All recent papers

Journal papers since 2005 (last updated on OCT30, 2019)

2020

Aya Ito-Ishida, Steven A Baker, Roy V Sillitoe, Yaling Sun, Jian Zhou, Yukiteru Ono, Junichi Iwakiri, Michisuke Yuzaki, Huda Y Zoghbi (2020) MeCP2 Levels Regulate the 3D Structure of Heterochromatic Foci in Mouse Neurons. J Neurosci 40(45):8746-8766. doi: 10.1523/JNEUROSCI.1281-19.2020.

Yoichiro Ito, Goro Terai, Misa Ishigami, Noriko Hashiba, Yasuyuki Nakamura, Takahiro Bamba, Ryota Kumokita, Tomohisa Hasunuma, Kiyoshi Asai, Jun Ishii, Akihiko Kondo (2020) Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression. Nucleic acids research Dec.

Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada (2020) PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores. Bioinformatics (Oxford, England) Sep.

Shun Sakuraba, Junichi Iwakiri, Michiaki Hamada, Tomoshi Kameda, Genichiro Tsuji, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai (2020) Free-Energy Calculation of Ribonucleic Inosines and Its Application to Nearest-Neighbor Parameters. Journal of chemical theory and computation Aug.

Hiroki Takizawa, Junichi Iwakiri, Goro Terai, Kiyoshi Asai (2020) Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model. Bioinformatics (Oxford, England) 36: Supplement_1. i227-i235 Jul.

Akito Taneda, Kiyoshi Asai (2020) COSMO: A dynamic programming algorithm for multicriteria codon optimization. Computational and structural biotechnology journal 18: 1811-1818 06.

Goro Terai, Kiyoshi Asai (2020) Improving the prediction accuracy of protein abundance in Escherichia coli using mRNA accessibility. Nucleic acids research 48: 14. 08.

Hiroki Takizawa, Junichi Iwakiri, Kiyoshi Asai (2020) RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. BMC bioinformatics 21: 1. 210 May.

Kensuke Ninomiya, Shungo Adachi, Tohru Natsume, Junichi Iwakiri, Goro Terai, Kiyoshi Asai, Tetsuro Hirose (2020) LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation. The EMBO journal 39: 3. 02.

Shen Tian, Goro Terai, Yoshiaki Kobayashi, Yasuaki Kimura, Hiroshi Abe, Kiyoshi Asai, Kumiko Ui-Tei (2020) A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs. RNA biology 17: 2. 264-280 02.

2019

Tsukasa Fukunaga, Junichi Iwakiri, Yukiteru Ono, Michiaki Hamada, LncRRIsearch: a web server for lncRNA-RNA interaction prediction integrated with tissue-specific expression and subcellular localization data, Frontiers in Genetics, 28 May 2019 DOI

Hirano A, Iwashita K, Ura T, Sakuraba S, Shiraki K, Arakawa T, Kameda T (2019) The binding affinity of uncharged aromatic solutes for negatively charged resins is enhanced by cations via cation-pi interactions: The case of sodium ion and arginine. Journal of chromatography A, in press. doi: 10.1016/j.chroma.2019.02.043

Risa Kawaguchi, Hisanori Kiryu, Junichi Iwakiri, Jun Sese (2019) reactIDR: Evaluation of the statistical reproducibility of high-throughput structural analyses towards a robust RNA structure prediction, BMC Bioinformatics, 20(Suppl 3):130

2018

Nishida S, Sakuraba S, Asai K, Hamada M (2018) Estimating energy parameters for RNA secondary structure predictions using both experimental and computational data. IEEE/ACM transactions on computational biology and bioinformatics, in press. doi: 10.1109/TCBB.2018.2813388

Anish M S Shrestha, Naruki Yoshikawa, Kiyoshi Asai (2018) Combining probabilistic alignments with read pair information improves accuracy of split-alignments. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty398

Hagio, Shun Sakuraba, Junichi Iwakiri, Ryota Mori, Kiyoshi Asai (2018) Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities. BMC bioinformatics 19(Suppl 1):38.

Martin C. Frith and Anish Shrestha: A Simplified Description of Child Tables for Sequence Similarity Search, IEEE/ACM Transactions on Computational Biology and Bioinformatics, pp(99):1-1 2018. doi: 10.1109/TCBB.2018.2796064

Chishima T, Iwakiri J, Hamada M (2018) Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs. Genes 9(1). pii: E23. doi: 10.3390/genes9010023.

