Michiaki Hamada

Michiaki Hamada

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Michiaki Hamada

Publications by authors named "Michiaki Hamada"

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Identification of RNA biomarkers for chemical safety screening in neural cells derived from mouse embryonic stem cells using RNA deep sequencing analysis.

Biochem Biophys Res Commun 2019 May 26;512(4):641-646. Epub 2018 Nov 26.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan; AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan; Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, 135-0064, Japan; Institute for Medical-oriented Structural Biology, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan; Graduate School of Medicine, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan.

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https://linkinghub.elsevier.com/retrieve/pii/S0006291X183257
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http://dx.doi.org/10.1016/j.bbrc.2018.11.141DOI Listing
May 2019

LncRRIsearch: A Web Server for lncRNA-RNA Interaction Prediction Integrated With Tissue-Specific Expression and Subcellular Localization Data.

Front Genet 2019 28;10:462. Epub 2019 May 28.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo, Japan.

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http://dx.doi.org/10.3389/fgene.2019.00462DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546843PMC
May 2019

Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference.

Bioinformatics 2019 Apr 16. Epub 2019 Apr 16.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University.

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http://dx.doi.org/10.1093/bioinformatics/btz266DOI Listing
April 2019

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning.

BMC Bioinformatics 2018 Dec 31;19(Suppl 19):524. Epub 2018 Dec 31.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.

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http://dx.doi.org/10.1186/s12859-018-2516-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311933PMC
December 2018

Identifying sequence features that drive ribosomal association for lncRNA.

BMC Genomics 2018 Dec 31;19(Suppl 10):906. Epub 2018 Dec 31.

Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.

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http://dx.doi.org/10.1186/s12864-018-5275-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6311901PMC
December 2018

A Novel Method for Assessing the Statistical Significance of RNA-RNA Interactions Between Two Long RNAs.

J Comput Biol 2018 Sep 2;25(9):976-986. Epub 2018 Jul 2.

2 Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University , Tokyo, Japan .

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http://dx.doi.org/10.1089/cmb.2017.0260DOI Listing
September 2018

Computational approaches for alternative and transient secondary structures of ribonucleic acids.

Brief Funct Genomics 2018 Jun;18(3):182-191

Waseda University.

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http://dx.doi.org/10.1093/bfgp/ely042DOI Listing
June 2018

Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data.

BMC Genomics 2018 May 29;19(1):414. Epub 2018 May 29.

AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.

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http://dx.doi.org/10.1186/s12864-018-4765-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5975437PMC
May 2018

In silico approaches to RNA aptamer design.

Authors:
Michiaki Hamada

Biochimie 2018 Feb 12;145:8-14. Epub 2017 Oct 12.

Bioinformatics Laboratory, Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 63-520, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan; Institute for Medical-oriented Structural Biology, Waseda University, 2-2, Wakamatsu-cho Shinjuku-ku, Tokyo 162-8480, Japan; Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan; Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.biochi.2017.10.005DOI Listing
February 2018

Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm.

Bioinformatics 2018 02;34(4):576-584

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btx643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860613PMC
February 2018

Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs.

Genes (Basel) 2018 Jan 9;9(1). Epub 2018 Jan 9.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.

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http://dx.doi.org/10.3390/genes9010023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793176PMC
January 2018

RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach.

Bioinformatics 2017 Sep;33(17):2666-2674

Faculty of Science and Engineering, Waseda University, Tokyo 169-8555, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btx287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860064PMC
September 2017

Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome.

Biol Direct 2017 06 8;12(1):15. Epub 2017 Jun 8.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.

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http://dx.doi.org/10.1186/s13062-017-0183-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465533PMC
June 2017

AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana.

Genes Genet Syst 2017 Mar 25;91(4):229-233. Epub 2016 Jul 25.

RIKEN Nishina Center.

