-Level Description Scheme of Protein Conformation. ISMB Kentaro Onizuka, Stephen T. C. Wong, Masato Ishikawa, Kiyoshi Asai
1993	A	`conf`	Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. ISMB Hidetoshi Tanaka, Masato Ishikawa, Kiyoshi Asai, Akihiko Konagaya
1993	J	`jnl`	Prediction of protein secondary structure by the hidden Markov model. Comput. Appl. Biosci. Kiyoshi Asai, Satoru Hayamizu, Ken'ichi Handa
1992	Misc	`conf`	Dividing the distributions of HMM and linear interpolation in speech recognition. ICASSP Kiyoshi Asai, Satoru Hayamizu, Ken'ichi Handa
1990	—	`conf`	A new method of consonant detection and classification using neural networks. ICSLP Shigeru Chiba, Kiyoshi Asai
1990	—	`conf`	Voiced-unvoiced classification using weighted distance measures. ICSLP Kiyoshi Asai, Shigeru Chiba