(Q35488841)

8 August 2017

title

Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences (English)

1 reference

8 August 2017

1 reference

1 reference

7

Christian R Landry

1 reference

Isabelle Gagnon-Arsenault

8 August 2017

5

object named as

Isabelle Gagnon-Arsenault

1 reference

8 August 2017

Alex N Nguyen Ba

1

1 reference

8 August 2017

Bob Strome

2

1 reference

8 August 2017

Jun Jie Hua

3

1 reference

8 August 2017

Jonathan Desmond

4

1 reference

8 August 2017

Eric L Weiss

6

1 reference

8 August 2017

Alan M Moses

8

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

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8 August 2017

issue

12

1 reference

8 August 2017

page(s)

e1003977

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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

Functional divergence and evolutionary turnover in mammalian phosphoproteomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Evolution and functional cross-talk of protein post-translational modifications

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Alternative splicing and subfunctionalization generates functional diversity in fungal proteomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The origins of the evolutionary signal used to predict protein-protein interactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Mitotic exit and separation of mother and daughter cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Network evolution: rewiring and signatures of conservation in signaling

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Proteome-wide discovery of evolutionary conserved sequences in disordered regions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Cascades of multisite phosphorylation control Sic1 destruction at the onset of S phase

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Phosphorylation network rewiring by gene duplication

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Large-scale discovery and characterization of protein regulatory motifs in 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=4256066

Phosphotyrosine Signaling: Evolving a New Cellular Communication System

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Posttranslational regulation impacts the fate of duplicated 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=4256066

ELM: the status of the 2010 eukaryotic linear motif resource

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Daughter-specific transcription factors regulate cell size control in budding yeast

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Global analysis of Cdk1 substrate phosphorylation sites provides insights into 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=4256066

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Turning a hobby into a job: how duplicated genes find new functions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The NDR/LATS family kinase Cbk1 directly controls transcriptional asymmetry

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Birth and rapid subcellular adaptation of a hominoid-specific CDC14 protein

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Functional diversification of duplicate genes through subcellular adaptation of encoded proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Regulation of the yeast Ace2 transcription factor during the cell cycle

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Gene duplication and the adaptive evolution of a classic genetic switch

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Natural history and evolutionary principles of gene duplication in fungi

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Mechanistic approaches to the study of evolution: the functional synthesis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

PAML 4: phylogenetic analysis by maximum likelihood

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Functional analysis of gene duplications in Saccharomyces cerevisiae

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Systematic discovery of new recognition peptides mediating protein interaction networks

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Expression divergence between duplicate 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=4256066

Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Linear motifs: evolutionary interaction switches.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Rapid evolution of expression and regulatory divergences after yeast gene duplication

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Regulation of cell cycle-specific gene expression through cyclin-dependent kinase-mediated phosphorylation of the forkhead transcription factor Fkh2p

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

HyPhy: hypothesis testing using phylogenies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Divergence of spatial gene expression profiles following species-specific gene duplications in human and 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=4256066

The Candida albicans CaACE2 gene affects morphogenesis, adherence and virulence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The DISOPRED server for the prediction of protein disorder

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Global analysis of protein localization in budding yeast

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Statistical significance for genomewide studies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Transcription regulation and animal diversity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier 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=4256066

A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Rck2, a member of the calmodulin-protein kinase family, links protein synthesis to high osmolarity MAP kinase signaling in budding yeast

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The regulation of protein function by multisite phosphorylation--a 25 year update

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Estimation of primate speciation dates using local molecular clocks

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Rck2 kinase is a substrate for the osmotic stress-activated mitogen-activated protein kinase Hog1.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Forkhead genes in transcriptional silencing, cell morphology and the cell cycle. Overlapping and distinct functions for FKH1 and FKH2 in Saccharomyces cerevisiae

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Preservation of duplicate genes by complementary, degenerative mutations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

A model recognition approach to the prediction of all-helical membrane protein structure and topology

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The role of phosphorylation and the CDC28 protein kinase in cell cycle-regulated nuclear import of the S. cerevisiae transcription factor SWI5.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

An update of DIVERGE software for functional divergence analysis of protein family

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Transcriptional divergence plays a role in the rewiring of protein interaction networks after gene duplication

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Predicting kinase substrates using conservation of local motif density

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The local-clock permutation test: a simple test to compare rates of molecular evolution on phylogenetic trees.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Moving from transcriptional to phospho-evolution: generalizing regulatory evolution?

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Evolution of alternative splicing after gene duplication

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

Duplicate genes increase gene expression diversity within and between species.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4256066

The Large-Sample Distribution of the Likelihood Ratio for Testing Composite Hypotheses

26 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003977

Large-scale prediction of function shift in protein families with a focus on enzymatic function

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003977

Inferring sequence regions under functional divergence in duplicate genes

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003977

The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25474245

12 December 2020

inferred from PubMed ID database lookup

Exposing the fitness contribution of duplicated genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25474245

12 December 2020

inferred from PubMed ID database lookup

Statistical methods for testing functional divergence after gene duplication

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25474245

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003977

1 reference

journals/ploscb/BaSHDGWLM14

8 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_sb4pugmddnedjal5je6ddhencm

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/sb4pugmddnedjal5je6ddhencm

24 November 2022

mapped directly with Wikidata item

PMC publication ID

4256066

1 reference

8 August 2017

1 reference