(Q21267236)

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Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend

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Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend (English)

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David M McGaughey

object named as

David M McGaughey

1

author given names

David M

author last names

McGaughey

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Dimensions Publication ID

19 August 2022

author name string

Zachary E Stine

2

author given names

Zachary E

author last names

Stine

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Dimensions Publication ID

19 August 2022

Jimmy L Huynh

3

author given names

Jimmy L

author last names

Huynh

1 reference

Dimensions Publication ID

19 August 2022

Ryan M Vinton

4

author given names

Ryan M

author last names

Vinton

1 reference

Dimensions Publication ID

19 August 2022

Andrew S McCallion

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author given names

Andrew S

author last names

McCallion

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Dimensions Publication ID

19 August 2022

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publication date

2009

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10

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1

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8

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Regulatory divergence modifies limb length between mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Evidence for widespread degradation of gene control regions in hominid genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Highly conserved non-coding sequences are associated with vertebrate development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

The human genome browser at UCSC

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Gene ontology: tool for the unification of biology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Ultraconserved Elements in the Human Genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Stages of embryonic development of the zebrafish

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Using galaxy to perform large-scale interactive data analyses

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Scanning Human Gene Deserts for Long-Range Enhancers

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

The homeobox gene Phox2b is essential for the development of autonomic neural crest derivatives

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Expression and interactions of the two closely related homeobox genes Phox2a and Phox2b during neurogenesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

19 March 2017

Aligning multiple genomic sequences with the threaded blockset aligner

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

7 April 2017

In vivo enhancer analysis of human conserved non-coding sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

7 April 2017

Gene regulatory networks and the evolution of animal body plans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

7 April 2017

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

7 April 2017

Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

OBO-Edit--an ontology editor for biologists

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Predicting tissue-specific enhancers in the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Genomic regulatory networks and animal development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

A common sex-dependent mutation in a RET enhancer underlies Hirschsprung disease risk.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Evolution and functional classification of vertebrate gene deserts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Comparative genomics at the vertebrate extremes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Germline mutations of the paired-like homeobox 2B (PHOX2B) gene in neuroblastoma

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Comparative genomic analysis as a tool for biological discovery

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

12 September 2017

Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

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Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

30 May 2018

Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

30 May 2018

Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

30 May 2018

Morphological evolution through multiple cis-regulatory mutations at a single gene.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

29 November 2018

Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

29 November 2018

Phox2b function in the enteric nervous system is conserved in zebrafish and is sox10-dependent

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

29 November 2018

PMX2B, a new candidate gene for Hirschsprung's disease.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

29 November 2018

A conserved retinoic acid response element required for early expression of the homeobox gene Hoxb-1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

29 November 2018

The apolipoprotein(a) gene is regulated by sex hormones and acute-phase inducers in YAC transgenic mice.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2630312

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Conservation of RET regulatory function from human to zebrafish without sequence similarity

1 reference

https://pubmed.ncbi.nlm.nih.gov/19128492

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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1 reference

https://pubmed.ncbi.nlm.nih.gov/19128492

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.1186/1471-2164-10-8

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9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2164-10-8

release_n2whbn5tkzaybmpbbx45v4ivki

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https://api.fatcat.wiki/v0/release/n2whbn5tkzaybmpbbx45v4ivki

24 November 2022

based on heuristic

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