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Secondary structure prediction for RNA sequences including N<sup>6</sup>-methyladenosine.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28817-4
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- Article
Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment.
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- International Journal of Molecular Sciences, 2022, v. 23, n. 5, p. 2452, doi. 10.3390/ijms23052452
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- Article
The RNA Ontology Consortium: An open invitation to the RNA community.
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- Journal of Nuclear Medicine Technology, 2006, v. 34, n. 1, p. 1
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- Article
Identification of new high affinity targets for Roquin based on structural conservation.
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- Nucleic Acids Research, 2018, v. 46, n. 22, p. 12109, doi. 10.1093/nar/gky908
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- Article
Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription.
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- Nucleic Acids Research, 2018, v. 46, n. 13, p. 6401, doi. 10.1093/nar/gky529
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- Article
Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.
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- Nucleic Acids Research, 2018, v. 46, n. 10, p. 4883, doi. 10.1093/nar/gky270
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- Article
Modeling RNA secondary structure folding ensembles using SHAPE mapping data.
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- Nucleic Acids Research, 2018, v. 46, n. 1, p. 314, doi. 10.1093/nar/gkx1057
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- Article
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.
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- Nucleic Acids Research, 2017, v. 45, n. 20, p. 11570, doi. 10.1093/nar/gkx815
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- Article
Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best.
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- Nucleic Acids Research, 2017, v. 45, n. 14, p. 8541, doi. 10.1093/nar/gkx512
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- Article
A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction.
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- Nucleic Acids Research, 2017, v. 45, n. 10, p. 6168, doi. 10.1093/nar/gkx170
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- Article
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.
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- Nucleic Acids Research, 2015, v. 43, n. 15, p. 7247, doi. 10.1093/nar/gkv706
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- Article
Dynalign II: common secondary structure prediction for RNA homologs with domain insertions.
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- Nucleic Acids Research, 2014, v. 42, n. 22, p. 13939, doi. 10.1093/nar/gku1172
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- Article
RNAstructure: web servers for RNA secondary structure prediction and analysis.
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- Nucleic Acids Research, 2013, v. 41, p. W471, doi. 10.1093/nar/gkt290
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- Article
Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure.
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- Nucleic Acids Research, 2013, v. 41, n. 6, p. 3819, doi. 10.1093/nar/gkt063
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- Article
Statistical evaluation of improvement in RNA secondary structure prediction.
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- Nucleic Acids Research, 2012, v. 40, n. 4, p. e26, doi. 10.1093/nar/gkr1081
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- Article
NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure.
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- Nucleic Acids Research, 2010, v. 38, p. D280, doi. 10.1093/nar/gkp892
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- Article
Stochastic sampling of the RNA structural alignment space.
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- Nucleic Acids Research, 2009, v. 37, n. 12, p. 4063, doi. 10.1093/nar/gkp276
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- Article
PARTS: Probabilistic Alignment for RNA joinT Secondary structure prediction.
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- Nucleic Acids Research, 2008, v. 36, n. 7, p. 2406, doi. 10.1093/nar/gkn043
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- Article
Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.
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- Nucleic Acids Research, 2008, v. 36, n. 11, p. 3738
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- Article
Efficient siRNA selection using hybridization thermodynamics.
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- Nucleic Acids Research, 2008, v. 36, n. 2, p. 640
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- Article
OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics.
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- Nucleic Acids Research, 2008, v. 36, n. suppl_2, p. W104
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- Article
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation.
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- Nucleic Acids Research, 2006, v. 34, n. 17, p. 4912, doi. 10.1093/nar/gkl472
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- Article
Nearest neighbor parameters for Watson–Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides.
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- Nucleic Acids Research, 2006, v. 34, n. 13, p. 3609, doi. 10.1093/nar/gkl232
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- Article
Secondary structure prediction for RNA sequences including N<sup>6</sup>-methyladenosine.
- Published in:
- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28817-4
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- Publication type:
- Article
Specific length and structure rather than high thermodynamic stability enable regulatory mRNA stem-loops to pause translation.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-28600-5
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- Article
A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-021-27790-8
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- Article
FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing.