Shun Sakuraba, Ikuo Fukuda (2018) Performance evaluation of the zero-multipole summation method in modern molecular dynamics software. Journal of Computational Chemistry 39(20) 1551-1560. doi: 10.1002/jcc.25228

Atsushi Hirano, Kazuki Iwashita, Shun Sakuraba, Kentaro Shiraki, Tsutomu Arakawa, Tomoshi Kameda (2018) Salt-dependent elution of uncharged aromatic solutes in ion-exchange chromatography. Journal of Chromatography A 1546 46-55. doi: 10.1016/j.chroma.2018.02.049

Kono H, Sakuraba S, Ishida H (2018) Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. PLoS computational biology 14(3) e1006024. doi: 10.1371/journal.pcbi.1006024

Kota Kasahara, Shun Sakuraba, Ikuo Fukuda (2018) Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation. The Journal of Physical Chemistry B 122(9) 2495-2503. doi: 10.1021/acs.jpcb.7b10830

Kitahara R, Sakuraba S, Kameda T, Okuda S, Xue M, Mulder FAA (2018) Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities. Protein science 27(3) 769-779. doi: 10.1002/pro.3371

2017

Anish M S Shrestha, Martin C Frith, Kiyoshi Asai, Hugues Richard (2017) Jointly aligning a group of DNA reads improves accuracy of identifying large deletions. Nucleic acids research 46(3), e18, doi:10.1093/nar/gkx1175

Terai, Satoshi Kamegai, Akito Taneda, Kiyoshi Asai (2017) Evolutionary design of multiple genes encoding the same protein. Bioinformatics 33: 11. 1613-1620.

Michiaki Hamada, Yukiteru Ono, Kiyoshi Asai, Martin C Frith (2017) Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinformatics 33: 6. 926-928.

Iwakiri J, Terai G, Hamada M (2017) Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome. Biol Direct. 2017 Jun 8;12(1):15. doi: 10.1186/s13062-017-0183-4.

Kawamura T, Wakamoto T, Kitazawa S, Sakuraba S, Kameda T, Kitahara R (2017) Analysis of O2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A. Biophysical journal 112(9) 1820-1828. doi: 10.1016/j.bpj.2017.03.029

Hirano A, Kameda T, Sakuraba S, Wada M, Tanaka T, Kataura H (2017) Disulfide bond formation of thiols by using carbon nanotubes. Nanoscale 17(9) 5389-5393. doi: 10.1039/c7nr01001j

2016

Osamu Yamada, Masayuki Machida, Akira Hosoyama, Masatoshi Goto, Toru Takahashi, Taiki Futagami, Youhei Yamagata, Michio Takeuchi, Tetsuo Kobayashi, Hideaki Koike, Keietsu Abe, Kiyoshi Asai, Masanori Arita, Nobuyuki Fujita, Kazuro Fukuda, Ken-Ichi Higa, Hiroshi Horikawa, Takeaki Ishikawa, Koji Jinno, Yumiko Kato, Kohtaro Kirimura, Osamu Mizutani, Kaoru Nakasone, Motoaki Sano, Yohei Shiraishi, Masatoshi Tsukahara, Katsuya Gomi (2016) Genome sequence of Aspergillus luchuensis NBRC 4314. DNA research : an international journal for rapid publication of reports on genes and genomes 23: 6. 507-515.

Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda (2016)
Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.
J. Chem. Theory Comput., 2016, 12 (9), pp 4688–4697
DOI: 10.1021/acs.jctc.6b00254

Toshitaka Kumagai, Tomoko Ishii, Goro Terai, Myco Umemura, Masayuki Machida, Kiyoshi Asai (2016)
Genome Sequence of Ustilaginoidea virens IPU010, a Rice Pathogenic Fungus Causing False Smut.
Genome announcements 4: 3. 05.

Michiaki Hamada, Yukiteru Ono, Hisanori Kiryu, Kengo Sato, Yuki Kato, Tsukasa Fukunaga, Ryota Mori, Kiyoshi Asai (2016)
Rtools: a web server for various secondary structural analyses on single RNA sequences.
Nucleic acids research 44 (W1): W302-W307.
doi: 10.1093/nar/gkw337

Goro Terai, Junichi Iwakiri, Tomoshi Kameda, Michiaki Hamada, Kiyoshi Asai (2016)
Comprehensive prediction of lncRNA-RNA interactions in human transcriptome.
BMC genomics 17 Suppl 1: 01.

Goro Terai, Satoshi Kamegai, Kiyoshi Asai (2016)
CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure.
Bioinformatics 32: 6. 828-834

Nozomi Nagano, Myco Umemura, Miho Izumikawa, Jin Kawano, Tomoko Ishii, Moto Kikuchi, Kentaro Tomii, Toshitaka Kumagai, Akira Yoshimi, Masayuki Machida, Keietsu Abe, Kazuo Shin-ya, Kiyoshi Asai (2016)
Class of cyclic ribosomal peptide synthetic genes in filamentous fungi.
Fungal genetics and biology 86: 58-70.

Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai (2016) Bioinformatics tools for lncRNA research.
Biochimica et biophysica acta 1859: 1. 23-30.

