Kiyoshi Asai

Kiyoshi Asai

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Kiyoshi Asai

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RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp.

BMC Bioinformatics 2020 May 24;21(1):210. Epub 2020 May 24.

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

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http://dx.doi.org/10.1186/s12859-020-3535-5DOI Listing
May 2020

Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data.

IEEE/ACM Trans Comput Biol Bioinform 2019 Sep-Oct;16(5):1645-1655. Epub 2018 Mar 12.

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http://dx.doi.org/10.1109/TCBB.2018.2813388DOI Listing
March 2020

A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs.

RNA Biol 2020 02 1;17(2):264-280. Epub 2019 Nov 1.

Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1080/15476286.2019.1678364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6973332PMC
February 2020

Combining probabilistic alignments with read pair information improves accuracy of split-alignments.

Bioinformatics 2018 11;34(21):3631-3637

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

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http://dx.doi.org/10.1093/bioinformatics/bty398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198854PMC
November 2018

Jointly aligning a group of DNA reads improves accuracy of identifying large deletions.

Nucleic Acids Res 2018 02;46(3):e18

Sorbonne Universités, UPMC Univ Paris 06, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 4 place Jussieu, 75005 Paris, France.

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http://dx.doi.org/10.1093/nar/gkx1175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5815140PMC
February 2018

Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.

BMC Bioinformatics 2018 02 19;19(Suppl 1):38. Epub 2018 Feb 19.

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

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http://dx.doi.org/10.1186/s12859-018-2018-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836843PMC
February 2018

Evolutionary design of multiple genes encoding the same protein.

Bioinformatics 2017 Jun;33(11):1613-1620

Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btx030DOI Listing
June 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

Genome Sequence of Ustilaginoidea virens IPU010, a Rice Pathogenic Fungus Causing False Smut.

Genome Announc 2016 May 5;4(3). Epub 2016 May 5.

Technology Research Association of Highly Efficient Gene Design, Sapporo, Hokkaido, Japan Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.

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http://dx.doi.org/10.1128/genomeA.00306-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859173PMC
May 2016

Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data.

PLoS One 2015 28;10(4):e0126289. Epub 2015 Apr 28.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126289PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4412624PMC
April 2016

CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure.

Bioinformatics 2016 03 20;32(6):828-34. Epub 2015 Nov 20.

National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv678DOI Listing
March 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

Class of cyclic ribosomal peptide synthetic genes in filamentous fungi.

Fungal Genet Biol 2016 Jan 15;86:58-70. Epub 2015 Dec 15.

Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan; Computational Biology Research Consortium (CBRC), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan.

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http://dx.doi.org/10.1016/j.fgb.2015.12.010DOI 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

Predicting RNA Duplex Dimerization Free-Energy Changes upon Mutations Using Molecular Dynamics Simulations.

J Phys Chem Lett 2015 Nov 20;6(21):4348-51. Epub 2015 Oct 20.

Biotechnology Research Institute for Drug Discovery, 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.jpclett.5b01984DOI Listing
November 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

Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in Ustilaginoidea virens.

Bioinformatics 2015 Apr 19;31(7):981-5. Epub 2014 Nov 19.

Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan, Fermlab Inc., Tokyo 135-0021, Japan, INTEC Inc., Tokyo 136-8637, Japan, and Department of Computational Biology, Graduate School of Frontier Sciences, the University of Tokyo, Chiba 277-8561, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btu753DOI Listing
April 2015

Editorial--The 25th International Conference on Genome Informatics (GIW/ISCB-ASIA 2014).

J Bioinform Comput Biol 2014 Dec;12(6):1402002

Human Genome Center, The Institute of Medical Science, The University of Tokyo, Japan.

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http://dx.doi.org/10.1142/S0219720014020028DOI Listing
December 2014

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

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

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 Res 2014 Aug 11;21(4):447-57. Epub 2014 Apr 11.

Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi-Nijo 17-2-1, Tsukisamu, Sapporo, Hokkaido 062-8517, Japan

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https://academic.oup.com/dnaresearch/article-lookup/doi/10.1
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http://dx.doi.org/10.1093/dnares/dsu010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131838PMC
August 2014

Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method.

J Chem Inf Model 2014 Feb 30;54(2):672-82. Epub 2014 Jan 30.

Molecular Profiling Research Center for Drug Discovery (molprof), 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/ci400525tDOI Listing
February 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

Finding protein-coding genes through human polymorphisms.

PLoS One 2013 22;8(1):e54210. Epub 2013 Jan 22.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054210PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3551959PMC
July 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

DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition.

Bioinformatics 2012 Dec 11;28(24):3218-24. Epub 2012 Oct 11.

Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, 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/bts612DOI Listing
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 mostly traditional approach improves alignment of bisulfite-converted DNA.

Nucleic Acids Res 2012 Jul 28;40(13):e100. Epub 2012 Mar 28.

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

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http://dx.doi.org/10.1093/nar/gks275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3401460PMC
July 2012

Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.

Nucleic Acids Res 2012 Jul 16;40(Web Server issue):W29-34. Epub 2012 May 16.

Graduate School of Information Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, Nara 630-0192, 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/gks412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394313PMC
July 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

Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations.

Bioinformatics 2012 Apr 28;28(8):1093-101. Epub 2012 Feb 28.

Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, Kashiwa, Chiba, Japan.

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http://bioinformatics.oxfordjournals.org/content/28/8/1093.f
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/bts097DOI Listing
April 2012

Transformations for the compression of FASTQ quality scores of next-generation sequencing data.

Bioinformatics 2012 Mar 13;28(5):628-35. Epub 2011 Dec 13.

Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Chiba-ken 277-8561, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btr689DOI Listing
March 2012

RecountDB: a database of mapped and count corrected transcribed sequences.

Nucleic Acids Res 2012 Jan 1;40(Database issue):D1089-92. Epub 2011 Dec 1.

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/nar/gkr1172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245132PMC
January 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

A detailed investigation of accessibilities around target sites of siRNAs and miRNAs.

Bioinformatics 2011 Jul 29;27(13):1788-97. Epub 2011 Apr 29.

Department of Computational Biology, Faculty of Frontier Science, The University of Tokyo, Chiba 277-8561, Japan.

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http://bioinformatics.oxfordjournals.org/content/early/2011/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btr276DOI 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

Discovery of short pseudogenes derived from messenger RNAs.

Nucleic Acids Res 2010 Mar 3;38(4):1163-71. Epub 2009 Dec 3.

INTEC Systems Institute Inc., Koto-ku 136-0075, Japan.

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http://dx.doi.org/10.1093/nar/gkp1098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831318PMC
March 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

A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila.

Nature 2009 Oct 7;461(7268):1296-9. Epub 2009 Oct 7.

Keio University School of Medicine, Tokyo 160-8582, Japan.

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http://dx.doi.org/10.1038/nature08501DOI Listing
October 2009

Transcripts of unknown function in multiple-signaling pathways involved in human stem cell differentiation.

Nucleic Acids Res 2009 Aug 16;37(15):4987-5000. Epub 2009 Jun 16.

Center for Biological Resources and Informatics, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.

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http://dx.doi.org/10.1093/nar/gkp426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2731886PMC
August 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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http://dx.doi.org/10.1093/nar/gkp367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703931PMC
July 2009

A local multiple alignment method for detection of non-coding RNA sequences.

Bioinformatics 2009 Jun 17;25(12):1498-505. Epub 2009 Apr 17.

Department of Computational biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.

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http://bioinformatics.oxfordjournals.org/content/25/12/1498.
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http://dx.doi.org/10.1093/bioinformatics/btp261DOI Listing
June 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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http://dx.doi.org/10.1093/bioinformatics/btn601DOI Listing
February 2009

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.

