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Journal Articles
- 2022
[j62]Masaki Tagashira
, Kiyoshi Asai:
ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures. Bioinform. 38(3): 710-719 (2022)- 2021
- [j61]Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada:
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores. Bioinform. 37(5): 589-595 (2021) - 2020
- [j60]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): i227-i235 (2020) - [j59]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): 210 (2020) - 2019
- [j58]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): 1645-1655 (2019) - 2018
- [j57]Anish Man Singh Shrestha, Naruki Yoshikawa, Kiyoshi Asai:
Combining probabilistic alignments with read pair information improves accuracy of split-alignments. Bioinform. 34(21): 3631-3637 (2018) - [j56]Taichi Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai:
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. BMC Bioinform. 19-S(1): 85-95 (2018) - 2017
- [j55]Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C. Frith:
Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinform. 33(6): 926-928 (2017) - [j54]Goro Terai, Satoshi Kamegai, Akito Taneda, Kiyoshi Asai:
Evolutionary design of multiple genes encoding the same protein. Bioinform. 33(11): 1613-1620 (2017) - 2016
- [j53]Goro Terai, Satoshi Kamegai, Kiyoshi Asai:
CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure. Bioinform. 32(6): 828-834 (2016) - [j52]Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai:
Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. BMC Genom. 17(S-1): 12 (2016) - [j51]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): W302-W307 (2016) - 2015
- [j50]Takahiro Tsukui, Nozomi Nagano, Myco Umemura, Toshitaka Kumagai, Goro Terai, Masayuki Machida, Kiyoshi Asai:
Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens. Bioinform. 31(7): 981-985 (2015) - [j49]Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai:
Learning chromatin states with factorized information criteria. Bioinform. 31(15): 2426-2433 (2015) - [j48]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): S6 (2015) - [j47]Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada:
A semi-supervised learning approach for RNA secondary structure prediction. Comput. Biol. Chem. 57: 72-79 (2015) - [j46]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): 761-762 (2015) - 2014
- [j45]Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada:
Reference-free prediction of rearrangement breakpoint reads. Bioinform. 30(18): 2559-2567 (2014) - [j44]Tetsuo Shibuya, Chuan Yi Tang, Paul Horton, Kiyoshi Asai:
Editorial. J. Bioinform. Comput. Biol. 12(6) (2014) - [j43]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): 672-682 (2014) - 2013
- [j42]Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada:
PBSIM: PacBio reads simulator - toward accurate genome assembly. Bioinform. 29(1): 119-121 (2013) - [j41]Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada:
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. Bioinform. 29(20): 2524-2528 (2013) - 2012
- [j40]Raymond Wan, Vo Ngoc Anh, Kiyoshi Asai:
Transformations for the compression of FASTQ quality scores of next-generation sequencing data. Bioinform. 28(5): 628-635 (2012) - [j39]Hisanori Kiryu, Kiyoshi Asai:
Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations. Bioinform. 28(8): 1093-1101 (2012) - [j38]Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara:
DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinform. 28(24): 3218-3224 (2012) - [j37]Michiaki Hamada, Kiyoshi Asai:
A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA). J. Comput. Biol. 19(5): 532-549 (2012) - [j36]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): 1089-1092 (2012) - [j35]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): 29-34 (2012) - 2011
- [j34]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): 85-93 (2011) - [j33]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): 1788-1797 (2011) - [j32]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): 3085-3092 (2011) - [j31]Michiaki Hamada, Kengo Sato, Kiyoshi Asai:
Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res. 39(2): 393-402 (2011) - [j30]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): 100-106 (2011) - 2010
- [j29]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) - [j28]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: 8 (2010) - [j27]Michiaki Hamada, Kengo Sato, Kiyoshi Asai:
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinform. 11: 586 (2010) - [j26]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): 727-742 (2010) - [j25]Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama, Kiyoshi Asai:
Conic Programming for Multitask Learning. IEEE Trans. Knowl. Data Eng. 22(7): 957-968 (2010) - 2009
- [j24]Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai:
Prediction of RNA secondary structure using generalized centroid estimators. Bioinform. 25(4): 465-473 (2009) - [j23]Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai:
Predictions of RNA secondary structure by combining homologous sequence information. Bioinform. 25(12) (2009) - [j22]Yasuo Tabei, Kiyoshi Asai:
A local multiple alignment method for detection of non-coding RNA sequences. Bioinform. 25(12): 1498-1505 (2009) - [j21]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): 3236-3243 (2009) - [j20]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): 89-92 (2009) - [j19]Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama:
CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res. 37(Web-Server-Issue): 277-280 (2009) - 2008
- [j18]Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
Rfold: an exact algorithm for computing local base pairing probabilities. Bioinform. 24(3): 367-373 (2008) - [j17]Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara:
