Kiyoshi Asai

发表

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

Yasuo Tabei, Kiyoshi Asai, K. Asai, 2009, Bioinform..

COSMO: A dynamic programming algorithm for multicriteria codon optimization

Kiyoshi Asai, Akito Taneda, K. Asai, 2020, Computational and structural biotechnology journal.

RNAfamProb Plus NeoFold: Estimations of Posterior Probabilities on RNA Structural Alignment and RNA Secondary Structures with Incorporating Homologous-RNA Sequences

Masaki Tagashira, Kiyoshi Asai, K. Asai, 2019, bioRxiv.

A New Direction for the Computational Biology Research Center

Kiyoshi Asai, 2007 .

Conic Programming for Multitask Learning

Masashi Sugiyama, Hisashi Kashima, Tsuyoshi Kato, 2010, IEEE Transactions on Knowledge and Data Engineering.

Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences

Masato Ishikawa, Kenta Nakai, Kiyoshi Asai, 1998, Bioinform..

Marginalized kernels for RNA sequence data analysis.

Kiyoshi Asai, Koji Tsuda, Taishin Kin, 2002, Genome informatics. International Conference on Genome Informatics.

Multi-Task Learning via Conic Programming

Masashi Sugiyama, Hisashi Kashima, Tsuyoshi Kato, 2007, NIPS.

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

Kiyoshi Asai, Hisanori Kiryu, Taishin Kin, 2007, Bioinform..

BESPA: Software Tools for Three-Dimensional Structure Reconstruction from Single Particle Images of Proteins

Kiyoshi Asai, Yutaka Ueno, Chikara Sato, 1999 .

Protein structure prediction based on multi-level description

Akira Aiba, Masato Ishikawa, Kiyoshi Asai, 1994, 1994 Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences.

Predictions of RNA secondary structure by combining homologous sequence information

Kiyoshi Asai, Michiaki Hamada, Hisanori Kiryu, 2009, Bioinform..

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

Koichiro Yamada, Kiyoshi Asai, Martin C. Frith, 2011, Nucleic Acids Res..

A Multi-Level Description Scheme of Protein Conformation

Stephen T. C. Wong, Masato Ishikawa, Kiyoshi Asai, 1993, ISMB.

Editorial

Chuan Yi Tang, Paul Horton, Kiyoshi Asai, 2014, J. Bioinform. Comput. Biol..

Learning chromatin states with factorized information criteria

Kiyoshi Asai, Michiaki Hamada, Ryohei Fujimaki, 2015, Bioinform..

A three-dimensional animation system for protein folding simulation

Masato Ishikawa, Kiyoshi Asai, Kentaro Onizuka, 1994, 1994 Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences.

Network-based de-noising improves prediction from microarray data

Paul Horton, Tsuyoshi Kato, Kiyoshi Asai, 2006, BMC Bioinformatics.

The em Algorithm for Kernel Matrix Completion with Auxiliary Data

Kiyoshi Asai, Shotaro Akaho, Koji Tsuda, 2003, J. Mach. Learn. Res..

RecountDB : a database of mapped and count corrected transcribed sequences

Paul Horton, Kiyoshi Asai, Martin C. Frith, 2011 .

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

Yasuo Tabei, Kiyoshi Asai, Koji Tsuda, 2006, Bioinform..

A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures

Kiyoshi Asai, Michiaki Hamada, Yasubumi Sakakibara, 2009, WABI.

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

Kiyoshi Asai, Michiaki Hamada, Hisanori Kiryu, 2009, Bioinform..

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

Tatsuya Akutsu, Kiyoshi Asai, Michiaki Hamada, 2011, Bioinform..

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

Kiyoshi Asai, Hisanori Kiryu, K. Asai, 2012, Bioinform..

Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method

Kiyoshi Asai, Kazuhiko Fukui, Takatsugu Hirokawa, 2014, J. Chem. Inf. Model..

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA)

Kiyoshi Asai, Michiaki Hamada, K. Asai, 2012, J. Comput. Biol..

CentroidFold: a web server for RNA secondary structure prediction

Kiyoshi Asai, Michiaki Hamada, Kengo Sato, 2009, Nucleic Acids Res..

Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions

Kiyoshi Asai, Masanori Arita, Kinya Okada, 2007, APBC.

Evolutionary design of multiple genes encoding the same protein

Kiyoshi Asai, Akito Taneda, Satoshi Kamegai, 2017, Bioinform..

