(Q35488229)

8 August 2017

title

Extensive error in the number of genes inferred from draft genome assemblies (English)

1 reference

8 August 2017

5

Wesley C Warren

1 reference

8 August 2017

6

Matthew W Hahn

1 reference

8 August 2017

James F Denton

1

1 reference

8 August 2017

Jose Lugo-Martinez

series ordinal

2

1 reference

8 August 2017

Abraham E Tucker

series ordinal

3

1 reference

8 August 2017

Daniel R Schrider

series ordinal

4

1 reference

8 August 2017

publication date

4 December 2014

1 reference

PLOS Computational Biology

8 August 2017

published in

1 reference

8 August 2017

volume

10

1 reference

8 August 2017

issue

12

1 reference

8 August 2017

page(s)

e1003998

1 reference

Creative Commons Attribution 4.0 International

8 August 2017

copyright license

start time

4 December 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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A physical, genetic and functional sequence assembly of the barley genome

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The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

12 July 2018

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Limitations of the rhesus macaque draft genome assembly and annotation.

12 July 2018

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Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

12 July 2018

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12 July 2018

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Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

12 July 2018

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12 July 2018

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RNA-Seq improves annotation of protein-coding genes in the cucumber genome.

12 July 2018

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Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies

12 July 2018

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The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming.

12 July 2018

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Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes)

12 July 2018

1 reference

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Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.

12 July 2018

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A vertebrate case study of the quality of assemblies derived from next-generation sequences

12 July 2018

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Error and error mitigation in low-coverage genome assemblies

12 July 2018

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The ecoresponsive genome of Daphnia pulex

12 July 2018

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The developmental transcriptome of Drosophila melanogaster

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Limitations of next-generation genome sequence assembly

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Scaffolding a Caenorhabditis nematode genome with RNA-seq

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Genome assembly quality: assessment and improvement using the neutral indel model

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Origins and functional impact of copy number variation in the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

All human-specific gene losses are present in the genome as pseudogenes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

The Sequence Alignment/Map format and SAMtools

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Lineage-specific biology revealed by a finished genome assembly of the mouse

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Fast and accurate short read alignment with Burrows-Wheeler transform

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Annotating genomes with massive-scale RNA sequencing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Assessing the gene space in draft genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Gene-boosted assembly of a novel bacterial genome from very short reads

12 July 2018

1 reference

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Genome assembly forensics: finding the elusive mis-assembly

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

A machine-learning approach to combined evidence validation of genome assemblies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Gene family evolution across 12 Drosophila genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Diet and the evolution of human amylase gene copy number variation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

The evolution of mammalian gene families

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Linking the human cytogenetic map with nucleotide sequence: the CCAP clone set.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Physical map-assisted whole-genome shotgun sequence assemblies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Initial sequence of the chimpanzee genome and comparison with the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Assembly of polymorphic genomes: algorithms and application to Ciona savignyi

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

wFleaBase: the Daphnia genome database

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

The diploid genome sequence of Candida albicans

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

An efficient algorithm for large-scale detection of protein families

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Microbial genes in the human genome: lateral transfer or gene loss?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Initial sequencing and analysis of the human genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Ab initio gene finding in Drosophila genomic DNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Comparative genomics of the eukaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

A whole-genome assembly of Drosophila

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Prediction of complete gene structures in human genomic DNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Comparative genome assembly.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

Nucleotide sequence database policies

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256071

HUMAN GENOME: A Low Number Wins the GeneSweep Pool

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003998

10.1371/JOURNAL.PCBI.1003998

21 January 2018

Identifiers

DOI

1 reference

journals/ploscb/DentonLTSWH14

8 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

8 August 2017

1 reference