Last Last updated on October 19, 2009 (JST). Some of the PDF links are subject to your licenses for the electrical journals.
[Sorted by Journals] [Sorted by Meetings]Kuniaki Saito, Sachi Inagaki, Toutai Mituyama, Yoshinori Kawamura, Yukiteru Ono, Eri Sakota, Hazuki Kotani, Kiyoshi Asai, Haruhiko Siomi & Mikiko C. Siomi: "A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila," Nature 2009 Oct29; 461(7268):1296-1299 doi:10.1038/nature08501
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," Bioinformatics Advance Access published October 6, 2009; doi: 10.1093/bioinformatics/btp580 PDF
Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama and Kiyoshi Asai: "Conic Programming for Multi-Task Learning," IEEE Transactions of Knowledge and Data Engeneering, to appear. http://www2.computer.org/portal/web/csdl/doi/10.1109/TKDE.2009.142
Kunio Kikuchi, Makiha Fukuda, Tomoya Ito, Mitsuko Inoue, Takahide Yokoi, Suenori Chiku, Toutai Mitsuyama, Kiyoshi Asai, Tetsuro Hirose, and Yasunori Aizawa: "Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation," Nucleic Acids Res. 2009 Aug;37(15):4987-5000; doi: doi:10.1093/nar/gkp426 Full Text
Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai: "Prediction of RNA secondary structure by combining homologous sequence information," Bioinformatics 2009 25(12):i330-i338; doi:10.1093/bioinformatics/btp228 Full Text PDF
Kengo Sato, Michiaki Hamada, Kiyoshi Asai and Toutai Mituyama: "CENTROIDFOLD: a web server for RNA secondary structure prediction," Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W277-280; doi:10.1093/nar/gkp367 Full Text PDF
Yasuo Tabei and Kiyoshi Asai: "A local multiple alignment method for detection of non-coding RNA sequences," Bioinformatics 2009 25(12):1498-1505; doi:10.1093/bioinformatics/btp261 Full Text PDF
Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, and Kiyoshi Asai: "Prediction of RNA secondary structure using generalized centroid estimators," Bioinformatics 2009 Feb 15;25(4):465-473; doi:10.1093/bioinformatics/btn601 Full Text PDF
Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, and Kiyoshi Asai: "The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs," Nucleic Acids Research 2009 37(Database issue): D89-D92; doi:10.1093/nar/gkn805 Full Text PDF
Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara: "Directed acyclic graph kernels for structural RNA analysis," BMC Bioinformatics 2008 Jul22; 9:318 Full Text
Asuka Azuma-Mukai, Hideo Oguri, Toutai Mituyama, Zhi Rong Qian, Kiyoshi Asai, Haruhiko Siomi, and Mikiko C. Siomi: "Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing," PNAS 2008 Jun 10; 105(23):7964-9 Full Text
Kinya Okada and Kiyoshi Asai: "Expansion of signaling genes for adaptive immune system evolution in early vertebrates," BMC Genomics 2008, 9:218 doi:10.1186/1471-2164-9-218 Full Text PDF
Yoshinori Kawamura, Kuniaki Saito, Taishin Kin, Yukiteru Ono, Kiyoshi Asai, Takafumi Sunohara, Tomoko N. Okada, Mikiko C. Siomi and Haruhiko Siomi: "Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells," Nature 453, 793-797 (5 June 2008) doi:10.1038/nature06938 Full Text PDF
Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai and Totai Mituyama: "Software.ncrna.org: web servers for analyses of RNA sequences," Nucleic Acids Research 2008 36(Web Server issue):W75-W78; doi:10.1093/nar/gkn222 Full Text PDF
Kinya Okada and Kiyoshi Asai: "Retention of genes involved in the adenohypophysis-mediated endocrine system in early vertebrates," Gene Available online 31 January 2008, Gene 412(2008) 71-83. Full Text
Yasuo Tabei, Hisanori Kiryu, Taishin Kin and Kiyoshi Asai: "A fast structural multiple alignment method for long RNA sequences," BMC Bioinformatics 2008, 9:33 doi:10.1186/1471-2105-9-33 Full Text PDF
Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai: "Rfold: An exact algorithm for computing local base pairing probabilities," Bioinformatics 2008 24(3): 367-373; doi:10.1093/bioinformatics/btm951 Full Text PDF
Goro Terai, Takashi Komori, Kiyoshi Asai and Taishin Kin: "miRRim: A novel system to find conserved miRNAs with high sensitivity and specificity," RNA 2007 Dec;13(12):2081-2090. doi:10.1261/rna.655107 Full Text PDF
Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai and Kengo Sato: "Stem Kernels for RNA Sequence Analyses," Journal of Bioinformatics and Computational Biology 2007 Oct;5(5): 1103-1122.