Ikebe J, Sakuraba S, Kono H (2016) H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation. PLoS computational biology 12(3) e1004788. doi: 10.1371/journal.pcbi.1004788

Yamamori Y, Ishizuka R, Karino Y, Sakuraba S, Matubayasi N (2016) Interaction-component analysis of the hydration and urea effects on cytochrome c. The Journal of chemical physics 144(8) 085102. doi: 10.1063/1.4941945

2015

Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka, Kiyoshi Asai (2015) Privacy-preserving search for chemical compound databases. BMC bioinformatics 16 Suppl 18: 12.

Shun Sakuraba, Kiyoshi Asai, Tomoshi Kameda (2015) Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations. The journal of physical chemistry letters 6: 21. 4348-4351 Nov.

Tsutomu Ikegami, Toyohiro Inatsugi, Isao Kojima, Myco Umemura, Hiroko Hagiwara, Masayuki Machida, Kiyoshi Asai (2015) Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data. PloS one 10: 4. 04.

Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai (2015) Learning chromatin states with factorized information criteria. Bioinformatics (Oxford, England) Mar.

Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada (2015) A semi-supervised learning approach for RNA secondary structure prediction. Computational biology and chemistry Feb.

Takahiro Tsukui, Nozomi Nagano, Myco Umemura, Toshitaka Kumagai, Goro Terai, Masayuki Machida, Kiyoshi Asai (2015) Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens. Bioinformatics (Oxford, England) 31: 7. 981-985 Apr.

2014

Ryota Mori, Michiaki Hamada, Kiyoshi Asai (2014) Efficient calculation of exact probability distributions of integer features on RNA secondary structures. BMC genomics 15 Suppl 10: 12.

Satoshi Yamasaki, Takatsugu Hirokawa, Kiyoshi Asai, Kazuhiko Fukui (2014) Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. Journal of chemical information and modeling 54: 2. 672-682 Feb.

Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada (2014) Reference-free prediction of rearrangement breakpoint reads. Bioinformatics (Oxford, England) 30: 18. 2559-2567 Sep.

Itaru Takeda, Myco Umemura, Hideaki Koike, Kiyoshi Asai, Masayuki Machida (2014) Motif-independent prediction of a secondary metabolism gene cluster using comparative genomics: application to sequenced genomes of Aspergillus and ten other filamentous fungal species. DNA research 21: 4. 447-457 Aug.

Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki, Hisanori Kiryu (2014) CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome biology 15: 1.

2013

[Umemura+2013] Myco Umemura, Hideaki Koike, Nozomi Nagano, Tomoko Ishii, Jin Kawano, Noriko Yamane, Ikuko Kozone, Katsuhisa Horimoto, Kazuo Shin-Ya, Kiyoshi Asai, Jiujiang Yu, Joan W Bennett, Masayuki Machida (2013) MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data. PLoS ONE 8(12): e84028.

[Iwakiri+2013] Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada (2013) Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions. Bioinformatics (Oxford, England) 29: 20. 2524-2528.

[Yonemoto+2013] Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada (2013) CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs. International journal of molecular sciences 14: 3. 6144-6156.

[Wijaya+2013] Edward Wijaya, Martin C Frith, Paul Horton, Kiyoshi Asai (2013) Finding protein-coding genes through human polymorphisms. PLoS ONE 8(1): e54210.

[Katayama+2013] Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul Jp Bonnal, Brad Chapman, Peter Ja Cock, Tore Eriksson, Paul Mk Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A Vos, David Withers, Chisato Yamasaki, Christian M Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi (2013) The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. Journal of biomedical semantics 4: 1. 02.

[Ono+2013] Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada (2013) PBSIM: PacBio reads simulator–toward accurate genome assembly. Bioinformatics 29: 1. 119-121.

2012

[Sato+2012] Kengo Sato, Yuki Kato, Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara (2012) DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition. Bioinformatics 28: 24. 3218-3224. Dec

[Terai+2012] Goro Terai, Hiroaki Okida, Kiyoshi Asai, Toutai Mituyama (2012) Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features. PLoS One 7: 9. Sep

[Ashida+2012] Hiroki Ashida, Kiyoshi Asai, Michiaki Hamada (2012) Shape-based alignment of genomic landscapes in multi-scale resolution. Nucleic Acids Res 40: 14. 6435-6448 Aug

[Frith+2012] Martin C Frith, Ryota Mori, Kiyoshi Asai (2012) A mostly traditional approach improves alignment of bisulfite-converted DNA. Nucleic Acids Res 40: 13. Jul

[KatoY+2012] Yuki Kato, Kengo Sato, Kiyoshi Asai, Tatsuya Akutsu (2012) Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming. Nucleic Acids Res 40: Web Server issue. W29-W34 Jul

[Hamada+2012] Michiaki Hamada, Kiyoshi Asai (2012) A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA). J Comput Biol 19: 5. 532-549 May

[Kiryu+2012] Hisanori Kiryu, Kiyoshi Asai (2012) Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations. Bioinformatics 28: 8. 1093-1101 Apr