Nucleic Acids Res 2009 Jan 23;37(Database issue):D89-92. Epub 2008 Oct 23.

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

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http://dx.doi.org/10.1093/nar/gkn805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686472PMC
January 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

Directed acyclic graph kernels for structural RNA analysis.

BMC Bioinformatics 2008 Jul 22;9:318. Epub 2008 Jul 22.

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

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-9-318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515856PMC
July 2008

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells.

Nature 2008 Jun 7;453(7196):793-7. Epub 2008 May 7.

Institute for Genome Research, University of Tokushima, Tokushima 770-8503, Japan.

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http://dx.doi.org/10.1038/nature06938DOI Listing
June 2008

Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing.

Proc Natl Acad Sci U S A 2008 Jun 4;105(23):7964-9. Epub 2008 Jun 4.

Institute for Genome Research, University of Tokushima, Tokushima 770-8503, Japan.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0800334105
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430345PMC
June 2008

Expansion of signaling genes for adaptive immune system evolution in early vertebrates.

BMC Genomics 2008 May 14;9:218. Epub 2008 May 14.

Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

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http://dx.doi.org/10.1186/1471-2164-9-218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2391169PMC
May 2008

Retention of genes involved in the adenohypophysis-mediated endocrine system in early vertebrates.

Gene 2008 Apr 31;412(1-2):71-83. Epub 2008 Jan 31.

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

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http://linkinghub.elsevier.com/retrieve/pii/S037811190800031
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http://dx.doi.org/10.1016/j.gene.2008.01.016DOI Listing
April 2008

Rfold: an exact algorithm for computing local base pairing probabilities.

Bioinformatics 2008 Feb 4;24(3):367-73. Epub 2007 Dec 4.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo, Japan.

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February 2008

A fast structural multiple alignment method for long RNA sequences.

BMC Bioinformatics 2008 Jan 23;9:33. Epub 2008 Jan 23.

Graduate School of Frontier Science, University of Tokyo, CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.

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http://dx.doi.org/10.1186/1471-2105-9-33DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375124PMC
January 2008

miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity.

RNA 2007 Dec 24;13(12):2081-90. Epub 2007 Oct 24.

Intec Web and Genome Informatics Corporation, Koto-ku, Tokyo, Japan, 136-0075.

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http://dx.doi.org/10.1261/rna.655107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2080609PMC
December 2007

Stem kernels for RNA sequence analyses.

J Bioinform Comput Biol 2007 Oct;5(5):1103-22

Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan.

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http://dx.doi.org/10.1142/s0219720007003028DOI Listing
October 2007

Murlet: a practical multiple alignment tool for structural RNA sequences.

Bioinformatics 2007 Jul 25;23(13):1588-98. Epub 2007 Apr 25.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btm146DOI Listing
July 2007

Coordinated expression of ncRNAs and HOX mRNAs in the human HOXA locus.

Biochem Biophys Res Commun 2007 Jun 9;357(3):724-30. Epub 2007 Apr 9.

Functional RNA Research Team, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koutou, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1016/j.bbrc.2007.03.200DOI Listing
June 2007

Identification and characterization of human non-coding RNAs with tissue-specific expression.

Biochem Biophys Res Commun 2007 Jun 17;357(4):991-6. Epub 2007 Apr 17.

Functional RNA Research Team, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.

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June 2007

Genomics of Aspergillus oryzae.

Biosci Biotechnol Biochem 2007 Mar 7;71(3):646-70. Epub 2007 Mar 7.

Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan.

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March 2007

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.

Bioinformatics 2007 Feb 20;23(4):434-41. Epub 2006 Dec 20.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan.

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February 2007

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.

Nucleic Acids Res 2007 Jan 11;35(Database issue):D145-8. Epub 2006 Nov 11.