Hisanori Kiryu, Yasuo Tabei, Taishin Kin, and Kiyoshi Asai: "Murlet: A practical multiple alignment tool for structural RNA sequences," Bioinformatics 2007 Jul 1;23(13): 1588-1598; doi:10.1093/bioinformatics/btm146 Full Text PDF
Yasnory T.F. Sasaki, Miho Sano, Takashi Ideue, Taishin Kin, Kiyoshi Asai and Tetsuro Hirose: "Identification and characterization of human non-coding RNAs with tissue-specific expression," Biochemical and Biophysical Research Communications, Volume 357, Issue 4, 15 June 2007, 991-996. doi:10.1016/j.bbrc.2007.04.034 PDF
Yasnory T.F. Sasaki, Miho Sano, Taishin Kin, Kiyoshi Asai and Tetsuro Hirose: "Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus," Biochemical and Biophysical Research Communications, Volume 357, Issue 3, 8 June 2007, 724-730. doi:10.1016/j.bbrc.2007.03.200 PDF
Tetsuo Kobayashi, Keietsu Abe, Kiyoshi Asai, Katsuya Gomi, Praveen Rao Juvvadi, Masashi Kato, Katuhiko Kitamoto, Michio Takeuchi, and Masayuki Machida: "Genomics of Aspergillus oryzae," Bioscience, Biotechnology, and Biochemistry 71(3), 646-670 (2007). PDF
Hisanori Kiryu, Taishin Kin, and Kiyoshi Asai: "Robust prediction of consensus secondary structures using averaged base pairing probability matrices," Bioinformatics 2007 23(4):434-441; doi:10.1093/bioinformatics/btl636 Full Text PDF
Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, and Kiyoshi Asai: "fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences," Nucleic Acids Research 2007 35(Database issue):D145-D148; doi:10.1093/nar/gkl837 Full Text PDF
Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, and Kiyoshi Asai: "Mining frequent stem patterns from unaligned RNA sequences," Bioinformatics 2006 22(20):2480-2487; doi:10.1093/bioinformatics/btl431 Full Text PDF
Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul B. Horton, Koji Tsuda, Wataru Fujibuchi: "Network-based de-noising improves prediction from microarray data," BMC Bioinformatics, vol. 7(Suppl 1):S4, March, 2006. PDF
Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai: "SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments," Bioinformatics 2006 22(14):1723-1729; doi:10.1093/bioinformatics/btl177 Full Text PDF
Yutaka Ueno, Katsunori Isono, Katsutoshi Takahashi, Yukio Shimonohara, Kiyoshi Asai: Statistical Evaluation of a Bottom-Up Clustering for Single Particle Molecular Images, Genome Informatics, 14, 125-135(2005). PDF
Machida, M., et al. (64 authors, Asai K is the 2nd): "Genome sequencing and analysis of Aspergillus oryzae", Nature 438, 1157-1161, doi:10.1038/nature04300 (2005). PDF
Nierman, W., et al. (84 authors, Asai K is the 80th): "Genome sequence of pathogenic and allergenic filamentous fungus Aspergillus fumigatus", Nature 438, 1151-1156, doi:10.1038/nature04332 (2005). PDF
Galagan, J.E., et al.(50 authors, Asai K is the 38th): "Sequencing of Aspergillus nidulans and comparative analysis with A. fumitatus and A. oryzae", Nature 438, 1105-1115, doi:10.1038/nature04341 (2005). PDF
Tsuyoshi Kato, Koji Tsuda, and Kiyoshi Asai: "Selective integration of multiple biological data for supervised network inference," Bioinformatics 2005 21(10):2488-2495; doi:10.1093/bioinformatics/bti339 PDF
Yutaka Ueno, Masanori Arita, Toshitaka Kumagai, and Kiyoshi Asai: "Processing sequence annotation data using the Lua programming language," Genome Informatics Vol.14, 154-163 (2003). PDF
Kinya Okada, Shigehiko Kanaya, and Kiyoshi Asai: "Accurate extraction of functional associations between proteins based on common interaction partners and common domains," Bioinformatics 2005 21(9):2043-2048; doi:10.1093/bioinformatics/bti305 PDF