[Wan+2012] Raymond Wan, Vo Ngoc Anh, Kiyoshi Asai (2012) Transformations for the compression of FASTQ quality scores of next-generation sequencing data. Bioinformatics 28: 5. 628-635 Mar

[Wijaya+2012] Edward Wijaya, Martin C Frith, Kiyoshi Asai, Paul Horton (2012) RecountDB: a database of mapped and count corrected transcribed sequences. Nucleic Acids Res 40: Database issue. D1089-D1092 Jan

2011

[Hamada+2011d] Michiaki Hamada, Edward Wijaya, Martin C Frith, Kiyoshi Asai (2011) Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinformatics 27: 22. 3085-3092 Nov

[Kiryu+2011] Hisanori Kiryu, Goro Terai, Osamu Imamura, Hiroyuki Yoneyama, Kenji Suzuki, Kiyoshi Asai (2011) A detailed investigation of accessibilities around target sites of siRNAs and miRNAs. Bioinformatics 27: 13. 1788-1797 Jul

[Hamada+2011c] Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai (2011) CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences. Nucleic Acids Res 39: Web Server issue. W100-W106 Jul

[Sato+2011] Kengo Sato, Yuki Kato, Michiaki Hamada, Tatsuya Akutsu, Kiyoshi Asai (2011) IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics 27: 13. i85-i93 Jul

[Adachi+2011] Hironori Adachi, Akira Ishiguro, Michiaki Hamada, Eri Sakota, Kiyoshi Asai, Yoshikazu Nakamura (2011) Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F. Biochimie 93: 7. 1081-1088 Jul

[Hamada+2011b] Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai (2011) Generalized centroid estimators in bioinformatics. PLoS One 6: 2. Feb

[Hamada+2011a] Michiaki Hamada, Kengo Sato, Kiyoshi Asai (2011) Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res 39: 2. 393-402 Jan

2010

[Hamada+2010] Michiaki Hamada, Kengo Sato, Kiyoshi Asai (2010) Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics 11: 586. Nov

[Saito+2010] Kuniaki Saito, Sachi Inagaki, Toutai Mituyama, Yoshinori Kawamura, Yukiteru Ono, Eri Sakota, Hazuki Kotani, Kiyoshi Asai, Haruhiko Siomi, Mikiko C Siomi (2009) A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila. Nature 461: 7268. 1296-1299 Oct

[KatoY+2010] Yuki Kato, Kengo Sato, Michiaki Hamada, Yoshihide Watanabe, Kiyoshi Asai, Tatsuya Akutsu (2010) RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 26: 18. i460-i466 Sep

[Katayama+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, Load Hendrix Barboza, Raoul Jp Bonnal, Richard Bruskiewich, Jan C Bryne, Jose M Fernendez, Akira Funahashi, Paul Mk Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, Rene Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi (2010) The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J Biomed Semantics 1: 1. Aug

[Kikuchi+2010] Kunio Kikuchi, Makiha Fukuda, Tomoya Ito, Mitsuko Inoue, Takahide Yokoi, Suenori Chiku, Toutai Mitsuyama, Kiyoshi Asai, Tetsuro Hirose, Yasunori Aizawa (2009) Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation. Nucleic Acids Res 37: 15. 4987-5000 Aug

[Sato+2010] Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasufumi Sakakibara (2010) A non-parametric Bayesian approach for predicting RNA secondary structures Journal of Bioinformatics and Computational Biology 8: 4. 727-742 Aug

[KatoT+2010] Tsuyoshi Kato, Hisashi Kashima, Masashi Sugiyama, Kiyoshi Asai (2010) Conic Programming for Multi-Task Learning IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING 22: 7. 957-968 Jul

[Terai+2010] Goro Terai, Aya Yoshizawa, Hiroaki Okida, Kiyoshi Asai, Toutai Mituyama (2010) Discovery of short pseudogenes derived from messenger RNAs. Nucleic Acids Res 38: 4. 1163-1171 Mar

2009

[Hamada+2009c] Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai (2009) CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics 25: 24. 3236-3243 Dec

[Sato+2009] Kengo Sato, Michiaki Hamada, Kiyoshi Asai, Toutai Mituyama (2009) CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res 37: Web Server issue. W277-W280 Jul

[Hamada+2009b] Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai (2009) Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics 25: 12. i330-i338 Jun

[Tabei+2009] Yasuo Tabei, Kiyoshi Asai (2009) A local multiple alignment method for detection of non-coding RNA sequences. Bioinformatics 25: 12. 1498-1505 Jun

[Hamada+2009a] Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai (2009) Large Scale Similarity Search for Locally Stable Secondary Structures among RNA Sequences IPSJ Transactions on Bioinformatics 2: 36-46 Mar

[Mituyama+2009] Toutai Mituyama, Kouichirou Yamada, Emi Hattori, Hiroaki Okida, Yukiteru Ono, Goro Terai, Aya Yoshizawa, Takashi Komori, Kiyoshi Asai (2009) The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res 37: Database issue. D89-D92 Jan