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

Aya Kojima, Kiyoshi Asai, Takashi Komori, 2006, Nucleic Acids Res..

The Multi-Scale 3D-1D Compatibility Scoring for Inverse Protein Folding Protein

Kiyoshi Asai, Kentaro Onizuka, Masato Ishikawa, 1994, ISMB.

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

Chuan Yi Tang, Paul Horton, Kiyoshi Asai, 2014, Journal of Bioinformatics and Computational Biology.

Secure Division Protocol and Applications to Privacy-preserving Chi-squared Tests

Koji Nuida, Goichiro Hanaoka, Kiyoshi Asai, 2018, 2018 International Symposium on Information Theory and Its Applications (ISITA).

Reference-free prediction of rearrangement breakpoint reads

Kiyoshi Asai, Kana Shimizu, Michiaki Hamada, 2014, Bioinform..

Sorting next generation sequencing data improves compression effectiveness

Kiyoshi Asai, Raymond Wan, K. Asai, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

Guest editorial for the 25th International Conference on Genome Informatics (GIW/ISCB-Asia 2014)

Chuan Yi Tang, Paul Horton, Kiyoshi Asai, 2015, TCBB.

Reconstructing Metabolic Pathways with New Enzyme Classification

Kiyoshi Asai, Masanori Arita, Takaaki Nishioka, 2000, German Conference on Bioinformatics.

PBSIM2: a simulator for long-read sequencers with a novel generative model of quality scores

Kiyoshi Asai, Michiaki Hamada, Yukiteru Ono, 2020, Bioinform..

Rfold: an exact algorithm for computing local base pairing probabilities

Kiyoshi Asai, Hisanori Kiryu, Taishin Kin, 2008, Bioinform..

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

Kiyoshi Asai, Ryota Mori, Junichi Iwakiri, 2018, BMC Bioinformatics.

Gene Discovery of G-Protein Coupled Receptors from Human Genome

Toshiyuki Sato, Kiyoshi Asai, Shuichi Tsutsumi, 2000 .

Directed acyclic graph kernels for structural RNA analysis

Kiyoshi Asai, Yasubumi Sakakibara, Kengo Sato, 2008, BMC Bioinformatics.

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

Kiyoshi Asai, Martin C. Frith, Michiaki Hamada, 2011, Bioinform..

Processing sequence annotation data using the Lua programming language.

Kiyoshi Asai, Yutaka Ueno, Masanori Arita, 2003, Genome informatics. International Conference on Genome Informatics.

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

Kenji Suzuki, Kiyoshi Asai, Hisanori Kiryu, 2011, Bioinform..

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

Kiyoshi Asai, Anish M. S. Shrestha, Naruki Yoshikawa, 2018, Bioinform..

Privacy-preserving search for chemical compound databases

Goichiro Hanaoka, Kiyoshi Asai, Kana Shimizu, 2015, BMC Bioinformatics.

Prediction of RNA secondary structure using generalized centroid estimators

Kiyoshi Asai, Michiaki Hamada, Hisanori Kiryu, 2009, Bioinform..

Automatic Discovery of Hidden Markov Representations for Functional Sites within DNA Sequences

Masato Ishikawa, Kiyoshi Asai, Tetsushi Yada, 1996 .

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

Tatsuya Akutsu, Kiyoshi Asai, Yasubumi Sakakibara, 2012, Bioinform..

Generalized Centroid Estimators in Bioinformatics

Kiyoshi Asai, Michiaki Hamada, Wataru Iwasaki, 2011, PloS one.

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

Yasuo Tabei, Hiroshi Matsui, Kiyoshi Asai, 2008, Nucleic Acids Res..

Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

Kiyoshi Asai, Michiaki Hamada, Kengo Sato, 2010, BMC Bioinformatics.

Marginalized kernels for biological sequences

Kiyoshi Asai, Koji Tsuda, Taishin Kin, 2002, ISMB.

A new method of consonant detection and classification using neural networks

Shigeru Chiba, Kiyoshi Asai, K. Asai, 1990, ICSLP.

Extracting relations between promoter sequences and their strengths from microarray data

Kiyoshi Asai, Hisanori Kiryu, Taku Oshima, 2005, Bioinform..

In search of true reads: A classification approach to next generation sequencing data selection

Kiyoshi Asai, Martin C. Frith, Edward Wijaya, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

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

Tatsuya Akutsu, Kiyoshi Asai, Michiaki Hamada, 2010, Bioinform..

