Kiyoshi Asai
Orcid: 0000-0003-0909-4982
According to our database1,
Kiyoshi Asai
authored at least 85 papers
between 1990 and 2022.
Collaborative distances:
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Bibliography
2022
ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures.
Bioinform., 2022
2021
PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores.
Bioinform., 2021
2020
RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp.
BMC Bioinform., 2020
Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model.
Bioinform., 2020
2019
Proceedings of the Encyclopedia of Bioinformatics and Computational Biology - Volume 2, 2019
Estimating Energy Parameters for RNA Secondary Structure Predictions Using Both Experimental and Computational Data.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019
2018
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.
BMC Bioinform., 2018
Combining probabilistic alignments with read pair information improves accuracy of split-alignments.
Bioinform., 2018
Proceedings of the International Symposium on Information Theory and Its Applications, 2018
2017
Bioinform., 2017
2016
Rtools: a web server for various secondary structural analyses on single RNA sequences.
Nucleic Acids Res., 2016
BMC Genom., 2016
CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure.
Bioinform., 2016
2015
BMC Bioinform., December, 2015
Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014).
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
Comput. Biol. Chem., 2015
Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in <i>Ustilaginoidea virens</i>.
Bioinform., 2015
2014
Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method.
J. Chem. Inf. Model., 2014
2013
Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions.
Bioinform., 2013
2012
Nucleic Acids Res., 2012
Rtips: fast and accurate tools for RNA 2D structure prediction using integer programming.
Nucleic Acids Res., 2012
A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA).
J. Comput. Biol., 2012
Transformations for the compression of FASTQ quality scores of next-generation sequencing data.
Bioinform., 2012
Bioinform., 2012
Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations.
Bioinform., 2012
2011
CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences.
Nucleic Acids Res., 2011
Nucleic Acids Res., 2011
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming.
Bioinform., 2011
A detailed investigation of accessibilities around target sites of siRNAs and miRNAs.
Bioinform., 2011
Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection.
Bioinform., 2011
2010
J. Bioinform. Comput. Biol., 2010
BMC Bioinform., 2010
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
J. Biomed. Semant., 2010
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming.
Bioinform., 2010
In search of true reads: A classification approach to next generation sequencing data selection.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010
2009
Nucleic Acids Res., 2009
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.
Nucleic Acids Res., 2009
Bioinform., 2009
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score.
Bioinform., 2009
Bioinform., 2009
Bioinform., 2009
2008
Nucleic Acids Res., 2008
BMC Bioinform., 2008
Bioinform., 2008
2007
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
Nucleic Acids Res., 2007
Bioinform., 2007
Robust prediction of consensus secondary structures using averaged base pairing probability matrices.
Bioinform., 2007
Proceedings of the Advances in Neural Information Processing Systems 20, 2007
Proceedings of the Bioinformatics Research and Development, First International Conference, 2007
Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions.
Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007
2006
BMC Bioinform., 2006
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.
Bioinform., 2006
2005
Accurate extraction of functional associations between proteins based on common interaction partners and common domains.
Bioinform., 2005
Extracting relations between promoter sequences and their strengths from microarray data.
Bioinform., 2005
Bioinform., 2005
2004
Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data.
Neural Process. Lett., 2004
Proceedings of the Structural, 2004
2003
J. Mach. Learn. Res., 2003
Proceedings of the Genetic and Evolutionary Computation, 2003
2002
Marginalized kernels for biological sequences.
Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002
Modeling splicing sites with pairwise correlations.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002
2000
Reconstructing Metabolic Pathways with New Enzyme Classification.
Proceedings of the German Conference on Bioinformatics (GCB 2000), 2000
1998
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
Bioinform., 1998
1997
A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997
1994
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994
Protein Structure Prediction Based on Multi-Level Description.
Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994
A Three-Dimensional Animation System for Protein Folding Simulation.
Proceedings of the 27th Annual Hawaii International Conference on System Sciences (HICSS-27), 1994
1993
Comput. Appl. Biosci., 1993
Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993
1992
Proceedings of the 1992 IEEE International Conference on Acoustics, 1992
1990
Proceedings of the First International Conference on Spoken Language Processing, 1990
Proceedings of the First International Conference on Spoken Language Processing, 1990