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A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs

International journal of molecular sciences, 2021-03, Vol.22 (5), p.2720

2021

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Ant colony optimization for predicting RNA folding pathways

Computational biology and chemistry, 2019-12, Vol.83, p.107118-107118, Article 107118

2019

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RNA inverse folding using Monte Carlo tree search

BMC bioinformatics, 2017-11, Vol.18 (1), p.468-468, Article 468

2017

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MODENA: a multi-objective RNA inverse folding

Advances and applications in bioinformatics and chemistry, 2011, Vol.4 (default), p.1-12

Taneda, Akito

2011

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COSMO: A dynamic programming algorithm for multicriteria codon optimization

Computational and structural biotechnology journal, 2020-01, Vol.18, p.1811-1818

2020

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An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

BMC bioinformatics, 2008-12, Vol.9 (1), p.521-521, Article 521

Taneda, Akito

2008

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Effects of Host-Adaptive Mutations on Hop Stunt Viroid Pathogenicity and Small RNA Biogenesis

International journal of molecular sciences, 2020-10, Vol.21 (19), p.7383

2020

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Multi-objective optimization for RNA design with multiple target secondary structures

BMC bioinformatics, 2015-09, Vol.16 (1), p.280-280, Article 280

Taneda, Akito

2015

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Accumulation of Potato spindle tuber viroid -specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars

Virology (New York, N.Y.), 2011-04, Vol.413 (1), p.72-83

2011

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RNAi-Mediated Down-Regulation of Dicer-Like 2 and 4 Changes the Response of 'Moneymaker' Tomato to Potato Spindle Tuber Viroid Infection from Tolerance to Lethal Systemic Necrosis, Accompanied by Up-Regulation of miR398, 398a-3p and Production of Excessive Amount of Reactive Oxygen Species

Viruses, 2019-04, Vol.11 (4), p.344

2019

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Riboswitch Design Using MODENA

Methods in molecular biology (Clifton, N.J.), 2025, Vol.2847, p.33

Taneda, Akito

2025

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Characterization of host-dependent mutations of apple fruit crinkle viroid replicating in newly identified experimental hosts suggests maintenance of stem-loop structures in the left-hand half of the molecule is important for replication

Journal of general virology, 2017-03, Vol.98 (3), p.506-516

2017

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Multi-objective pairwise RNA sequence alignment

Bioinformatics, 2010-10, Vol.26 (19), p.2383-2390

TANEDA, Akito

2010

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A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments

IPSJ Transactions on Bioinformatics, 2011, Vol.4, pp.2-8

Taneda, Akito

2011

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Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location

Genome, 2024-01, Vol.67 (1), p.1-12

2024

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Multi-objective genetic algorithm for pseudoknotted RNA sequence design

Frontiers in genetics, 2012, Vol.3, p.36-36

Taneda, Akito

2012

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Evolutionary design of multiple genes encoding the same protein

Bioinformatics (Oxford, England), 2017-06, Vol.33 (11), p.1613-1620

2017

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Endogenous short interfering RNAs of chalcone synthase genes associated with inhibition of seed coat pigmentation in soybean [Glycine max]

Breeding Science, 2009, Vol.59(4), pp.419-426

2009

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Changes in relative expression levels of viroid-specific small RNAs and microRNAs in tomato plants infected with severe and mild symptom-inducing isolates of Potato spindle tuber viroid

Journal of general plant pathology : JGPP, 2015-01, Vol.81 (1), p.49-62

2015

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Characterization of a new Apple dimple fruit viroid variant that causes yellow dimple fruit formation in ‘Fuji’ apple trees

Journal of general plant pathology : JGPP, 2010-10, Vol.76 (5), p.324-330

2010

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Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia

BMC genomics, 2013-01, Vol.14 (1), p.63-63, Article 63

2013

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Adplot: detection and visualization of repetitive patterns in complete genomes

Bioinformatics, 2004-03, Vol.20 (5), p.701-708

TANEDA, Akito

2004

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A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments

Information and Media Technologies, 2011, Vol.6(2), pp.331-337

Taneda, Akito

2011

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Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

Plant molecular biology, 2012-02, Vol.78 (3), p.259-273

2012

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1D-03 Induction mechanisms of RNA silencing of two linked transgenes revealed by deep sequencing analysis

Genes & Genetic Systems, 2011, Vol.86 (6), p.414-414

2011

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A Web Server for Designing Molecular Switches Composed of Two Interacting RNAs

Ant colony optimization for predicting RNA folding pathways

RNA inverse folding using Monte Carlo tree search

MODENA: a multi-objective RNA inverse folding

COSMO: A dynamic programming algorithm for multicriteria codon optimization

An efficient genetic algorithm for structural RNA pairwise alignment and its application to non-coding RNA discovery in yeast

Effects of Host-Adaptive Mutations on Hop Stunt Viroid Pathogenicity and Small RNA Biogenesis

Multi-objective optimization for RNA design with multiple target secondary structures

Accumulation of Potato spindle tuber viroid -specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars

RNAi-Mediated Down-Regulation of Dicer-Like 2 and 4 Changes the Response of 'Moneymaker' Tomato to Potato Spindle Tuber Viroid Infection from Tolerance to Lethal Systemic Necrosis, Accompanied by Up-Regulation of miR398, 398a-3p and Production of Excessive Amount of Reactive Oxygen Species

Riboswitch Design Using MODENA

Characterization of host-dependent mutations of apple fruit crinkle viroid replicating in newly identified experimental hosts suggests maintenance of stem-loop structures in the left-hand half of the molecule is important for replication

Multi-objective pairwise RNA sequence alignment

A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments

Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location

Multi-objective genetic algorithm for pseudoknotted RNA sequence design

Evolutionary design of multiple genes encoding the same protein

Endogenous short interfering RNAs of chalcone synthase genes associated with inhibition of seed coat pigmentation in soybean [Glycine max]

Changes in relative expression levels of viroid-specific small RNAs and microRNAs in tomato plants infected with severe and mild symptom-inducing isolates of Potato spindle tuber viroid

Characterization of a new Apple dimple fruit viroid variant that causes yellow dimple fruit formation in ‘Fuji’ apple trees

Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia

Adplot: detection and visualization of repetitive patterns in complete genomes

A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments

Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

1D-03 Induction mechanisms of RNA silencing of two linked transgenes revealed by deep sequencing analysis

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