Learning Kernels from Distance Constraints

Tsuyoshi Kato, Kiyoshi Asai, Wataru Fujibuchi, 2006 .

Prediction of protein secondary structure by the hidden Markov model

Satoru Hayamizu, Kiyoshi Asai, Ken'ichi Handa, 1993, Comput. Appl. Biosci..

Approximating Incomplete Kernel Matrices by the em Algorithm

Kiyoshi Asai, Shotaro Akaho, Koji Tsuda, 2002, ArXiv.

A New Plug-In Software Architecture Applied for a Portable Molecular Structure Browser

Kiyoshi Asai, Yutaka Ueno, 1997, ISMB.

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

Kiyoshi Asai, Satoshi Kamegai, Goro Terai, 2016, Bioinform..

A Non-Parametric Bayesian Approach for Predicting RNA Secondary Structures

Kiyoshi Asai, Michiaki Hamada, Yasubumi Sakakibara, 2009, J. Bioinform. Comput. Biol..

PBSIM: PacBio reads simulator - toward accurate genome assembly

Kiyoshi Asai, Michiaki Hamada, Yukiteru Ono, 2013, Bioinform..

Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data

Kiyoshi Asai, Koji Tsuda, Shinsuke Uda, 2004, Neural Processing Letters.

Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities

Akihiko Konagaya, Masato Ishikawa, Hidetoshi Tanaka, 1993, ISMB.

Selective integration of multiple biological data for supervised network inference

Tsuyoshi Kato, Kiyoshi Asai, Koji Tsuda, 2005, Bioinform..

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

Kiyoshi Asai, Michiaki Hamada, K. Asai, 2014, Methods in molecular biology.

Improving the accuracy of predicting secondary structure for aligned RNA sequences

Kiyoshi Asai, Michiaki Hamada, Kengo Sato, 2010, Nucleic Acids Res..

Voiced-unvoiced classification using weighted distance measures

Shigeru Chiba, Kiyoshi Asai, K. Asai, 1990, ICSLP.

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

Kiyoshi Asai, Michiaki Hamada, Junichi Iwakiri, 2013, Bioinform..

Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model

Kiyoshi Asai, Junichi Iwakiri, Hiroki Takizawa, 2020, Bioinform..

Stem Kernels for RNA Sequence Analyses

Kiyoshi Asai, Yasubumi Sakakibara, Kengo Sato, 2007, BIRD.

Stem Kernels for RNA Sequence Analyses

Kiyoshi Asai, Kris Popendorf, Yasubumi Sakakibara, 2007, BIRD.

A semi-supervised learning approach for RNA secondary structure prediction

Kiyoshi Asai, Michiaki Hamada, Haruka Yonemoto, 2015, Comput. Biol. Chem..

Mining frequent stem patterns from unaligned RNA sequences

Taku Kudo, Kiyoshi Asai, Koji Tsuda, 2006, Bioinform..

GA-Based Inference of Euler Angles for Single Particle Analysis

Hitoshi Iba, Kiyoshi Asai, Yutaka Ueno, 2003, GECCO.

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

Tatsuya Akutsu, Kiyoshi Asai, Kengo Sato, 2012, Nucleic Acids Res..

Murlet: a practical multiple alignment tool for structural RNA sequences

Yasuo Tabei, Kiyoshi Asai, Hisanori Kiryu, 2007, Bioinform..

Training alignment parameters for arbitrary sequencers with LAST-TRAIN

Kiyoshi Asai, Martin C. Frith, Michiaki Hamada, 2016, Bioinform..

The 3rd DBCLS BioHackathon : Improving life science with semantic web technologies

Akira R. Kinjo, Fumikazu Konishi, Hammad Afzal, 2013 .

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

Kiyoshi Asai, Nozomi Nagano, Goro Terai, 2015, Bioinform..

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

Akira R. Kinjo, Kiyoko F. Aoki-Kinoshita, Kiyoshi Asai, 2010, J. Biomed. Semant..

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

Kiyoshi Asai, Raymond Wan, Vo Ngoc Anh, 2012, Bioinform..

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

Kiyoshi Asai, Tsukasa Fukunaga, Michiaki Hamada, 2016, Nucleic Acids Res..

Maximum Likelihood Superposition of Protein Structures

Tsuyoshi Kato, Kiyoshi Asai, Koji Tsuda, 2003 .

