(Q33777987)

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Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

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scholarly article

1 reference

Europe PubMed Central

29 July 2017

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data (English)

1 reference

Europe PubMed Central

29 July 2017

Caenorhabditis elegans

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high-throughput sequencing

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based on heuristic

inferred from title

object named as

Joel Rozowsky

9

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object named as

Frank Slack

13

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Mark Bender Gerstein

17

object named as

Mark B Gerstein

1 reference

Europe PubMed Central

29 July 2017

16

object named as

Valerie Reinke

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Europe PubMed Central

29 July 2017

Michael P. Snyder

14

object named as

Michael Snyder

1 reference

Europe PubMed Central

29 July 2017

Ladeana Hillier

5

object named as

Ladeana W Hillier

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Europe PubMed Central

29 July 2017

15

object named as

Robert H Waterston

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Europe PubMed Central

29 July 2017

David M. Miller III

12

object named as

David M Miller

1 reference

Europe PubMed Central

29 July 2017

11

object named as

Masaomi Kato

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Europe PubMed Central

29 July 2017

author name string

Zhi John Lu

1

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Europe PubMed Central

29 July 2017

Kevin Y Yip

2

1 reference

Europe PubMed Central

29 July 2017

Guilin Wang

3

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Europe PubMed Central

29 July 2017

Chong Shou

4

1 reference

Europe PubMed Central

29 July 2017

Ekta Khurana

6

1 reference

Europe PubMed Central

29 July 2017

Ashish Agarwal

7

1 reference

Europe PubMed Central

29 July 2017

Raymond Auerbach

8

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Europe PubMed Central

29 July 2017

Chao Cheng

10

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Europe PubMed Central

29 July 2017

publication date

22 December 2010

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Europe PubMed Central

29 July 2017

Genome Research

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Europe PubMed Central

29 July 2017

21

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29 July 2017

276-285

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29 July 2017

2

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Europe PubMed Central

29 July 2017

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

1 reference

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4 July 2018

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response

1 reference

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4 July 2018

Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data

1 reference

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4 July 2018

De novo prediction of structured RNAs from genomic sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

TERRA: telomeric repeat-containing RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Unlocking the secrets of the genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Infernal 1.0: inference of RNA alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Rfam: updates to the RNA families database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Specific expression of long noncoding RNAs in the mouse brain

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

The phylogenetic relationships of Caenorhabditis and other rhabditids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Biogenesis and germline functions of piRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

miRBase: tools for microRNA genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Structured RNAs in the ENCODE selected regions of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Identification and classification of conserved RNA secondary structures in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Accurate multiplex polony sequencing of an evolved bacterial genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Genome sequencing in microfabricated high-density picolitre reactors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Fast and reliable prediction of noncoding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

MSARI: multiple sequence alignments for statistical detection of RNA secondary structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

MicroRNAs: genomics, biogenesis, mechanism, and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Widespread selection for local RNA secondary structure in coding regions of bacterial genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

Noncoding RNA gene detection using comparative sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

4 July 2018

ddbRNA: detection of conserved secondary structures in multiple alignments.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

30 October 2018

Intronic MicroRNA: Discovery and Biological Implications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

30 October 2018

Prediction of structured non-coding RNAs in the genomes of the nematodesCaenorhabditis elegans andCaenorhabditis briggsae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3032931

30 October 2018

Identifiers

10.1101/GR.110189.110

1 reference

Europe PubMed Central

29 July 2017

1 reference

Europe PubMed Central

29 July 2017

1 reference

Europe PubMed Central

29 July 2017

ResearchGate publication ID

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