EGASP: the human ENCODE Genome Annotation Assessment Project (Q21184139)

Europe PubMed Central

25 November 2020

30 April 2021

EGASP: the human ENCODE Genome Annotation Assessment Project (English)

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25 November 2020

1 reference

30 April 2021

Stilianos Antonarakis

series ordinal

7

object named as

Stylianos Antonarakis

author given names

Stylianos

author last names

Antonarakis

1 reference

17 August 2022

10

Ewan Birney

Ewan

Birney

1 reference

17 August 2022

8

Michael Ashburner

Michael

Ashburner

1 reference

17 August 2022

16

Tim Hubbard

Tim

Hubbard

1 reference

17 August 2022

4

Alexandre Reymond

Alexandre

Reymond

1 reference

17 August 2022

6

France Denoeud

France

Denoeud

1 reference

17 August 2022

13

Catherine Ucla

Catherine

Ucla

1 reference

17 August 2022

15

Jennifer Harrow

Jennifer

Harrow

1 reference

17 August 2022

2

Paul Flicek

Paul

Flicek

1 reference

1048969371

17 August 2022

Roderic Guigó i Serra

1

Roderic Guigó

Roderic

Guigó

1 reference

17 August 2022

Julien Lagarde

5

Julien

Lagarde

1 reference

17 August 2022

Josep F Abril

3

Josep F

Abril

1 reference

17 August 2022

Eduardo Eyras

12

Eduardo

Eyras

1 reference

17 August 2022

Vladimir B Bajic

9

Vladimir B

Bajic

1 reference

17 August 2022

17

Suzanna E Lewis

Suzanna E

Lewis

1 reference

17 August 2022

14

Thomas R Gingeras

Thomas R

Gingeras

1 reference

17 August 2022

11

Robert

Castelo

Robert Castelo

1 reference

17 August 2022

Martin G Reese

18

Martin G

Reese

1 reference

1048969371

GENCODE: producing a reference annotation for ENCODE

17 August 2022

language of work or name

English

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publication date

2006

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7 August 2006

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25 November 2020

30 April 2021

2 references

25 November 2020

30 April 2021

7 Suppl 1

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issue

Suppl 1

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page(s)

S2.1-31

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Tandem chimerism as a means to increase protein complexity in the human genome

19 March 2017

1 reference

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ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Recognition of unknown conserved alternatively spliced exons

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Gene finding in the chicken genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The DNA sequence of the human X chromosome

19 March 2017

1 reference

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Entrez Gene: gene-centered information at NCBI

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

DNA sequence and analysis of human chromosome 9

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The DNA sequence and analysis of human chromosome 13

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Eval: a software package for analysis of genome annotations

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Reevaluating human gene annotation: a second-generation analysis of chromosome 22

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Initial sequencing and analysis of the human genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Finishing the euchromatic sequence of the human genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The DNA sequence and comparative analysis of human chromosome 10

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The DNA sequence and analysis of human chromosome 6

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The DNA sequence and comparative analysis of human chromosome 20

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The Sequence of the Human Genome

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The UCSC Genome Browser Database

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Prediction of complete gene structures in human genomic DNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Nineteen additional unpredicted transcripts from human chromosome 21

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Large-scale transcriptional activity in chromosomes 21 and 22

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Evaluation of gene-finding programs on mammalian sequences

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

A computational approach for identifying pseudogenes in the ENCODE regions

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The ENCODE (ENCyclopedia Of DNA Elements) Project

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

The Ensembl automatic gene annotation system

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Assessing the accuracy of prediction algorithms for classification: an overview

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Pairagon N-SCAN_EST: a model-based gene annotation pipeline

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Automatic annotation of eukaryotic genes, pseudogenes and promoters

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

ECgene: genome-based EST clustering and gene modeling for alternative splicing

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Identification and analysis of alternative splicing events conserved in human and mouse

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Recent advances in gene structure prediction

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Identification of rat genes by TWINSCAN gene prediction, RT-PCR, and direct sequencing

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Splicing double: insights from the second spliceosome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Comparing the success of different prediction software in sequence analysis: a review

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Gene structure prediction and alternative splicing analysis using genomically aligned ESTs

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

MaskerAid: a performance enhancement to RepeatMasker

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Genome annotation assessment in Drosophila melanogaster

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Gene prediction and verification in a compact genome with numerous small introns

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

SLAM web server for comparative gene finding and alignment

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Comparative gene prediction in human and mouse

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

An assessment of gene prediction accuracy in large DNA sequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Vertebrate gene finding from multiple-species alignments using a two-level strategy

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Integrating genomic homology into gene 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=1810551

Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Exogean: a framework for annotating protein-coding genes in eukaryotic genomic DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Large multiple organism gene finding by collapsed Gibbs sampling.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

ExonHunter: a comprehensive approach to gene finding

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Human chromosome 21 gene expression atlas in the mouse.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

Evaluation of gene structure prediction programs.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1810551

29 November 2018

Identifiers

DOI

10.1186/GB-2006-7-S1-S2

1 reference

1048969371

0 references

1 reference

1 reference

PubMed publication ID

16925836

1 reference