Directed acyclic graph kernels for structural RNA analysis. BMC Bioinform. 9 (2008) - [j16]Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
A fast structural multiple alignment method for long RNA sequences. BMC Bioinform. 9 (2008) - [j15]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): 75-78 (2008) - 2007
- [j14]Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinform. 23(4): 434-441 (2007) - [j13]Hisanori Kiryu, Yasuo Tabei, Taishin Kin, Kiyoshi Asai:
Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinform. 23(13): 1588-1598 (2007) - [j12]Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato:
Stem Kernels for RNA Sequence Analyses. J. Bioinform. Comput. Biol. 5(5): 1103-1122 (2007) - [j11]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): 145-148 (2007) - 2006
- [j10]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): 1723-1729 (2006) - [j9]Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai:
Mining frequent stem patterns from unaligned RNA sequences. Bioinform. 22(20): 2480-2487 (2006) - [j8]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) - 2005
- [j7]Hisanori Kiryu, Taku Oshima, Kiyoshi Asai:
Extracting relations between promoter sequences and their strengths from microarray data. Bioinform. 21(7): 1062-1068 (2005) - [j6]Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai:
Accurate extraction of functional associations between proteins based on common interaction partners and common domains. Bioinform. 21(9): 2043-2048 (2005) - [j5]Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai:
Selective integration of multiple biological data for supervised network inference. Bioinform. 21(10): 2488-2495 (2005) - 2004
- [j4]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): 63-72 (2004) - 2003
- [j3]Koji Tsuda, Shotaro Akaho, Kiyoshi Asai:
The em Algorithm for Kernel Matrix Completion with Auxiliary Data. J. Mach. Learn. Res. 4: 67-81 (2003) - 1998
- [j2]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): 317-325 (1998) - 1993
- [j1]Kiyoshi Asai, Satoru Hayamizu, Ken'ichi Handa:
Prediction of protein secondary structure by the hidden Markov model. Comput. Appl. Biosci. 9(2): 141-146 (1993)
Conference and Workshop Papers
- 2018
- [c21]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: 530-534 - 2010
- [c20]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: 561-566 - [c19]Raymond Wan, Kiyoshi Asai:
Sorting next generation sequencing data improves compression effectiveness. BIBM Workshops 2010: 567-572 - 2009
- [c18]Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara:
A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. WABI 2009: 286-297 - 2007
- [c17]Kinya Okada, Kiyoshi Asai, Masanori Arita:
Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions. APBC 2007: 317-326 - [c16]Yasubumi Sakakibara, Kiyoshi Asai, Kengo Sato:
Stem Kernels for RNA Sequence Analyses. BIRD 2007: 278-291 - [c15]Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama, Kiyoshi Asai:
Multi-Task Learning via Conic Programming. NIPS 2007: 737-744 - 2004
- [c14]Tsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai:
A New Variational Framework for Rigid-Body Alignment. SSPR/SPR 2004: 171-179 - 2003
- [c13]Shusuke Saeki, Kiyoshi Asai, Katsutoshi Takahashi, Yutaka Ueno, Katsunori Isono, Hitoshi Iba:
GA-Based Inference of Euler Angles for Single Particle Analysis. GECCO 2003: 2288-2300 - 2002
- [c12]Masanori Arita, Koji Tsuda, Kiyoshi Asai:
Modeling splicing sites with pairwise correlations. ECCB 2002: 27-34 - [c11]Koji Tsuda, Taishin Kin, Kiyoshi Asai:
Marginalized kernels for biological sequences. ISMB 2002: 268-275 - 2000
- [c10]Masanori Arita, Kiyoshi Asai, Takaaki Nishioka:
Reconstructing Metabolic Pathways with New Enzyme Classification. German Conference on Bioinformatics 2000: 99-106 - 1997
- [c9]Yutaka Ueno, Kiyoshi Asai:
A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser. ISMB 1997: 329-332 - 1994
- [c8]Masayuki Akahoshi, Kentaro Onizuka, Masato Ishikawa, Kiyoshi Asai:
A Three-Dimensional Animation System for Protein Folding Simulation. HICSS (5) 1994: 173-182 - [c7]Kentaro Onizuka, Hiroshi Tsuda, Masato Ishikawa, Akira Aiba, Kiyoshi Asai, Katunobu Ito:
Protein Structure Prediction Based on Multi-Level Description. HICSS (5) 1994: 355-364 - [c6]Kentaro Onizuka, Masayuki Akahoshi, Masato Ishikawa, Kiyoshi Asai:
The Multi-Scale 3D-1D Compatibility Scoring for Inverse Protein Folding Protein. ISMB 1994: 314-321 - 1993
- [c5]Kentaro Onizuka, Stephen T. C. Wong, Masato Ishikawa, Kiyoshi Asai:
A Multi-Level Description Scheme of Protein Conformation. ISMB 1993: 301-309 - [c4]Hidetoshi Tanaka, Masato Ishikawa, Kiyoshi Asai, Akihiko Konagaya:
Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. ISMB 1993: 395-401 - 1992
- [c3]Kiyoshi Asai, Satoru Hayamizu, Ken'ichi Handa:
Dividing the distributions of HMM and linear interpolation in speech recognition. ICASSP 1992: 29-32 - 1990
- [c2]Kiyoshi Asai, Shigeru Chiba:
Voiced-unvoiced classification using weighted distance measures. ICSLP 1990: 205-208 - [c1]Shigeru Chiba, Kiyoshi Asai:
A new method of consonant detection and classification using neural networks. ICSLP 1990: 1065-1068
Reference Works
- 2019
- [r1]Junichi Iwakiri, Kiyoshi Asai:
RNA Structure Prediction. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 575-584
Informal and Other Publications
- 2013
- [i2]Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai:
Generalized Centroid Estimators in Bioinformatics. CoRR abs/1305.4339 (2013) - 2002
- [i1]Koji Tsuda, Shotaro Akaho, Kiyoshi Asai:
Approximating Incomplete Kernel Matrices by the em Algorithm. CoRR cs.LG/0211007 (2002)
Coauthor Index
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