2008

[Sato+2009b] Kengo Sato, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara (2008) Directed acyclic graph kernels for structural RNA analysis. BMC Bioinformatics 9: 318. Jul

[Azuma-Mukai+2008] Asuka Azuma-Mukai, Hideo Oguri, Toutai Mituyama, Zhi Rong Qian, Kiyoshi Asai, Haruhiko Siomi, Mikiko C Siomi (2008) Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing. Proc Natl Acad Sci U S A 105: 23. 7964-7969 Jun

[Kawamura+2008] Yoshinori Kawamura, Kuniaki Saito, Taishin Kin, Yukiteru Ono, Kiyoshi Asai, Takafumi Sunohara, Tomoko N Okada, Mikiko C Siomi, Haruhiko Siomi (2008) Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells. Nature 453: 7196. 793-797 Jun

[Okada+2008b] Kinya Okada, Kiyoshi Asai (2008) Expansion of signaling genes for adaptive immune system evolution in early vertebrates. BMC Genomics 9: 218. May

[Asai+2008] Kiyoshi Asai, Hisanori Kiryu, Michiaki Hamada, Yasuo Tabei, Kengo Sato, Hiroshi Matsui, Yasubumi Sakakibara, Goro Terai, Toutai Mituyama (2008) Software.ncrna.org: web servers for analyses of RNA sequences. Nucleic Acids Res 36: Web Server issue. W75-W78 Jul

[Okada+2008a] Kinya Okada, Kiyoshi Asai (2008) Retention of genes involved in the adenohypophysis-mediated endocrine system in early vertebrates. Gene 412: 1-2. 71-83 Apr

[Kiryu+2008] Hisanori Kiryu, Taishin Kin, Kiyoshi Asai (2008) Rfold: an exact algorithm for computing local base pairing probabilities. Bioinformatics 24: 3. 367-373 Feb
[Hamada+2008] Michiaki Hamada, Hisanori Kiryu, Kengo Sato, Toutai Mituyama, Kiyoshi Asai (2009) Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 25: 4. 465-473 Feb

[Tabei+2008] Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai (2008) A fast structural multiple alignment method for long RNA sequences. BMC Bioinformatics 9: 33. Jan

2007

[Terai+2007] Goro Terai, Takashi Komori, Kiyoshi Asai, Taishin Kin (2007) miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. RNA 13: 12. 2081-2090 Dec

[Sakakibara+2007] Yasubumi Sakakibara, Kris Popendorf, Nana Ogawa, Kiyoshi Asai, Kengo Sato (2007) Stem kernels for RNA sequence analyses. J Bioinform Comput Biol 5: 5. 1103-1122 Oct

[Kiryu+2007b] Hisanori Kiryu, Yasuo Tabei, Taishin Kin, Kiyoshi Asai (2007) Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics 23: 13. 1588-1598 Jul

[Sasaki+2007a] Yasnory T F Sasaki, Miho Sano, Taishin Kin, Kiyoshi Asai, Tetsuro Hirose (2007) Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus. Biochem Biophys Res Commun 357: 3. 724-730 Jun

[Sasaki+2007b] Yasnory T F Sasaki, Miho Sano, Takashi Ideue, Taishin Kin, Kiyoshi Asai, Tetsuro Hirose (2007) Identification and characterization of human non-coding RNAs with tissue-specific expression. Biochem Biophys Res Commun 357: 4. 991-996 Jun

[Kobayashi+2007] Tetsuo Kobayashi, Keietsu Abe, Kiyoshi Asai, Katsuya Gomi, Praveen Rao Juvvadi, Masashi Kato, Katsuhiko Kitamoto, Michio Takeuchi, Masayuki Machida (2007) Genomics of Aspergillus oryzae. Biosci Biotechnol Biochem 71: 3. 646-670 Mar

[Kiryu+2007a] Hisanori Kiryu, Taishin Kin, Kiyoshi Asai (2007) Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics 23: 4. 434-441 Feb

[Kin+2007] Taishin Kin, Kouichirou Yamada, Goro Terai, Hiroaki Okida, Yasuhiko Yoshinari, Yukiteru Ono, Aya Kojima, Yuki Kimura, Takashi Komori, Kiyoshi Asai (2007) fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res 35: Database issue. D145-D148 Jan

2006

[Hamada+2006] Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai (2006) Mining frequent stem patterns from unaligned RNA sequences. Bioinformatics 22: 20. 2480-2487 Oct

[Tabei+2006] Yasuo Tabei, Koji Tsuda, Taishin Kin, Kiyoshi Asai (2006) SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinformatics 22: 14. 1723-1729 Jul