Hisanori Kiryu, Taku Oshima, and Kiyoshi Asai: "Extracting relations between promoter sequences and their strengths from microarray data," Bioinformatics 2005 21(7):1062-1068; doi:10.1093/bioinformatics/bti094 PDF
K. Tsuda, S. Uda, T. Kin and K. Asai: "Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data," Neural Processing Letters 19, 63-72(2004). PDF
Iba H, Saeki S, Asai K, Takahashi K, Ueno Y, Isono K: "Inference of Euler angles for single-particle analysis by means of evolutionary algorithms." Biosystems. 2003 Nov;72(1-2):43-55. PDF PubMed
Shusuke Saeki, Kiyoshi Asai, Katsutoshi Takahashi, Yutaka Ueno, Katsunori Isono and Hitoshi Iba: "Inference of Euler Angles for Single Particle Analysis by Using Genetic Algorithms," Genome Informatics Vol.13, 133-142 (2002). PDF
Koji Tsuda, Shotaro Akaho, Kiyoshi Asai: "The em algorithm for kernel matrix completion with auxiliary data," Journal of Machine Learning Research, 4, pp.67-81 (2003). PDF
Taishin Kin, Koji Tsuda and Kiyoshi Asai: "Marginalized Kernels for RNA Sequence Data Analysis," Genome Informatics Vol.13, 112-122 (GIW2002 Best Paper Award, 2002). PubMed PDF
Masanori Arita, Koji Tsuda, and Kiyoshi Asai: "Modeling Splicing Sites with Pairwise Correlations," Bioinformatics 2002 18:27S--34S (European Conference on Computational Biology 2002). PDF
Koji Tsuda, Taishin Kin, Kiyoshi Asai: "Marginalized kernels for biological sequences," Bioinformatics 2002 18:268S--275S (ISMB2002). PDF
Yutaka Ueno and Kiyoshi Asai: "MOSBY: a molecular structure viewer program with portability and extensibility," Journal of Molecular Graphics and Modelling 20 (2002) 411-413.
C. Sato, Y. Ueno, K. Asai, K. Takahashi,M. Sato A. Engel and Y. Fujiyoshi: "The voltage-sensitive sodium channel is a bell-shaped molecule with several cavities," Nature 409, 1047-1051 (2001). PDF
K. Asai, Y. Ueno, C. Sato and K. Takahashi: "Clustering and Averaging of Images in Single-Particle Analysis," Genome Informatics, Vol.11, 151-160 (2000). PDF
M. Arita, K. Asai and T. Nishioka: "Reconstructing Metabolic Pathways with New Enzyme Classification," Proceedings of 15th German Conference in Bioinformatics 99-106 (GCB'00, 2000).
K.Asai: "Sequence Information and Stochastic Models," Journal of JSAI, Vol.15, No.1, pp.35--42 (2000).
C. Kim, A. Konagaya and K. Asai: "A Generic Criterion for Gene Recognitions in Genome Sequences," Genome Informatics, Vol.10, 13-22 (1999). PDF
M. Arita, K. Asai and T. Nishioka: "Finding Precursor Compounds in Secondary Metabolism," Genome Informatics, Vol.10, 113-120 (1999). PDF
Y. Ueno, K. Asai and M. Arita: "Integrating Application Programs for Bioinformatics Using a Web Browser," Genome Informatics, Vol.10, 166-175 (1999). PDF
T.Yada, Y.Totoki, K.Asai and M.Ishikawa: "Generation of Hidden Markov Model Describing Complex Motif in DNA Sequences," JPSJ Transactions, 40, 750-767 (1999).
T. Yada, Y. Totoki, M. Ishikawa, K. Asai and K. Nakai: "Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences," Bioinformatics Vol.14, no.4, 317- 325 (1998). PDF
K. Asai, K. Itou, Y. Ueno and T. Yada: "Recognition of Human Genes by Stochastic Parsing," Pacific Symposium on Biocomputing 98, 228-239 (1998). PDF
Y. Ueno and K. Asai: "A High-throughput Graphics Library Designed for a Protable Molecular Structure Viewer," Pacific Symposium on Biocomputing 98, 201-212 (1998). PDF
K. Asai, Y. Ueno, K. Itou and T. Yada: "Automatic Gene Recognition without Using Training Data," Genome Informatics Vol.8, 15-24 (1997). PDF
Y. Ueno and K. Asai: "A New Plug-in Software Architechture Applied for a Portable Molecular Structure Browser," International Conference on Intelligent Systems for Molecular Biology, 329-332 (ISMB97, 1997).