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- Nature Methods, 2010, v. 7, n. 12, p. 995, doi. 10.1038/nmeth.1529
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- Article
A sequence similar to tRNA<sub>3</sub><sup>Lys</sup> gene is embedded in HIV-1 U3–R and promotes minus-strand transfer.
- Published in:
- Nature Structural & Molecular Biology, 2010, v. 17, n. 1, p. 83, doi. 10.1038/nsmb.1687
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- Article
Predicting RNA secondary structure by free energy minimization.
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- Theoretical Chemistry Accounts: Theory, Computation, & Modeling, 2006, v. 116, n. 1-3, p. 160, doi. 10.1007/s00214-005-0027-7
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- Article
RNA design via structure-aware multifrontier ensemble optimization.
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- Bioinformatics, 2023, v. 39, p. i563, doi. 10.1093/bioinformatics/btad252
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- Article
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families.
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- Bioinformatics, 2022, v. 38, n. 16, p. 3892, doi. 10.1093/bioinformatics/btac415
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- Article
Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41799-1
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- Article
Secondary structures that regulate mRNA translation provide insights for ASO-mediated modulation of cardiac hypertrophy.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41799-1
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- Article
Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures.
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- PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0130200
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- Article
Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing.
- Published in:
- eLife, 2022, p. 1, doi. 10.7554/eLife.73888
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- Article
CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation.
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- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12028-5
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- Article
mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances.
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- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06792-z
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- Article
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences.
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- BMC Bioinformatics, 2011, v. 12, n. 1, p. 108, doi. 10.1186/1471-2105-12-108
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- Article
RNAstructure: software for RNA secondarystructure prediction and analysis.
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- BMC Bioinformatics, 2010, v. 11, p. 129, doi. 10.1186/1471-2105-11-129
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- Article
Genome-Wide DNA Changes Acquired by Candida albicans Caspofungin-Adapted Mutants.
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- Microorganisms, 2023, v. 11, n. 8, p. 1870, doi. 10.3390/microorganisms11081870
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- Article
The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes.
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- Nucleic Acids Research, 2005, v. 33, n. 16, p. 5082, doi. 10.1093/nar/gki789
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- Article
Accelerating calculations of RNA secondary structure partition functions using GPUs.
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- Algorithms for Molecular Biology, 2013, v. 8, n. 1, p. 2, doi. 10.1186/1748-7188-8-29
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- Article
In vivo secondary structural analysis of Influenza A virus genomic RNA.
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- Cellular & Molecular Life Sciences, 2023, v. 80, n. 5, p. 1, doi. 10.1007/s00018-023-04764-1
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- Article
Structure-Function Model for Kissing Loop Interactions That Initiate Dimerization of Ty1 RNA.
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- Viruses (1999-4915), 2017, v. 9, n. 5, p. 93, doi. 10.3390/v9050093
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- Article
Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference.
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- Systematic Biology, 2011, v. 60, n. 1, p. 60, doi. 10.1093/sysbio/syq074
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- Article
Bridging the gap between in vitro and in vivo RNA folding.
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- Quarterly Reviews of Biophysics, 2016, v. 49, p. 1, doi. 10.1017/S003358351600007X
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- Article
High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States.
- Published in:
- PLoS Biology, 2008, v. 6, n. 4, p. e96, doi. 10.1371/journal.pbio.0060096
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- Article
Efficient parameter estimation for RNA secondary structure prediction.
- Published in:
- Bioinformatics, 2007, v. 23, n. 13, p. i19, doi. 10.1093/bioinformatics/btm223
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- Article
Predicting a set of minimal free energy RNA secondary structures common to two sequences.
- Published in:
- Bioinformatics, 2005, v. 21, n. 10, p. 2246, doi. 10.1093/bioinformatics/bti349
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- Article
LinearCoFold and LinearCoPartition: linear-time algorithms for secondary structure prediction of interacting RNA molecules.
- Published in:
- Nucleic Acids Research, 2023, v. 51, n. 18, p. e94, doi. 10.1093/nar/gkad664
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- Article