[KatoT+2006] Tsuyoshi Kato, Yukio Murata, Koh Miura, Kiyoshi Asai, Paul B Horton, Tsuda Koji, Wataru Fujibuchi (2006) Network-based de-noising improves prediction from microarray data. BMC Bioinformatics 7 Suppl 1: Mar

2005

[Nierman+2005] William C Nierman, Arnab Pain, Michael J Anderson, Jennifer R Wortman, H Stanley Kim, Javier Arroyo, Matthew Berriman, Keietsu Abe, David B Archer, Clara Bermejo, Joan Bennett, Paul Bowyer, Dan Chen, Matthew Collins, Richard Coulsen, Robert Davies, Paul S Dyer, Mark Farman, Nadia Fedorova, Natalie Fedorova, Tamara V Feldblyum, Reinhard Fischer, Nigel Fosker, Audrey Fraser, Jose L Garcia, Maria J Garcia, Arlette Goble, Gustavo H Goldman, Katsuya Gomi, Sam Griffith-Jones, Ryan Gwilliam, Brian Haas, Hubertus Haas, David Harris, H Horiuchi, Jiaqi Huang, Sean Humphray, Javier Jimenez, Nancy Keller, Hoda Khouri, Katsuhiko Kitamoto, Tetsuo Kobayashi, Sven Konzack, Resham Kulkarni, Toshitaka Kumagai, Anne Lafon, Anne Lafton, Jean-Paul Latge, Weixi Li, Angela Lord, Charles Lu, William H Majoros, Gregory S May, Bruce L Miller, Yasmin Mohamoud, Maria Molina, Michel Monod, Isabelle Mouyna, Stephanie Mulligan, Lee Murphy, Susan O’Neil, Ian Paulsen, Miguel A Penalva, Mihaela Pertea, Claire Price, Bethan L Pritchard, Michael A Quail, Ester Rabbinowitsch, Neil Rawlins, Marie-Adele Rajandream, Utz Reichard, Hubert Renauld, Geoffrey D Robson, Santiago Rodriguez de Cordoba, Jose M Rodriguez-Pena, Catherine M Ronning, Simon Rutter, Steven L Salzberg, Miguel Sanchez, Juan C Sanchez-Ferrero, David Saunders, Kathy Seeger, Rob Squares, Steven Squares, Michio Takeuchi, Fredj Tekaia, Geoffrey Turner, Carlos R Vazquez de Aldana, Janice Weidman, Owen White, John Woodward, Jae-Hyuk Yu, Claire Fraser, James E Galagan, Kiyoshi Asai, Masayuki Machida, Neil Hall, Bart Barrell, David W Denning (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438: 7071. 1151-1156 Dec

[Machida+2005] Masayuki Machida, Kiyoshi Asai, Motoaki Sano, Toshihiro Tanaka, Toshitaka Kumagai, Goro Terai, Ken-Ichi Kusumoto, Toshihide Arima, Osamu Akita, Yutaka Kashiwagi, Keietsu Abe, Katsuya Gomi, Hiroyuki Horiuchi, Katsuhiko Kitamoto, Tetsuo Kobayashi, Michio Takeuchi, David W Denning, James E Galagan, William C Nierman, Jiujiang Yu, David B Archer, Joan W Bennett, Deepak Bhatnagar, Thomas E Cleveland, Natalie D Fedorova, Osamu Gotoh, Hiroshi Horikawa, Akira Hosoyama, Masayuki Ichinomiya, Rie Igarashi, Kazuhiro Iwashita, Praveen Rao Juvvadi, Masashi Kato, Yumiko Kato, Taishin Kin, Akira Kokubun, Hiroshi Maeda, Noriko Maeyama, Jun-ichi Maruyama, Hideki Nagasaki, Tasuku Nakajima, Ken Oda, Kinya Okada, Ian Paulsen, Kazutoshi Sakamoto, Toshihiko Sawano, Mikio Takahashi, Kumiko Takase, Yasunobu Terabayashi, Jennifer R Wortman, Osamu Yamada, Youhei Yamagata, Hideharu Anazawa, Yoji Hata, Yoshinao Koide, Takashi Komori, Yasuji Koyama, Toshitaka Minetoki, Sivasundaram Suharnan, Akimitsu Tanaka, Katsumi Isono, Satoru Kuhara, Naotake Ogasawara, Hisashi Kikuchi (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438: 7071. 1157-1161 Dec

