A New Chicken Genome Assembly Provides Insight into Avian Genome Structure (Q36194303)

12 August 2017

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure (English)

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12 August 2017

6

Tina Graves

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Patrick Minx

4

Patrick Minx

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12 August 2017

Francoise Thibaud-Nissen

10

Francoise Thibaud-Nissen

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12 August 2017

5

Milinn Kremitzki

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12 August 2017

13

C Titus Brown

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12 August 2017

William Chow

21

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Tamer Mansour

Tamer A Mansour

12

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David W Burt

David W Burt

30

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Kerstin Howe

Kerstin Howe

22

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Claudio V Mello

26

Claudio V Mello

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12 August 2017

25

Peter Lovell

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12 August 2017

1

Wesley C Warren

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12 August 2017

9

Kim D Pruitt

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12 August 2017

23

Janet E Fulton

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12 August 2017

LaDeana W Hillier

2

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12 August 2017

Chad Tomlinson

3

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12 August 2017

Chris Markovic

7

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12 August 2017

Nathan Bouk

8

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12 August 2017

Valerie Schneider

11

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12 August 2017

Aleksey Zimin

14

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12 August 2017

Rachel Hawken

15

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12 August 2017

Mitch Abrahamsen

16

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12 August 2017

Alexis B Pyrkosz

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12 August 2017

Mireille Morisson

18

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12 August 2017

Valerie Fillon

19

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12 August 2017

Alain Vignal

20

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12 August 2017

Marcia M Miller

24

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12 August 2017

Morgan Wirthlin

27

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12 August 2017

Andrew S Mason

28

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12 August 2017

Richard Kuo

29

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12 August 2017

Jerry B Dodgson

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12 August 2017

Hans H Cheng

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12 August 2017

14 November 2016

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12 August 2017

109-117

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describes a project that uses

12 August 2017

MUMmer

MUMmer

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CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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GMAP and GSNAP for Genomic Sequence Alignment: Enhancements to Speed, Accuracy, and Functionality

1 October 2017

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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

1 October 2017

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A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1.

1 October 2017

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Brief review of the chicken Major Histocompatibility Complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance

1 October 2017

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Parallel Selection Revealed by Population Sequencing in Chicken

1 October 2017

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The genetics of feed conversion efficiency traits in a commercial broiler line

1 October 2017

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UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View

1 October 2017

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Third Report on Chicken Genes and Chromosomes 2015.

1 October 2017

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High speed BLASTN: an accelerated MegaBLAST search tool

1 October 2017

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Using VarScan 2 for Germline Variant Calling and Somatic Mutation Detection

1 October 2017

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Conserved syntenic clusters of protein coding genes are missing in birds

1 October 2017

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The InterPro protein families database: the classification resource after 15 years

1 October 2017

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Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

1 October 2017

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Resolving the complexity of the human genome using single-molecule sequencing

1 October 2017

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The GOA database: gene Ontology annotation updates for 2015

1 October 2017

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1 October 2017

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SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

1 October 2017

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Sequence of a complete chicken BG haplotype shows dynamic expansion and contraction of two gene lineages with particular expression patterns

1 October 2017

1 reference

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InterProScan 5: genome-scale protein function classification

1 October 2017

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Clone DB: an integrated NCBI resource for clone-associated data

1 October 2017

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Hybrid error correction and de novo assembly of single-molecule sequencing reads

1 October 2017

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Graph accordance of next-generation sequence assemblies

1 October 2017

1 reference

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Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Whole-genome resequencing reveals loci under selection during chicken domestication

1 October 2017

1 reference

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Fast and accurate short read alignment with Burrows-Wheeler transform

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Splign: algorithms for computing spliced alignments with identification of paralogs

1 October 2017

1 reference

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High-throughput functional annotation and data mining with the Blast2GO suite

1 October 2017

1 reference

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NCBI BLAST: a better web interface

1 October 2017

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LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

De novo identification of LTR retrotransposons in eukaryotic genomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Additional gene ontology structure for improved biological reasoning

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like Loci

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

WindowMasker: window-based masker for sequenced genomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

The chicken leukocyte receptor complex: a highly diverse multigene family encoding at least six structurally distinct receptor types

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Versatile and open software for comparing large genomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

BLAT—The BLAST-Like Alignment Tool

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Map Manager QTX, cross-platform software for genetic mapping

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Size and structure of the bird genome--I. DNA content of 48 species of Neognathae

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Corrigendum: Assembling large genomes with single-molecule sequencing and locality-sensitive hashing.

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Genomics: Bird sequencing project takes off.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Assembly errors cause false tandem duplicate regions in the chicken (Gallus gallus) genome sequence

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Extended gene map reveals tripartite motif, C-type lectin, and Ig superfamily type genes within a subregion of the chicken MHC-B affecting infectious disease

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

A physical map of the chicken genome

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

LTR_STRUC: a novel search and identification program for LTR retrotransposons

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

At least one class I gene in restriction fragment pattern-Y (Rfp-Y), the second MHC gene cluster in the chicken, is transcribed, polymorphic, and shows divergent specialization in antigen binding region.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

Development of a genetic map of the chicken with markers of high utility.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5217101

22 September 2018

Identifiers

DOI

10.1534/G3.116.035923

1 reference

12 August 2017

1 reference

12 August 2017

PubMed publication ID

27852011

1 reference