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

Kiyoshi Asai, Junichi Iwakiri, Hiroki Takizawa, 2020, BMC Bioinformatics.

Modeling splicing sites with pairwise correlations

Kiyoshi Asai, Masanori Arita, Koji Tsuda, 2002, ECCB.

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

Hitoshi Iba, Kiyoshi Asai, Yutaka Ueno, 2002, Genome informatics. International Conference on Genome Informatics.

A fast structural multiple alignment method for long RNA sequences

Yasuo Tabei, Kiyoshi Asai, Hisanori Kiryu, 2008, BMC Bioinformatics.

Comprehensive prediction of lncRNA–RNA interactions in human transcriptome

Kiyoshi Asai, Michiaki Hamada, Junichi Iwakiri, 2016, BMC Genomics.

A New Variational Framework for Rigid-Body Alignment

Tsuyoshi Kato, Kiyoshi Asai, Koji Tsuda, 2004, SSPR/SPR.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Fumikazu Konishi, Hammad Afzal, Gos Micklem, 2013, J. Biomed. Semant..

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

Kiyoshi Asai, Takashi Komori, Yukiteru Ono, 2008, Nucleic Acids Res..

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

Kiyoshi Asai, Shigehiko Kanaya, Kinya Okada, 2005, Bioinform..

ConsAlifold: considering RNA structural alignments improves prediction accuracy of RNA consensus secondary structures

Masaki Tagashira, Kiyoshi Asai, 2022, Bioinform..

Efficient calculation of exact probability distributions of integer features on RNA secondary structures

Kiyoshi Asai, Michiaki Hamada, K. Asai, 2014, BMC Genomics.

Improved Accuracy in RNA-Protein Rigid Body Docking by Incorporating Force Field for Molecular Dynamics Simulation into the Scoring Function.

Kiyoshi Asai, Michiaki Hamada, Junichi Iwakiri, 2016, Journal of chemical theory and computation.

Kernel Analysis for Noisy Microarray Data

Kiyoshi Asai, Wataru Fujibuchi, Tsuyoshi Kato, 2006 .

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

Tatsuya Akutsu, Kiyoshi Asai, Michiaki Hamada, 2010, Bioinform..

Difficulties in vector-parallel processing of Monte Carlo codes

Kiyoshi Asai, Kenji Higuchi, Yukihiro Hasegawa, 1997 .

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

Kiyoshi Asai, Michiaki Hamada, K. Asai, 2012, Nucleic acids research.

Genomics of Aspergillus oryzae

Kiyoshi Asai, Katsuhiko Kitamoto, Masashi Kato, 2007, Bioscience, biotechnology, and biochemistry.

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

Kiyoshi Asai, Toutai Mituyama, Mikiko C. Siomi, 2008, Proceedings of the National Academy of Sciences.

MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data

Kiyoshi Asai, Katsuhisa Horimoto, Nozomi Nagano, 2013, PloS one.

A mostly traditional approach improves alignment of bisulfite-converted DNA

Kiyoshi Asai, Martin C. Frith, M. Frith, 2012, Nucleic acids research.

Motif-Independent Prediction of a Secondary Metabolism Gene Cluster Using Comparative Genomics: Application to Sequenced Genomes of Aspergillus and Ten Other Filamentous Fungal Species

Kiyoshi Asai, Itaru Takeda, Hideaki Koike, 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

Classification of Proteins via Successive State Splitting Algorithm of Hidden Markov Network

Hidetoshi Tanaka, Kiyoshi Asai, Kentaro Onizuka, 1993 .

A New Variational Framework for Rigid -

Kiyoshi Asai, Koji Tsuda, Kentaro Tomii, 2004 .

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

Kiyoshi Asai, Michiaki Hamada, Yoshikazu Nakamura, 2011, Biochimie.

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

Kiyoshi Asai, Taishin Kin, Taishin Kin, 2007, Biochemical and biophysical research communications.

Finding Protein-Coding Genes through Human Polymorphisms

Paul Horton, Kiyoshi Asai, Martin C. Frith, 2013, PloS one.

Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features

Kiyoshi Asai, Toutai Mituyama, Goro Terai, 2012, PloS one.

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

Kiyoshi Asai, Tsukasa Fukunaga, Haruka Ozaki, 2014, Genome Biology.

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

Hitoshi Iba, Kiyoshi Asai, Yutaka Ueno, 2003, Bio Systems.