K. Asai, T. Yada, K. Itou: "Finding Genes by Hidden Markov Models with a Protein Motif Dictionary," Genome Informatics Vol.7, 88-97 (1996). PDF
T. Yada, M. Ishikawa, H. Tanaka and K. Asai: "Extraction of Hidden Markov Model Representations of Signal Patterns in DNA Sequences," Pacific Symposium on Biocomputing 96, 686-696 (PSB96, 1996).
T.Yada, M.Ishikawa, H.Tanaka and K.Asai: "Extraction of Signal Patterns from DNA Sequences by Hidden Markov Models and Genetic Algorithm," JPSJ Transactions, 37, 1117-1129 (1996). PDF
K. Onizuka, M. Akahoshi, M. Ishikawa and K. Asai: "The Multi Level 3D-1D Compatibility Scoring," International Conference on Intelligent Systems for Molecular Biology, 314-321 (ISMB94, 1994).
K. Onizuka, H. Tsuda, M. Ishikawa and A. Aiba: "Protein Structure Prediction Based on Multi-Level Description," 27th Annual Hawaii International Conference on System Sciences, Vol.5, 355-364 (27th HICSS, 1994).
M. Akahoshi, K. Onizuka, M. Ishikawa and K. Asai: "A Three-Dimentional Animation System for Protein Folding Simulation," 27th Annual Hawaii International Conference on System Sciences, Vol.5, 173-182 (27th HICSS, 1994).
K. Asai, S. Hayamizu and K. Handa: "Prediction of protein secondary structure by the hidden Markov model," Computer Applications in the Biosciences (currently Bioinformatics), Vol.9, no.2, 141-146 (CABIOS, 1993).
K. Asai, H. Tanaka, K. Itou and K. Onizuka: "Are the Hidden Markov Models Promising in Protein Research ?" Genome Informatics Vol.4, 130-139 (1993).
K. Onizuka, K. Asai and M. Ishikawa: "Protein 3D Structure Prediction Based on Multi-Level Description," Genome Informatics Vol.4, 140-151 (1993).
K. Onizuka, K. Asai and M. Ishikawa: "A Scheme for Protein Tertiary Structure Prediction Based on Stochastic Reasoning," 13th International Joint Conference on Artificial Inteligence, Artificial Inteligence and Genome, W26:49-58 (IJCAI93, 1993).
H. Tanaka, K. Onizuka and K. Asai: "Classification of Proteins via Successive State Splitting of Hidden Markov Network," 13th International Joint Conference on Artificial Inteligence, Artificial Inteligence and Genome, W26:25-30 (IJCAI93, 1993).
K. Onizuka, K. Asai, M. Ishikawa and T. C. Wong: "A Multi Level Description Scheme of Protein Conformation," International Conference on Inteligent Systems for Molecular Biology, 301-309 (ISMB93, 1993)
H. Tanaka, M. Ishikawa, K. Asai and A. Konagaya: "Hidden Markov Models and Iterative Aligners: Study of their Equivalence and Possibilities," International Conference on Inteligent Systems for Molecular Biology, 395-401 (ISMB93, 1993)
K. Asai, S. Hayamizu and K. Onizuka: "HMM with Protein Structure Grammar," 26th Hawaii International Conference on System Sciences, Vol.1, 783-791 (26th HICSS, 1993).
K. Asai, S. Hayamizu and K. Handa: "Dividing the Distributions of HMM and Linear Interpolation in Speech Recognition," International Conference on Acoustics, Speech, and Signal Processing, I29-32 (ICASSP92, 1992). PDF
K. Asai and S. Chiba: "Voiced-Unvoiced Classification Using Weighted Distance Measures," International Conference on Speken Language Processing, 205-208. (ICSLP90, 1990).
S. Chiba and K. Asai: "A New Method of Consonant Detection and Classification Using Neural Networks," International Conference on Speken Language Processing, 1065-1068. (ICSLP90, 1990).
Yasuo Tabei, Taishin Kin, Koji Tsuda and Kiyoshi Asai: "Searching non-coding RNAs from genome using fixed-length stem fragments," Poster in Pacific Symposium on Biocomputing 2006 (PSB2006).
Ysuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai: "An Alignment Algorithm by Matching Fixed-Length Stem Fragments for Comparing RNA Sequences," Poster in The 14th International Conference on Genome Informatics (GIW2005).
