Kiyoshi Asai

According to our database1, Kiyoshi Asai authored at least 80 papers between 1990 and 2020.

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Bibliography

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
RNA Structure Prediction.
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

Secure Division Protocol and Applications to Privacy-preserving Chi-squared Tests.
Proceedings of the International Symposium on Information Theory and Its Applications, 2018

2017
Evolutionary design of multiple genes encoding the same protein.
Bioinform., 2017

Training alignment parameters for arbitrary sequencers with LAST-TRAIN.
Bioinform., 2017

2016
Rtools: a web server for various secondary structural analyses on single RNA sequences.
Nucleic Acids Res., 2016

Comprehensive prediction of lncRNA-RNA interactions in human transcriptome.
BMC Genom., 2016

CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure.
Bioinform., 2016

2015
Guest Editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014).
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

A semi-supervised learning approach for RNA secondary structure prediction.
Comput. Biol. Chem., 2015

Ustiloxins, fungal cyclic peptides, are ribosomally synthesized in <i>Ustilaginoidea virens</i>.
Bioinform., 2015

Learning chromatin states with factorized information criteria.
Bioinform., 2015

2014
Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method.
J. Chem. Inf. Model., 2014

Editorial.
J. Bioinform. Comput. Biol., 2014

Reference-free prediction of rearrangement breakpoint reads.
Bioinform., 2014

2013
Generalized Centroid Estimators in Bioinformatics
CoRR, 2013

PBSIM: PacBio reads simulator - toward accurate genome assembly.
Bioinform., 2013

Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions.
Bioinform., 2013

2012
RecountDB: a database of mapped and count corrected transcribed sequences.
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

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

Improving the accuracy of predicting secondary structure for aligned RNA sequences.
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
Conic Programming for Multitask Learning.
IEEE Trans. Knowl. Data Eng., 2010

A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures.
J. Bioinform. Comput. Biol., 2010

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

2009
CENTROIDFOLD: a web server for RNA secondary structure prediction.
Nucleic Acids Res., 2009

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.
Nucleic Acids Res., 2009

A local multiple alignment method for detection of non-coding RNA sequences.
Bioinform., 2009

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score.
Bioinform., 2009

Predictions of RNA secondary structure by combining homologous sequence information.
Bioinform., 2009

Prediction of RNA secondary structure using generalized centroid estimators.
Bioinform., 2009

2008
Software.ncrna.org: web servers for analyses of RNA sequences.
Nucleic Acids Res., 2008

A fast structural multiple alignment method for long RNA sequences.
BMC Bioinform., 2008

Directed acyclic graph kernels for structural RNA analysis.
BMC Bioinform., 2008

Rfold: an exact algorithm for computing local base pairing probabilities.
Bioinform., 2008

2007
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
Nucleic Acids Res., 2007

Stem Kernels for RNA Sequence Analyses.
J. Bioinform. Comput. Biol., 2007

Murlet: a practical multiple alignment tool for structural RNA sequences.
Bioinform., 2007

Robust prediction of consensus secondary structures using averaged base pairing probability matrices.
Bioinform., 2007

Multi-Task Learning via Conic Programming.
Proceedings of the Advances in Neural Information Processing Systems 20, 2007

Stem Kernels for RNA Sequence Analyses.
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
Network-based de-noising improves prediction from microarray data.
BMC Bioinform., 2006

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.
Bioinform., 2006

Mining frequent stem patterns from unaligned RNA sequences.
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

Selective integration of multiple biological data for supervised network inference.
Bioinform., 2005

2004
Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data.
Neural Process. Lett., 2004

A New Variational Framework for Rigid-Body Alignment.
Proceedings of the Structural, 2004

2003
The em Algorithm for Kernel Matrix Completion with Auxiliary Data.
J. Mach. Learn. Res., 2003

GA-Based Inference of Euler Angles for Single Particle Analysis.
Proceedings of the Genetic and Evolutionary Computation, 2003

2002
Approximating Incomplete Kernel Matrices by the em Algorithm
CoRR, 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
The Multi-Scale 3D-1D Compatibility Scoring for Inverse Protein Folding Protein.
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
Prediction of protein secondary structure by the hidden Markov model.
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

A Multi-Level Description Scheme of Protein Conformation.
Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology, 1993

1992
Dividing the distributions of HMM and linear interpolation in speech recognition.
Proceedings of the 1992 IEEE International Conference on Acoustics, 1992

1990
A new method of consonant detection and classification using neural networks.
Proceedings of the First International Conference on Spoken Language Processing, 1990

Voiced-unvoiced classification using weighted distance measures.
Proceedings of the First International Conference on Spoken Language Processing, 1990


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