(Q33636096)

28 July 2017

title

FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome (English)

1 reference

28 July 2017

0 references

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10

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28 July 2017

20

Kerstin Lindblad-Toh

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Jessica Alföldi

18

Jessica Alföldi

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Fabrice Legeai

2

Fabrice Legeai

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Thomas Derrien

Thomas Derrien

22

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Susanna Cirera

Susanna Cirera

11

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Merete Fredholm

12

Merete Fredholm

1 reference

28 July 2017

21

Christophe Hitte

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28 July 2017

8

Edouard Cadieu

1 reference

28 July 2017

1

Valentin Wucher

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28 July 2017

15

Céline Le Béguec

1 reference

28 July 2017

13

Nadine Botherel

1 reference

28 July 2017

7

Vidhya Jagannathan

1 reference

28 July 2017

Benoît Hédan

3

1 reference

28 July 2017

Guillaume Rizk

4

1 reference

28 July 2017

Lætitia Lagoutte

5

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28 July 2017

Tosso Leeb

6

1 reference

28 July 2017

Audrey David

9

1 reference

28 July 2017

Peter A J Leegwater

14

1 reference

28 July 2017

Hille Fieten

16

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28 July 2017

Jeremy Johnson

17

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28 July 2017

Catherine André

19

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28 July 2017

language of work or name

English

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publication date

3 January 2017

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28 July 2017

published in

Nucleic Acids Research

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28 July 2017

volume

45

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28 July 2017

issue

8

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28 July 2017

page(s)

e57

1 reference

Creative Commons Attribution-NonCommercial 4.0 International

28 July 2017

copyright license

start time

4 January 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Bioinformatics Pipeline for Transcriptome Sequencing Analysis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Evolution to the rescue: using comparative genomics to understand long non-coding RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Ensembl comparative genomics resources

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

NONCODE 2016: an informative and valuable data source of long non-coding RNAs.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

GREENC: a Wiki-based database of plant lncRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

LncRNA-ID: Long non-coding RNA IDentification using balanced random forests.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Prediction of long noncoding RNA functions with co-expression network in esophageal squamous cell carcinoma

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Tree of life reveals clock-like speciation and diversification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Pseudogene-derived lncRNAs: emerging regulators of gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Genomic data integration for ecological and evolutionary traits in non-model organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

GATB: Genome Assembly & Analysis Tool Box.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Diversity and dynamics of the Drosophila transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Genome-wide discovery and characterization of maize long non-coding RNAs.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

A single-molecule long-read survey of the human transcriptome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Long noncoding RNAs usher in a new era in the biology of enhancers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

STAR: ultrafast universal RNA-seq aligner

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

GENCODE: the reference human genome annotation for The ENCODE Project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Landscape of transcription in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The emergence of lncRNAs in cancer biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

LUPA: a European initiative taking advantage of the canine genome architecture for unravelling complex disorders in both human and dogs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

BlastR--fast and accurate database searches for non-coding RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Evolution and functions of long noncoding RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The antisense transcriptomes of human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

How does eukaryotic gene prediction work?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Evolution at the nucleotide level: the problem of multiple whole-genome alignment

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The transcriptional landscape of the mammalian genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

ROCR: visualizing classifier performance in R

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Assessing the accuracy of prediction algorithms for classification: an overview

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Quorum sensing triggers the stochastic escape of individual cells from Pseudomonas putida biofilms

21 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1306

Melanoma addiction to the long non-coding RNA SAMMSON.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1306

New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1306

A network-based approach to identify substrate classes of bacterial glycosyltransferases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1306

Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1306

Discovery and annotation of long noncoding RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1306

Transcription: Enhancers make non-coding RNA.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

Using geneid to identify genes

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5416892

[15] k-tuple frequency analysis: From intron/exon discrimination to T-cell epitope mapping

30 October 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKW1306

21 January 2018

Identifiers

DOI

10.1093/NAR/GKW1306

1 reference

28 July 2017

1 reference

28 July 2017

1 reference