Tsuyoshi Kato, Koji Tsuda, Kentaro Tomii, Kiyoshi Asai: "Maximum likelihood superposition of protein structures," Genome Informatics 14, pp.488--489 (2003).
T. Nagano, S. Suwa and K. Asai: "Classification of C2H2 Zinc Finger Domains Using Support Vector Machines," Genome Informatics Vol.13, pp.314-315 (GIW02, 2002).
M. Suwa, M. Arita, S. Matsumoto, S. Tsutsumi, H. Aburatani, K. Asai and Y. Akiyama: "SEVENS: Comprehensive Collection of Human Seven Transmembrane Helix Receptors," Genome Informatics Vol.13, pp.511-512 (GIW02, 2002).
M. Suwa, T. Sato, I. Okouchi, M. Arita, S. Matsumoto, S. Tsutsumi, H. Aburatani, K. Asai and Y. Akiyama: "An Automated System for Finding Seven Transmembrane Helix Receptors from Human Genome," Genome Informatics Vol.12, pp.425-426 (GIW01, 2001).
M. Suwa, T. Sato, I. Okouchi, M. Mikoshiba, Y. Akiyama, K. Asai, S. Matsumoto, S. Tsutsumi, H. Aburatani: "Gene Discovery of G-Protein Coupled Receptors from Human Genome," Genome Informatics Vol.11, pp.410-411 (GIW00, 2000).
Y. Ueno, K. Takahashi, K. Asai, C. Sato: "BESPA: Software Tools for Three-Dimensional Structure Reconstruction from Single Particle Images of Proteins," Genome Informatics Vol.10, pp.241-242 (GIW99, 1999).
K.Asai, Y.Ueno, K.Itou and T.Yada: "Hidden Markov Models with Multiple Streams for Gene Annotation," International Conference for Intelligent Systems for Molecular Biology (ISMB99, 1999).
K.Asai, K.Itou and T.Yada: "Integrating Multiple Evidences by Hidden Markov Models," Genome Informatics Vol.9, pp.347-348 (GIW98, 1998).
K.Asai, Y.Ueno, K.Itou and T.Yada: "Finding Genes by Hidden Markov Models with Protein Motifs," Gene Discovery in silico (1997).
Y.Ueno and K.Asai: "A New Software For Visialization of Large Proteins," Genome Informatics Vol.7, pp.208-209 (GIW96, 1996).
T.Yada, Y.Totoki, M.Ishikawa and K.Asai: "Automatic Discovery of Hidden Markov Representations for Functional Sites within DNA Sequences," Genome Informatics Vol.7, pp.210-211 (GIW96, 1996).
K.Asai and H.Tanaka: "Stochastic Models and Grammars for Bioinformatics," 28th Annual Hawaii International Conference on System Sciences, (28th HICSS, 1995).
K.Asai, K.Onizuka, M.Akahoshi, H.Tanaka and K.Itou: "Automatic Labeling of Protein Structures by Hidden Markov Models," Genome Informatics Vol.5, 1994, pp.156-157 (GIW94, 1994).
T.Yada, M.Ishikawa, H.Tanaka and K.Asai: "DNA Sequence Analysis using Hidden Markov Model and Genetic Algorithm," Genome Informatics Vol.5 1994, pp.178-179 (GIW94, 1994).
H.Tanaka, K.Onizuka, M.Ishikawa and K.Asai: "Classification of Proteins via Successive State Splitting Algorithm of Hidden Markov Network," Genome Informatics Vol.4, 224-230 (GIW93, 1993).
M.Akahoshi, K.Onizuka, M.Ishikawa and K.Asai: "A Three-Dimensional Graphics System for Protein Structure Analysis," Genome Informatics Vol.4, 418-429 (GIW93, 1993).
K.Asai: "Toward more flexible use of hidden Markov models in computational biology," Statistical Analysis of DNA and Protein Sequences, at Newton Institute in Chambridge (1997).
K.Asai: "Stochastic Models and Grammars for Molecular Biology," International Symposium on ``Genome Project and Computer Science'' (1995).
T.Yada and K.Asai "Application of Genetic Algorithm to Extraction of Signal Patterns from DNA Sequences," Genetic Algorithm, Chapter 8 (Sangyo Tosho, in Japanese, 1997).
K.Asai: "Structure Prediction of Protein Learned from Speech Recognition Technology," Challenge to Genome Informatics, Chapter 9 (Kyoritsu Shuppan, in Japanese, 1994).