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) Aomi 2-42, Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/nar/gkl837DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669753PMC
January 2007

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

Statistical evaluation of a bottom-up clustering for single particle molecular images.

Genome Inform 2005 ;16(2):125-35

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Tokyo, 135-0064, Japan.

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September 2006

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.

Bioinformatics 2006 Jul 11;22(14):1723-9. Epub 2006 May 11.

Department of Computational Biology, Graduate School of Frontier Science, University of Tokyo, CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.

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http://dx.doi.org/10.1093/bioinformatics/btl177DOI Listing
July 2006

Network-based de-noising improves prediction from microarray data.

BMC Bioinformatics 2006 Mar 20;7 Suppl 1:S4. Epub 2006 Mar 20.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810315PMC
March 2006

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.

Authors:
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 García Maria J García 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 Jiménez Nancy Keller Hoda Khouri Katsuhiko Kitamoto Tetsuo Kobayashi Sven Konzack Resham Kulkarni Toshitaka Kumagai Anne Lafon Anne Lafton Jean-Paul Latgé 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 Peñalva 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 Córdoba Jose M Rodríguez-Peña Catherine M Ronning Simon Rutter Steven L Salzberg Miguel Sanchez Juan C Sánchez-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

Nature 2005 Dec;438(7071):1151-6

The Institute for Genomic Research, Rockville, Maryland 20850, USA.

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December 2005

[Prediction and analyses of functional RNAs].

Authors:
Kiyoshi Asai

Tanpakushitsu Kakusan Koso 2005 Dec;50(16 Suppl):2282-7

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December 2005

Modeling splicing sites with pairwise correlations.

Bioinformatics 2002 ;18 Suppl 2:S27-34

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

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September 2005

Accurate extraction of functional associations between proteins based on common interaction partners and common domains.

Bioinformatics 2005 May 4;21(9):2043-8. Epub 2005 Feb 4.

Graduate School of Information Sciences, Nara Institute of Science and Technology, Ikoma, Japan.

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May 2005

Selective integration of multiple biological data for supervised network inference.

Bioinformatics 2005 May 22;21(10):2488-95. Epub 2005 Feb 22.

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

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http://dx.doi.org/10.1093/bioinformatics/bti339DOI Listing
May 2005

Extracting relations between promoter sequences and their strengths from microarray data.

Bioinformatics 2005 Apr 28;21(7):1062-8. Epub 2004 Oct 28.

Graduate School of Information Sciences, Nara Institute of Science and Technology 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.

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http://dx.doi.org/10.1093/bioinformatics/bti094DOI Listing
April 2005

Processing sequence annotation data using the Lua programming language.

Genome Inform 2003 ;14:154-63

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-43-17 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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March 2005

Marginalized kernels for biological sequences.

Bioinformatics 2002 ;18 Suppl 1:S268-75

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi Koto-ku, Tokyo 135-0064, Japan.

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http://dx.doi.org/10.1093/bioinformatics/18.suppl_1.s268DOI Listing
October 2004

Marginalized kernels for RNA sequence data analysis.

Genome Inform 2002 ;13:112-22

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.

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November 2003

Inference of Euler angles for single particle analysis by using Genetic Algorithms.

Genome Inform 2002 ;13:133-42

Graduate School of Frontier Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

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November 2003

Inference of Euler angles for single-particle analysis by means of evolutionary algorithms.

Biosystems 2003 Nov;72(1-2):43-55

Graduate School of Frontier Science, The University of Tokyo, Hongo 7-3-1 Bunkyo-ku, Tokyo 113-8656, Japan.

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http://dx.doi.org/10.1016/s0303-2647(03)00134-5DOI Listing
November 2003

MOSBY: a molecular structure viewer program with portability and extensibility.

J Mol Graph Model 2002 Mar;20(5):411-3

Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.

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http://dx.doi.org/10.1016/s1093-3263(01)00140-1DOI Listing
March 2002