De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. (Q34331168)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

title

De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

0 references

0 references

1 reference

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Danielle J Whittaker

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Ram Podicheti

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

12

Ellen D Ketterson

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

author name string

Mark P Peterson

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Shruthi Ambreth

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Suhas Sureshchandra

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Aaron Buechlein

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Jeong-Hyeon Choi

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Zhao Lai

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Keithanne Mockatis

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

Haixu Tang

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

language of work or name

English

0 references

publication date

9 July 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

volume

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

page(s)

305

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

7 February 2020

limma

object named as

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/3476391

based on heuristic

inferred from PubMed Central ID database lookup

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

maintained by WikiProject

1 reference

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Three periods of regulatory innovation during vertebrate evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

The ecoresponsive genome of Daphnia pulex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Next generation sequencing and analysis of a conserved transcriptome of New Zealand's kiwi

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Gene discovery in the horned beetle Onthophagus taurus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Nebulin: a study of protein repeat evolution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Parallel evolution of opsin gene expression in African cichlid fishes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Natural selection on testosterone production in a wild songbird population

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

6 July 2018

The genome of a songbird

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Comparative venom gland transcriptome surveys of the saw-scaled vipers (Viperidae: Echis) reveal substantial intra-family gene diversity and novel venom transcripts

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

KEGG for representation and analysis of molecular networks involving diseases and drugs

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Global characterization of Artemisia annua glandular trichome transcriptome using 454 pyrosequencing

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

BioMart Central Portal--unified access to biological data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Characterization of amphioxus nebulin and its similarity to human nebulin

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Patterns of exon-intron architecture variation of genes in eukaryotic genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

BioMart--biological queries made easy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

NCBI Reference Sequences: current status, policy and new initiatives

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Hormone-mediated suites as adaptations and evolutionary constraints

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Quantitative assessment of relationship between sequence similarity and function similarity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Low sex steroids, high steroid receptors: Increasing the sensitivity of the nonreproductive brain.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

The evolutionary significance of cis-regulatory mutations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Physiological effects on demography: a long-term experimental study of testosterone's effects on fitness

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

From genomics to chemical genomics: new developments in KEGG

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Pathway level analysis of gene expression using singular value decomposition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Phylogeny and diversification of the largest avian radiation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Nebulin: the nebulous, multifunctional giant of striated muscle

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Intrinsic errors in genome annotation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

RefSeq and LocusLink: NCBI gene-centered resources

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

The COG database: new developments in phylogenetic classification of proteins from complete genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Gene ontology: tool for the unification of biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

KEGG: kyoto encyclopedia of genes and genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Role of the archistriatal nucleus taeniae in the sexual behavior of male Japanese quail (Coturnix japonica): a comparison of function with the medial nucleus of the amygdala in mammals.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

A genomic perspective on protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Single-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate–Phenol–Chloroform Extraction

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Testosterone and avian life histories: the effect of experimentally elevated testosterone on corticosterone and body mass in dark-eyed juncos

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Promiscuous mating produces offspring with higher lifetime fitness.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Phenotypic integration and independence: Hormones, performance, and response to environmental change

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Sequencing goes 454 and takes large-scale genomics into the wild

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Sex-role reversal is reflected in the brain of African black coucals (Centropus grillii).

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Adaptive phenotypic plasticity and the successful colonization of a novel environment

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Complete genomic structure of the human nebulin gene and identification of alternatively spliced transcripts.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Rapid evolution of a sexually selected trait following population establishment in a novel habitat

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Genetic and morphological evolution following a founder event in the dark-eyed junco, Junco hyemalis thurberi

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Androgen-metabolizing enzymes show region-specific changes across the breeding season in the brain of a wild songbird.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3476391

Practical limits of function prediction

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22776250

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

ANIMAL MIGRATION AS A MOVING TARGET FOR CONSERVATION: INTRA-SPECIES VARIATION AND RESPONSES TO ENVIRONMENTAL CHANGE, AS ILLUSTRATED IN A SOMETIMES MIGRATORY SONGBIRD.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22776250

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2164-13-305

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json

7 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22776250%20AND%20SRC:MED&resulttype=core&format=json