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Journal ArticleDOI

Non-coding RNA genes and the modern RNA world.

Sean R. Eddy
- 01 Dec 2001 - 
- Vol. 2, Iss: 12, pp 919-929
TLDR
Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.
Abstract
Non-coding RNA (ncRNA) genes produce functional RNA molecules rather than encoding proteins. However, almost all means of gene identification assume that genes encode proteins, so even in the era of complete genome sequences, ncRNA genes have been effectively invisible. Recently, several different systematic screens have identified a surprisingly large number of new ncRNA genes. Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.

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Citations
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Journal ArticleDOI

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.

TL;DR: TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between sequences with the thermodynamic folding model.
Journal ArticleDOI

Transcriptomics: Advances and approaches

TL;DR: With the development of next-generation high-throughput sequencing technology, transcriptome analysis has been progressively improving the authors' understanding of RNA-based gene regulatory network, and especially the recent advances in this inspiring field of study are discussed.
Journal ArticleDOI

Roles for long non-coding RNAs in physiology and disease

TL;DR: A steadily increasing number of studies could establish functional roles for some of these lncRNAs in developmental processes, cancer and tissue homeostasis.
Journal ArticleDOI

Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures

TL;DR: The pair stochastic tree adjoining grammars (PSTAGs) are proposed for modeling RNA secondary structures including pseudoknots and shown to be more efficient and biologically plausible than by other conventional methods.
Book ChapterDOI

Rich parameterization improves RNA structure prediction

TL;DR: This work argues that with suitable learning techniques, not being tied to features whose weights could be determined experimentally, and having a large enough set of examples, one could define much richer feature representations than was previously explored, while still allowing efficient inference.
References
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Journal ArticleDOI

Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 - 
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI

The sequence of the human genome.

J. Craig Venter, +272 more
- 16 Feb 2001 - 
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Journal ArticleDOI

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

TL;DR: Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin- 4 regulates lin- 14 translation via an antisense RNA-RNA interaction.
Journal ArticleDOI

The Complete Genome Sequence of Escherichia coli K-12

TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Journal ArticleDOI

Genetic regulatory mechanisms in the synthesis of proteins.

TL;DR: The synthesis of enzymes in bacteria follows a double genetic control, which appears to operate directly at the level of the synthesis by the gene of a shortlived intermediate, or messenger, which becomes associated with the ribosomes where protein synthesis takes place.
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Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 -