[Galaran+2005] James E Galagan, Sarah E Calvo, Christina Cuomo, Li-Jun Ma, Jennifer R Wortman, Serafim Batzoglou, Su-In Lee, Meray Ba?turkmen, Christina C Spevak, John Clutterbuck, Vladimir Kapitonov, Jerzy Jurka, Claudio Scazzocchio, Mark Farman, Jonathan Butler, Seth Purcell, Steve Harris, Gerhard H Braus, Oliver Draht, Silke Busch, Christophe D’Enfert, Christiane Bouchier, Gustavo H Goldman, Deborah Bell-Pedersen, Sam Griffiths-Jones, John H Doonan, Jaehyuk Yu, Kay Vienken, Arnab Pain, Michael Freitag, Eric U Selker, David B Archer, Miguel A Penalva, Berl R Oakley, Michelle Momany, Toshihiro Tanaka, Toshitaka Kumagai, Kiyoshi Asai, Masayuki Machida, William C Nierman, David W Denning, Mark Caddick, Michael Hynes, Mathieu Paoletti, Reinhard Fischer, Bruce Miller, Paul Dyer, Matthew S Sachs, Stephen A Osmani, Bruce W Birren (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 7071. 1105-1115 Dec

[KatoT+2005] Tsuyoshi Kato, Koji Tsuda, Kiyoshi Asai (2005) Selective integration of multiple biological data for supervised network inference. Bioinformatics 21: 10. 2488-2495 May

[Okada+2005] Kinya Okada, Shigehiko Kanaya, Kiyoshi Asai (2005) Accurate extraction of functional associations between proteins based on common interaction partners and common domains. Bioinformatics 21: 9. 2043-2048 May

[Kiryu+2005] Hisanori Kiryu, Taku Oshima, Kiyoshi Asai (2005) Extracting relations between promoter sequences and their strengths from microarray data. Bioinformatics 21: 7. 1062-1068 Apr

Recent Meeting Presentations

2019

  1. Junichi Iwakiri, Martin C. Frith, Michiaki Hamada, Kiyoshi Asai, Computational analysis pipeline for recent RNA-seq methods involving induced-substitutions, FRONTIERS OF GENOME SCIENCE: The International symposium organized by “Platform for Advanced Genome Science”, Tokyo, January 2019

2018

  1. Akihiro Imaeda, Ryota Oikawa, Kiyoshi Asai, Junichi Iwakiri, Shun Sakuraba, Naoko Abe, Fumiaki Tomoike, Yasuaki Kimura, Hiroshi Abe, Synthesis of mRNA with site-specific N6-methyladenosine and its translation efficiency, ISNAC2018(第45回国際核酸化学シンポジウム),Kyoto,2018年11月
  2. 寺井 悟朗、高橋 俊介、中村 朋美、柘植 謙爾、石井 純、浅井 潔 DNAシャッフリングを利用した出芽酵母におけるコドン最適化ルールの抽出 第41回日本分子生物学会年会 2018年11月
  3. Naruki Yoshikawa, Kiyoshi Asai, Anish M.S. Shrestha: Combining probabilistic alignments with read pair information improves accuracy of split-alignments, Poster at the 16th Asia Pacific Bioinformatics Conference, 2018, Kanagawa [Poster]
  4. Anish M.S. Shrestha, Martin C. Frith, Kiyoshi Asai, Hugues Richard: Jointly aligning a group of DNA reads improves accuracy of identifying large deletions, HiTSeq 2018, Chicago. [Talk]
  5. 中川 真理子、Hugues Richard、浅井 潔、Anish MS Shrestha、RNA-Seqリードのジョイントアラインメントを用いた正確なスプライスサイト予測、第41回分子生物学会年会[poster]
  6. 二宮賢介、足達俊吾、 夏目徹、岩切淳一、寺井悟朗、浅井潔、廣瀬哲郎 核内ストレス体によるストレス回復期のスプライシング制御 第20回日本RNA学会年会 2018年07月
  7. 寺井 悟朗、高橋 俊介、中村 朋美、石井 純、柘植 謙爾、浅井 潔 Combi-OGAB法を用いた最適コドンの探索 日本農芸化学会2018年度大会 2018年3月
  8. 岩切淳一,Martin C. Frith,浜田道昭,浅井潔,先進的RNA-seqのデータ解析を改善するマッピングパラメータ学習,第20回日本RNA学会年会,大阪,2018年7月
    今枝昭裕,笈川涼太,浅井潔,岩切淳一,桜庭俊,阿部奈保子,友池史明,木村康明,阿部洋,N6-アルキルアデノシンの導入位置を制御したmRNAの合成とその翻訳能,第20回日本RNA学会年会,大阪,2018年7月

2017

  1. Takafumi Chishima, Junichi Iwakiri, Michiaki Hamada, Identification of Transposable Elements which contribute to tissue specific expression of lncRNAs, 第6回生命医薬情報学連合大会(IIBMP), 北海道,2017年9月
  2. Mei Takeda, Junichi Iwakiri, Michiaki Hamada, Estimation of mapping parameters for PAR-CLIP data using LAST-TRAIN, 第6回生命医薬情報学連合大会(IIBMP), 北海道,2017年9月
  3. 福永 津嵩,岩切 淳一,小野 幸輝,浜田 道昭, lncRNA-mRNAの網羅的相互作用予測へ向けた高速なRNA-RNA相互作用予測ソフトウェアRIblastの開発,第19回日本RNA学会年会,富山,2017年7月
  4. 千島 崇史,岩切 淳一,浜田 道昭,lncRNAの組織特異的な発現に関与するTransposable Elementの同定,第19回日本RNA学会年会,富山,2017年7月
  5. 福永 津嵩,岩切 淳一,小野 幸輝,浜田 道昭,ヒトlncRNA-RNAの網羅的相互作用予測及びデータベースの構築,第五回NGS現場の会,宮城,2017年5月
  6. Junichi Iwakiri, Kiyoshi Asai, Computational analysis of CLIP-seq data in public databases, Advanced Genome Science International Symposium “The Start of New Genomics”, Tokyo, 2017

