R<scp>NA</scp> Secondary Structure Analysis Using the Vienna <scp>RNA</scp> Package

Hofacker, Ivo L.

doi:10.1002/0471250953.bi1202s26

Cited by 136 publications

(106 citation statements)

References 19 publications

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“…Recent years have witnessed the emergence of elegant RNA folding models that accurately capture secondary structure formation of loops and simple helices (8)(9)(10)(11)(12). However, more complex motifs, such as multiloops, remain challenging to model (1), and thus, algorithmically designed RNAs frequently misfold in vitro.…”

mentioning

confidence: 99%

RNA design rules from a massive open laboratory

Lee¹,

Kladwang²,

Lee³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

289

234

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Significance Self-assembling RNA molecules play critical roles throughout biology and bioengineering. To accelerate progress in RNA design, we present EteRNA, the first internet-scale citizen science “game” scored by high-throughput experiments. A community of 37,000 nonexperts leveraged continuous remote laboratory feedback to learn new design rules that substantially improve the experimental accuracy of RNA structure designs. These rules, distilled by machine learning into a new automated algorithm EteRNABot, also significantly outperform prior algorithms in a gauntlet of independent tests. These results show that an online community can carry out large-scale experiments, hypothesis generation, and algorithm design to create practical advances in empirical science.

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mentioning

confidence: 99%

RNA design rules from a massive open laboratory

Lee¹,

Kladwang²,

Lee³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

289

234

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“…Growing evidence indicates that synonymous variation in coding regions can alter mRNA levels by affecting mRNA stability. 35,36 An in silico analysis performed by using RNA structure software package (version 4.5) revealed that c.621C>T greatly alters the predicted PAR-2 mRNA secondary structure (Fig 3, A). The calculated minimum free energy level of the PAR-2 mRNA with the ''T'' allele at c.621 was approximately 47.16 kcal/mol lower than that of the mRNA with the ''C'' allele, leading to the expectation that PAR-2 mRNA with the ''T'' allele is more stable than the mRNA with the ''C'' allele.…”

Section: Discussionmentioning

confidence: 99%

“…34,35 Full-length mRNA sequences were compared with the wild-type mRNA sequence. The amount of minimum free energy of centroid secondary structure in the dot-bracket notation was calculated.…”

Section: Mrna Structure Modeling Of Par-2 Sequencesmentioning

confidence: 99%

A synonymous variation in protease-activated receptor-2 is associated with atopy in Korean children

Lee

Kim

Gee

et al. 2011

Journal of Allergy and Clinical Immunology

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“…The potential variations in folding of the RNA secondary structure caused by the synonymous and the non-synonymous mutation of AIRE variants were identified using the Vienna RNA package software [29,31].…”

Section: Quantitative Analysis Of Tcr Clonotypes By Dna Amplificationmentioning

confidence: 99%

The role of AIRE polymorphisms in melanoma

Conteduca

Ferrera

Pastorino

et al. 2010

Clinical Immunology

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Polymorphisms of AIRE, a transcription factor that up-regulates intrathymic expression of tissue-specific antigens including melanoma-associated antigens (MAAs), may variably affect the selection of MAAs-specific thymocytes, generating T-cell repertoires protecting or predisposing individuals to melanoma. We found that AIRE single nucleotide polymorphisms (SNPs) rs1055311, rs1800520 and rs1800522 were significantly more frequent in healthy subjects than in melanoma patients, independently from sex, age and stages of melanoma. The presence of these SNPs was associated with increased frequency of two T-cell clonotypes specific for MAGE-1 linking their protective effect to selection/expansion of MAA-specific T cells. Interestingly, mRNA transcribed on the rs1800520 SNP showed increased free energy than the wild type suggesting that its reduced stability may be responsible for the different activity of the polymorphic AIRE molecule. This finding may contribute at identifying subjects with increased risk of developing melanoma or patients with melanoma that may take benefit from immunotherapy.

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RNA Secondary Structure Analysis Using the Vienna RNA Package

Cited by 136 publications

References 19 publications

RNA design rules from a massive open laboratory

RNA design rules from a massive open laboratory

A synonymous variation in protease-activated receptor-2 is associated with atopy in Korean children

The role of AIRE polymorphisms in melanoma

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