(Q28596126)

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Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover

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scholarly article

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20 June 2019

30 June 2019

14 September 2019

18 October 2020

30 October 2020

Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover (English)

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genetic variation

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14 September 2019

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18 October 2020

molecular evolution

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30 October 2020

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based on heuristic

inferred from title

author name string

Robert S Young

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publication date

July 2016

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1 July 2016

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20 June 2019

30 June 2019

14 September 2019

18 October 2020

30 October 2020

5 references

20 June 2019

30 June 2019

14 September 2019

18 October 2020

30 October 2020

38

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7

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654-63

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copyright license

Creative Commons Attribution

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20 June 2019

30 June 2019

14 September 2019

18 October 2020

30 October 2020

copyright status

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describes a project that uses

object named as

edgeR

1 reference

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

Lagging-strand replication shapes the mutational landscape of the genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

An integrated map of genetic variation from 1,092 human genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

An expansive human regulatory lexicon encoded in transcription factor footprints

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

An integrated encyclopedia of DNA 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=4949557

17 March 2017

Rapid turnover of long noncoding RNAs and the evolution of gene expression

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Human-specific loss of regulatory DNA and the evolution of human-specific traits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Massive turnover of functional sequence in human and other mammalian genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Emergence of a new gene from an intergenic region

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

MicroRNAs: target recognition and regulatory functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Species-specific transcription in mice carrying human chromosome 21

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

The diploid genome sequence of an individual human

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Genome-wide identification of human functional DNA using a neutral indel model

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 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=4949557

17 March 2017

The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Human-mouse alignments with BLASTZ

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Initial sequencing and comparative analysis of the mouse genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

17 March 2017

Initial sequencing and analysis 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=4949557

17 March 2017

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

6 April 2017

A map of the cis-regulatory sequences in the mouse genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

7 April 2017

The regulated retrotransposon transcriptome of mammalian cells

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

7 April 2017

Evolution and functions of long noncoding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

7 April 2017

Relative impact of nucleotide and copy number variation on gene expression phenotypes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

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=4949557

7 April 2017

Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Abundant contribution of short tandem repeats to gene expression variation in humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Large-scale whole-genome sequencing of the Icelandic population

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Enhancer evolution across 20 mammalian species

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Conservation of trans-acting circuitry during mammalian regulatory evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

A comparative encyclopedia of DNA elements in the mouse genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

A promoter-level mammalian expression atlas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

The evolution of lineage-specific regulatory activities in the human embryonic limb

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Divergence of mammalian higher order chromatin structure is associated with developmental loci

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Next-generation sequencing platforms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Evolution of the human-specific microRNA miR-941.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

CTCF: insights into insulator function during development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Animal transcription networks as highly connected, quantitative continua

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Natural genetic variation caused by small insertions and deletions 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=4949557

29 September 2017

Origins, evolution, and phenotypic impact of new genes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

A human-specific de novo protein-coding gene associated with human brain functions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Insertion and deletion processes in recent human history

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Enhancers: the abundance and function of regulatory sequences beyond promoters

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

The deep evolution of metazoan microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Human-specific gain of function in a developmental enhancer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

The biological effects of simple tandem repeats: lessons from the repeat expansion diseases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

A macaque's-eye view of human insertions and deletions: differences in mechanisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Mammalian RNA polymerase II core promoters: insights from genome-wide studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

The UCSC genome browser database: update 2007.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Human-specific insertions and deletions inferred from mammalian genome sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

An initial map of insertion and deletion (INDEL) variation 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=4949557

29 September 2017

Evolutionary turnover of mammalian transcription start sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Positive selection on the human genome.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Elevated rates of protein secretion, evolution, and disease among tissue-specific genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

29 September 2017

Comparative epigenomic annotation of regulatory DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

3 June 2018

Sequence shortening in the rodent ancestor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

3 June 2018

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4949557

3 June 2018

Common deletion polymorphisms in the human genome.

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201500192

21 January 2018

The frequent evolutionary birth and death of functional promoters in mouse and human

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201500192

21 January 2018

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201500192

21 January 2018

The majority of recent short DNA insertions in the human genome are tandem duplications.

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201500192

21 January 2018

Transposable elements have rewired the core regulatory network of human embryonic stem cells

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201500192

21 January 2018

Rapidly evolving human promoter regions.

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201500192

21 January 2018

Evidence of abundant purifying selection in humans for recently acquired regulatory functions

1 reference

https://api.crossref.org/works/10.1002%2FBIES.201500192

21 January 2018

The g-value paradox

1 reference

https://pubmed.ncbi.nlm.nih.gov/27231054

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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