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Authors: Kiyoshi Asai
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Journal Article

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

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Masaki Tagashira and Kiyoshi Asai
Bioinformatics, Volume 38, Issue 3, February 2022, Pages 710–719, https://doi.org/10.1093/bioinformatics/btab738
Published: 25 October 2021
Journal Article

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

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Yukiteru Ono and others
Bioinformatics, Volume 37, Issue 5, March 2021, Pages 589–595, https://doi.org/10.1093/bioinformatics/btaa835
Published: 25 September 2020
Journal Article

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

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Hiroki Takizawa and others
Bioinformatics, Volume 36, Issue Supplement_1, July 2020, Pages i227–i235, https://doi.org/10.1093/bioinformatics/btaa469
Published: 13 July 2020
Journal Article

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

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Anish M S Shrestha and others
Bioinformatics, Volume 34, Issue 21, November 2018, Pages 3631–3637, https://doi.org/10.1093/bioinformatics/bty398
Published: 18 May 2018
Journal Article

Evolutionary design of multiple genes encoding the same protein

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Goro Terai and others
Bioinformatics, Volume 33, Issue 11, June 2017, Pages 1613–1620, https://doi.org/10.1093/bioinformatics/btx030
Published: 27 January 2017
Journal Article

Training alignment parameters for arbitrary sequencers with LAST-TRAIN

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Michiaki Hamada and others
Bioinformatics, Volume 33, Issue 6, March 2017, Pages 926–928, https://doi.org/10.1093/bioinformatics/btw742
Published: 23 November 2016
Journal Article

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

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Goro Terai and others
Bioinformatics, Volume 32, Issue 6, March 2016, Pages 828–834, https://doi.org/10.1093/bioinformatics/btv678
Published: 20 November 2015
Journal Article

Learning chromatin states with factorized information criteria

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Michiaki Hamada and others
Bioinformatics, Volume 31, Issue 15, August 2015, Pages 2426–2433, https://doi.org/10.1093/bioinformatics/btv163
Published: 24 March 2015
Journal Article

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

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Takahiro Tsukui and others
Bioinformatics, Volume 31, Issue 7, April 2015, Pages 981–985, https://doi.org/10.1093/bioinformatics/btu753
Published: 19 November 2014
Journal Article

Reference-free prediction of rearrangement breakpoint reads

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Edward Wijaya and others
Bioinformatics, Volume 30, Issue 18, September 2014, Pages 2559–2567, https://doi.org/10.1093/bioinformatics/btu360
Published: 29 May 2014
Journal Article

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

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Junichi Iwakiri and others
Bioinformatics, Volume 29, Issue 20, October 2013, Pages 2524–2528, https://doi.org/10.1093/bioinformatics/btt453
Published: 09 August 2013
Journal Article

PBSIM: PacBio reads simulator—toward accurate genome assembly

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Yukiteru Ono and others
Bioinformatics, Volume 29, Issue 1, January 2013, Pages 119–121, https://doi.org/10.1093/bioinformatics/bts649
Published: 04 November 2012
Journal Article

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

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Kengo Sato and others
Bioinformatics, Volume 28, Issue 24, December 2012, Pages 3218–3224, https://doi.org/10.1093/bioinformatics/bts612
Published: 11 October 2012
Journal Article

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

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Hisanori Kiryu and Kiyoshi Asai
Bioinformatics, Volume 28, Issue 8, April 2012, Pages 1093–1101, https://doi.org/10.1093/bioinformatics/bts097
Published: 28 February 2012
Journal Article

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

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Raymond Wan and others
Bioinformatics, Volume 28, Issue 5, March 2012, Pages 628–635, https://doi.org/10.1093/bioinformatics/btr689
Published: 13 December 2011
Journal Article

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

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Michiaki Hamada and others
Bioinformatics, Volume 27, Issue 22, November 2011, Pages 3085–3092, https://doi.org/10.1093/bioinformatics/btr537
Published: 05 October 2011
Journal Article

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

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Kengo Sato and others
Bioinformatics, Volume 27, Issue 13, July 2011, Pages i85–i93, https://doi.org/10.1093/bioinformatics/btr215
Published: 14 June 2011
Journal Article

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

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Hisanori Kiryu and others
Bioinformatics, Volume 27, Issue 13, July 2011, Pages 1788–1797, https://doi.org/10.1093/bioinformatics/btr276
Published: 29 April 2011
Journal Article

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

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Yuki Kato and others
Bioinformatics, Volume 26, Issue 18, September 2010, Pages i460–i466, https://doi.org/10.1093/bioinformatics/btq372
Published: 04 September 2010
Journal Article

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

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Michiaki Hamada and others
Bioinformatics, Volume 25, Issue 24, December 2009, Pages 3236–3243, https://doi.org/10.1093/bioinformatics/btp580
Published: 06 October 2009