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http://dx.doi.org/10.1266/ggs.15-00078DOI Listing
March 2017

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

Bioinformatics 2017 03;33(6):926-928

Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btw742DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5351549PMC
March 2017

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 Sep 17;12(9):4688-97. Epub 2016 Aug 17.

Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1021/acs.jctc.6b00254DOI Listing
September 2016

Rtools: a web server for various secondary structural analyses on single RNA sequences.

Nucleic Acids Res 2016 07 29;44(W1):W302-7. Epub 2016 Apr 29.

Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, 135-0064 Tokyo, Japan Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkw337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987903PMC
July 2016

Bioinformatics tools for lncRNA research.

Biochim Biophys Acta 2016 Jan 10;1859(1):23-30. Epub 2015 Aug 10.

Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan; Computational Biology Research Consortium (CBRC), in National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6, Aomi, Koto-ku, Tokyo 135-0064, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S18749399150016
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http://dx.doi.org/10.1016/j.bbagrm.2015.07.014DOI Listing
January 2016

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome.

BMC Genomics 2016 Jan 11;17 Suppl 1:12. Epub 2016 Jan 11.

Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.

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http://dx.doi.org/10.1186/s12864-015-2307-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4895283PMC
January 2016

RNA secondary structure prediction from multi-aligned sequences.

Authors:
Michiaki Hamada

Methods Mol Biol 2015 ;1269:17-38

Faculty of Science and Engineering, Waseda university, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo, 169-8555, Japan,

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http://dx.doi.org/10.1007/978-1-4939-2291-8_2DOI Listing
September 2015

A semi-supervised learning approach for RNA secondary structure prediction.

Comput Biol Chem 2015 Aug 20;57:72-9. Epub 2015 Feb 20.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan; Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7, Aomi, Koto-ku, Tokyo 135-0064, Japan. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S14769271150001
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http://dx.doi.org/10.1016/j.compbiolchem.2015.02.002DOI Listing
August 2015

Learning chromatin states with factorized information criteria.

Bioinformatics 2015 Aug 24;31(15):2426-33. Epub 2015 Mar 24.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btv163DOI Listing
August 2015

RNA structural alignments, part II: non-Sankoff approaches for structural alignments.

Methods Mol Biol 2014 ;1097:291-301

Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan.

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http://dx.doi.org/10.1007/978-1-62703-709-9_14DOI Listing
November 2014

Fighting against uncertainty: an essential issue in bioinformatics.

Authors:
Michiaki Hamada

Brief Bioinform 2014 Sep 26;15(5):748-67. Epub 2013 Jun 26.

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http://dx.doi.org/10.1093/bib/bbt038DOI Listing
September 2014

Reference-free prediction of rearrangement breakpoint reads.

Bioinformatics 2014 Sep 29;30(18):2559-67. Epub 2014 May 29.

Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562 and Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btu360DOI Listing
September 2014

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions.

Bioinformatics 2013 Oct 9;29(20):2524-8. Epub 2013 Aug 9.

Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan and Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt453DOI Listing
October 2013

CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs.

Int J Mol Sci 2013 Mar 18;14(3):6144-56. Epub 2013 Mar 18.

Department of Computational Biology, Graduate School of Frontier Sciences,the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan.

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http://dx.doi.org/10.3390/ijms14036144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3634467PMC
March 2013

PBSIM: PacBio reads simulator--toward accurate genome assembly.

Bioinformatics 2013 Jan 4;29(1):119-21. Epub 2012 Nov 4.

Information and Mathematical Science and Bioinformatics Co., Ltd., Toshima-ku, Tokyo 170-0013, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bts649DOI Listing
January 2013

Direct updating of an RNA base-pairing probability matrix with marginal probability constraints.

Authors:
Michiaki Hamada

J Comput Biol 2012 Dec;19(12):1265-76

The University of Tokyo, Graduate School of Frontier Science, Kashiwa, Japan.

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http://dx.doi.org/10.1089/cmb.2012.0215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514005PMC
December 2012

Shape-based alignment of genomic landscapes in multi-scale resolution.

