Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome (Q24563506)

1

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Wayne A Decatur

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Carrie A Davis

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Manuel Ares

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Maurille J Fournier

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Todd M Lowe

Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics

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language of work or name

English

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publication date

2004

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published in

Nucleic Acids Research

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volume

32

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issue

14

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page(s)

4281-96

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cites work

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Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus.

24 March 2017

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Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs

24 March 2017

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Identification of novel small RNAs using comparative genomics and microarrays

24 March 2017

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Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

24 March 2017

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Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

24 March 2017

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Basic local alignment search tool

24 March 2017

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T-Coffee: A novel method for fast and accurate multiple sequence alignment

24 March 2017

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Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast.

24 March 2017

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Pseudouridylation (Psi) of U2 snRNA in S. cerevisiae is catalyzed by an RNA-independent mechanism

24 March 2017

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Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs

24 March 2017

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A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae

24 March 2017

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The tandem affinity purification (TAP) method: a general procedure of protein complex purification

24 March 2017

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The expanding snoRNA world

24 March 2017

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Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions

24 March 2017

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Large-scale transcriptional activity in chromosomes 21 and 22

24 March 2017

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microRNAs: tiny regulators with great potential

24 March 2017

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Computational identification of noncoding RNAs in E. coli by comparative genomics

24 March 2017

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Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

24 March 2017

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RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse

24 March 2017

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Homologs of small nucleolar RNAs in Archaea

24 March 2017

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Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes

24 March 2017

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A computational screen for methylation guide snoRNAs in yeast

24 March 2017

1 reference

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Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs

24 March 2017

1 reference

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The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation

24 March 2017

1 reference

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SGD: Saccharomyces Genome Database

24 March 2017

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Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA

7 April 2017

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The RNA world of the nucleolus: two major families of small RNAs defined by different box elements with related functions

7 April 2017

1 reference

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Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis

7 April 2017

1 reference

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Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in the peptidyl transferase center

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

27 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

Ribosomal RNA pseudouridines and pseudouridine synthases

27 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

Mapping pseudouridines in RNA molecules

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

RNAMotif, an RNA secondary structure definition and search algorithm

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

A comprehensive database for the small nucleolar RNAs from Saccharomyces cerevisiae

27 September 2017

1 reference

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A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

Analysis of the yeast genome: identification of new non-coding and small ORF-containing RNAs

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

Efficient association of U2 snRNPs with pre-mRNA requires an essential U2 RNA structural element

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

Pattern searching/alignment with RNA primary and secondary structures: an effective descriptor for tRNA

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

From sequences to shapes and back: a case study in RNA secondary structures.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=514388

28 November 2018

Identifiers

DOI

10.1093/NAR/GKH768

1 reference

3398546

3398546

1 reference

1 reference

1 reference