2016

  1. Kiyoshi Asai,Algorithms for Marginal Probabilities on RNA Secondary Structures, ALGO2016 Invited Talk, Aug.23, 2016
  2. Hideaki Noshiro, Kiyoshi Asai, Anish M.S. Shrestha: ZBDD-based representation and mining of RNA secondary structure ensemble, Poster at the 39th Annual Meeting of the Molecular Biology Society of Japan, 2016, Yokohama
  3. Junichi Iwakiri, Goro Terai, Michiaki Hamada, Computational prediction of lncRNA-mRNA interactions by integrating tissue-specificity of human transcripts, The 21st Annual Meeting of the RNA Society, 346, Kyoto, June 2016
  4. Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai, Tomoshi Kameda, Improved accuracy in RNA-protein rigid body docking by incorporating force field for molecular dynamics simulation into the scoring function, The 21st Annual Meeting of the RNA Society, 348, Kyoto, June 2016
  5. 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, The 21st Annual Meeting of the RNA Society, 348, Kyoto, June 2016
  6. Wataru Okada, Junichi Iwakiri, Michiaki Hamada, Investigation of evolutionarily conserved NEAT1-NEAT1 interactions, The 21st Annual Meeting of the RNA Society, 356, Kyoto, June 2016
  7. 萩尾太一、桜庭俊、浅井潔、 RNAの準最適二次構造の予測、第39回日本分子生物学会年会(最優秀ポスター賞)
  8. 松田 崇、浅井潔、配列解析を考慮した行列分解によるインフルエンザ HI 試験データの欠損値予測、第39回日本分子生物学会年会(最優秀ポスター賞)

2015

  1. 岩切 淳一,浅井 潔.CLIP-seqデータの統合解析の現状と今後の展望,BMB2015(第38回日本分子生物学会年会,第88回日本生化学会大会 合同大会),神戸,2015年12月
  2. 亀田倫史、岩切淳一、浜田道昭、由良敬、浅井潔、蛋白質・RNA複合体の立体構造予測、第53回日本生物物理学会、2015年9月、金沢大学
  3. 岩切 淳一,寺井 悟朗,亀田 倫史,浅井 潔,浜田 道昭.RNA 発現量を用いた組織特異的 lncRNA-mRNA 相互作用予測,第17回日本RNA学会,北海道,2015年7月
  4. 寺井 悟朗,岩切 淳一,亀田 倫史,浜田 道昭,浅井 潔.ヒトトランスクリプトームにおける網羅的 lncRNA-RNA 相互作用予測,第17回日本RNA学会,北海道,2015年7月
  5. 由良 敬,岩切 淳一,浜田 道昭,浅井 潔,亀田 倫史,分子動力学計算を用いた蛋白質・RNA 複合体立体構造予測,第17回日本RNA学会,北海道,2015年7月
  6. Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada, A semi-supervised learning approach for RNA secondary structure prediction, The thirteenth Asia Pacific Bioinformatics Conference (APBC2015)

2014

  1. 岩切 淳一, 亀田 倫史,浅井 潔,浜田 道昭.RNA‐タンパク質相互作用予測法の開発,第16回日本RNA学会,愛知,2014年7月
  2. 由良 敬,岩切 淳一,浜田 道昭,浅井 潔,亀田 倫史.分子動力学計算を用いた蛋白質・RNA 複合体立体構造予測,第16回日本RNA学会,愛知,2014年7月
  3. Ryota Mori, Michiaki Hamada and Kiyoshi Asai, Efficient calculation of exact probability distributions of integer features on RNA secondary structures, GIW/ISCB-ASIA2014 (Oral Presentation)

2013

  1. 岩切 淳一, 亀田 倫史,浅井 潔,浜田 道昭.タンパク質-RNA相互作用におけるRNA2次構造認識機構:塩基対確率に基づく解析,第15回日本RNA学会年会,愛媛,2013年7月
  2. 亀田 倫史, 岩切 淳一, 浜田 道昭, 浅井 潔.蛋白質-RNA の複合体立体構造予測,第15回日本RNA学会年会,愛媛,2013年7月

2011

Kiyoshi Asai, Algorithms for RNA sequence analysis, International Conference on Genome Informatics 2011 (GIW2011), Invited Talk, Busan