(Q38989042)

25 June 2018

review article

1 reference

title

The state of play in higher eukaryote gene annotation (English)

1 reference

25 June 2018

author

Jonathan M Mudge

series ordinal

1

1 reference

25 June 2018

author name string

Jonathan M Mudge

series ordinal

1

1 reference

8 September 2017

24 October 2016

1 reference

25 June 2018

published in

Nature Reviews Genetics

1 reference

25 June 2018

volume

17

1 reference

25 June 2018

issue

12

1 reference

25 June 2018

page(s)

758-772

1 reference

25 June 2018

https://scigraph.springernature.com/pub.10.1038/nrg.2016.119

exact match

0 references

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30 June 2018

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30 June 2018

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30 June 2018

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30 June 2018

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Ribosomal profiling adds new coding sequences to the proteome

30 June 2018

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CTCF Binding Polarity Determines Chromatin Looping.

30 June 2018

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30 June 2018

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FlyBase: establishing a Gene Group resource for Drosophila melanogaster

30 June 2018

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30 June 2018

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30 June 2018

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30 June 2018

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Creating reference gene annotation for the mouse C57BL6/J genome assembly

30 June 2018

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Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins

30 June 2018

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30 June 2018

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Functional and genetic diversity of leukocyte immunoglobulin-like receptor and implication for disease associations

30 June 2018

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Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

30 June 2018

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Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

30 June 2018

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Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.

30 June 2018

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30 June 2018

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30 June 2018

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30 June 2018

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The awesome power of ribosome profiling.

30 June 2018

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30 June 2018

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Non-coding RNA: what is functional and what is junk?

30 June 2018

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Genomic variation. Impact of regulatory variation from RNA to protein

30 June 2018

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The selection and function of cell type-specific enhancers

30 June 2018

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A copy number variation map of the human genome

30 June 2018

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Proteomics. Tissue-based map of the human proteome

30 June 2018

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30 June 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

2 December 2018

https://api.crossref.org/works/10.1038%2FNRG.2016.119

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7 January 2021

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12 December 2020

based on heuristic

The landscape of long noncoding RNAs in the human transcriptome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible

30 June 2018

1 reference

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VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

30 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Comparative genomics reveals insights into avian genome evolution and adaptation

30 June 2018

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Rfam 12.0: updates to the RNA families database

30 June 2018

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Genenames.org: the HGNC resources in 2015

30 June 2018

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Proteogenomics: concepts, applications and computational strategies

30 June 2018

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30 June 2018

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lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs

30 June 2018

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Widespread intron retention in mammals functionally tunes transcriptomes

30 June 2018

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High-resolution transcriptome analysis with long-read RNA sequencing

30 June 2018

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Comparative analysis of pseudogenes across three phyla

30 June 2018

1 reference

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Considerations when investigating lncRNA function in vivo.

30 June 2018

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Progranulin transcripts with short and long 5' untranslated regions (UTRs) are differentially expressed via posttranscriptional and translational repression

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Regulation of natural mRNAs by the nonsense-mediated mRNA decay pathway

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Application of resequencing to rice genomics, functional genomics and evolutionary analysis

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

A draft map of the human proteome

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

A promoter-level mammalian expression atlas

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Function-based identification of mammalian enhancers using site-specific integration

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Genome-guided transcript assembly by integrative analysis of RNA sequence data.

30 June 2018

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Transcriptional enhancers: from properties to genome-wide predictions

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

CTCF: an architectural protein bridging genome topology and function

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Enhancer RNAs: the new molecules of transcription

30 June 2018

1 reference

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Finding the missing honey bee genes: lessons learned from a genome upgrade

30 June 2018

1 reference

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Tackling structures of long noncoding RNAs

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

miRBase: annotating high confidence microRNAs using deep sequencing data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Current status and new features of the Consensus Coding Sequence database

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Assessment of transcript reconstruction methods for RNA-seq

30 June 2018

1 reference

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Functional transcriptomics in the post-ENCODE era

30 June 2018

1 reference

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Web Apollo: a web-based genomic annotation editing platform

30 June 2018

1 reference

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Gene expression regulation by upstream open reading frames and human disease

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Major histocompatibility complex genomics and human disease

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Structural and functional annotation of the porcine immunome

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

30 June 2018

1 reference

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APPRIS: annotation of principal and alternative splice isoforms

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

STAR: ultrafast universal RNA-seq aligner

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

GENCODE: the reference human genome annotation for The ENCODE Project

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

An integrated encyclopedia of DNA elements in the human genome

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

The GENCODE pseudogene resource

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Rapid turnover of long noncoding RNAs and the evolution of gene expression

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Hi-C: a comprehensive technique to capture the conformation of genomes

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

30 June 2018

1 reference

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A beginner's guide to eukaryotic genome annotation

30 June 2018

1 reference

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A quantitative atlas of polyadenylation in five mammals

30 June 2018

1 reference

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Community gene annotation in practice

30 June 2018

1 reference

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Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

30 June 2018

1 reference

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The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter"

30 June 2018

1 reference

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Protein-RNA interactions: new genomic technologies and perspectives

30 June 2018

1 reference

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Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Synthetic spike-in standards for RNA-seq experiments

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

The origins, evolution, and functional potential of alternative splicing in vertebrates

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Noisy splicing drives mRNA isoform diversity in human cells.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Pig genome sequence--analysis and publication strategy

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Most "dark matter" transcripts are associated with known genes

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

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

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Locus Reference Genomic sequences: an improved basis for describing human DNA variants.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Widespread transcription at neuronal activity-regulated enhancers

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

An oestrogen-receptor-α-bound human chromatin interactome

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

TopHat: discovering splice junctions with RNA-Seq

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

ChIP-based methods for the identification of long-range chromatin interactions

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Biogenesis of small RNAs in animals

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

The vertebrate genome annotation (Vega) database

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

What is a gene, post-ENCODE? History and updated definition

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Genome-wide mapping of in vivo protein-DNA interactions

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

EGASP: the human ENCODE Genome Annotation Assessment Project

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Gene prediction with a hidden Markov model and a new intron submodel

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

The non-coding Air RNA is required for silencing autosomal imprinted genes

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Prediction of complete gene structures in human genomic DNA

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Analyzing the first drafts of the human proteome.

30 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Predicting alternative splicing.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Ribosome profiling: new views of translation, from single codons to genome scale

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Orchestrated intron retention regulates normal granulocyte differentiation.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Structural variation: the genome's hidden architecture.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

PseudoPipe: an automated pseudogene identification pipeline

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5876476

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

21 August 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.119

Mitochondrial transport in neurons: impact on synaptic homeostasis and neurodegeneration

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.119

Ideas fly at gene-finding jamboree

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.119

Function of alternative splicing

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.119

An update on LNCipedia: a database for annotated human lncRNA sequences

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRG.2016.119

31 March 2020

Identifiers

DOI

10.1038/NRG.2016.119

1 reference

25 June 2018

Dimensions Publication ID

0 references

1 reference

25 June 2018

PubMed ID

27773922

1 reference

25 June 2018