Nucleic Acids Res 2012 Aug 4;40(14):6435-48. Epub 2012 May 4.

Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8561, Japan.

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https://academic.oup.com/nar/article/40/14/6435/2414915
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http://dx.doi.org/10.1093/nar/gks354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413149PMC
August 2012

A classification of bioinformatics algorithms from the viewpoint of maximizing expected accuracy (MEA).

J Comput Biol 2012 May 7;19(5):532-49. Epub 2012 Feb 7.

Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.

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http://dx.doi.org/10.1089/cmb.2011.0197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342518PMC
May 2012

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.

Bioinformatics 2011 Nov 5;27(22):3085-92. Epub 2011 Oct 5.

Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btr537DOI Listing
November 2011

Antagonistic RNA aptamer specific to a heterodimeric form of human interleukin-17A/F.

Biochimie 2011 Jul 19;93(7):1081-8. Epub 2011 Apr 19.

Department of Basic Medical Sciences, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.

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http://dx.doi.org/10.1016/j.biochi.2011.04.003DOI Listing
July 2011

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences.

Nucleic Acids Res 2011 Jul 11;39(Web Server issue):W100-6. Epub 2011 May 11.

Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.

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http://dx.doi.org/10.1093/nar/gkr290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125741PMC
July 2011

IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.

Bioinformatics 2011 Jul;27(13):i85-93

Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btr215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3117384PMC
July 2011

Generalized centroid estimators in bioinformatics.

PLoS One 2011 Feb 18;6(2):e16450. Epub 2011 Feb 18.

Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0016450PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041832PMC
February 2011

Improving the accuracy of predicting secondary structure for aligned RNA sequences.

Nucleic Acids Res 2011 Jan 15;39(2):393-402. Epub 2010 Sep 15.

Mizuho Information & Research Institute, Inc, Chiyoda-ku, Tokyo, Japan.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkq792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025558PMC
January 2011

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy.

BMC Bioinformatics 2010 Nov 30;11:586. Epub 2010 Nov 30.

Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, Japan.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-11-586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3003279PMC
November 2010

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.

Bioinformatics 2010 Sep;26(18):i460-6

Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btq372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935440PMC
September 2010

Parameters for accurate genome alignment.

BMC Bioinformatics 2010 Feb 9;11:80. Epub 2010 Feb 9.

Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1186/1471-2105-11-80DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829014PMC
February 2010

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score.

Bioinformatics 2009 Dec 6;25(24):3236-43. Epub 2009 Oct 6.

Mizuho Information & Research Institute, Inc, 2-3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101-8443, Japan.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btp580DOI Listing
December 2009

CENTROIDFOLD: a web server for RNA secondary structure prediction.

Nucleic Acids Res 2009 Jul 12;37(Web Server issue):W277-80. Epub 2009 May 12.

Japan Biological Informatics Consortium, 2-45 Aomi, Koto-ku, Tokyo 135-8073, Japan.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkp367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703931PMC
July 2009

Prediction of RNA secondary structure using generalized centroid estimators.

Bioinformatics 2009 Feb 18;25(4):465-73. Epub 2008 Dec 18.

Mizuho Information & Research Institute, Inc, 2-3 Kanda-Nishikicho, Chiyoda-ku, Tokyo 101-8443, Japan.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btn601DOI Listing
February 2009

Software.ncrna.org: web servers for analyses of RNA sequences.

Nucleic Acids Res 2008 Jul 25;36(Web Server issue):W75-8. Epub 2008 Apr 25.

Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwa-no-ha, Chiba 277-8561, Japan.

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http://dx.doi.org/10.1093/nar/gkn222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447773PMC
July 2008

Mining frequent stem patterns from unaligned RNA sequences.

Bioinformatics 2006 Oct 14;22(20):2480-7. Epub 2006 Aug 14.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2-43 Aomi, Koto-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btl431DOI Listing
October 2006