PLAZA: a comparative genomics resource to study gene and genome evolution in plants (Q38432649)

3 September 2017

title

PLAZA: a comparative genomics resource to study gene and genome evolution in plants (English)

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3 September 2017

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3 September 2017

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3 September 2017

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3 September 2017

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3 September 2017

Thomas Van Parys

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author name string

Sebastian Proost

series ordinal

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3 September 2017

Kenny Billiau

series ordinal

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3 September 2017

Thomas Van Parys

series ordinal

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3 September 2017

publication date

29 December 2009

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3 September 2017

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3 September 2017

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3 September 2017

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3 September 2017

page(s)

3718-3731

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The flowering world: a tale of duplications

3 September 2017

cites work

1 reference

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The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species

31 August 2018

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Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition

31 August 2018

1 reference

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The 1001 genomes project for Arabidopsis thaliana

31 August 2018

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Old dogs, new tricks: regulatory evolution in conserved genetic modules leads to novel morphologies in plants

31 August 2018

1 reference

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Web-queryable large-scale data sets for hypothesis generation in plant biology

31 August 2018

1 reference

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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

31 August 2018

1 reference

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

31 August 2018

1 reference

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GRASSIUS: a platform for comparative regulatory genomics across the grasses

31 August 2018

1 reference

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Genomic insights into marine microalgae

31 August 2018

1 reference

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InterPro: the integrative protein signature database

31 August 2018

1 reference

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Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Reconciliation with non-binary species trees.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Importance of lineage-specific expansion of plant tandem duplicates in the adaptive response to environmental stimuli

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Arabidopsis reactome: a foundation knowledgebase for plant systems biology

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

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

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

How to usefully compare homologous plant genes and chromosomes as DNA sequences

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

PlantTribes: a gene and gene family resource for comparative genomics in plants

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

GreenPhylDB: a database for plant comparative genomics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Gramene: a growing plant comparative genomics resource

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The Chlamydomonas genome reveals the evolution of key animal and plant functions

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Assessing performance of orthology detection strategies applied to eukaryotic genomes

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

PlnTFDB: an integrative plant transcription factor database

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The gain and loss of genes during 600 million years of vertebrate evolution

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Leafing through the genomes of our major crop plants: strategies for capturing unique information

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

OrthologID: automation of genome-scale ortholog identification within a parsimony framework

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Phytome: a platform for plant comparative genomics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Orthologs, paralogs, and evolutionary genomics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The map-based sequence of the rice genome

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

SynBrowse: a synteny browser for comparative sequence analysis

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Genome cluster database. A sequence family analysis platform for Arabidopsis and rice

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Exploring the plant transcriptome through phylogenetic profiling

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Recent developments in computational approaches for uncovering genomic homology

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

MUSCLE: multiple sequence alignment with high accuracy and high throughput

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Expressed sequence tags: alternative or complement to whole genome sequences?

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The hidden duplication past of Arabidopsis thaliana

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

An efficient algorithm for large-scale detection of protein families

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Genome annotation: from sequence to biology

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Gene ontology: tool for the unification of biology

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Histone acetylation in chromatin structure and transcription

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The major cytoplasmic histone acetyltransferase in yeast: links to chromatin replication and histone metabolism

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Synonymous nucleotide divergence: what is "saturation"?

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

The organization structure and regulatory elements of Chlamydomonas histone genes reveal features linking plant and animal genes

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Human histone genes map to multiple chromosomes

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Single-copy flanking sequences in human histone gene clusters map to chromosomes 1 and 6

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Synteny and Collinearity in Plant Genomes

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2814516

Genome sequencing. The greening of plant genomics

31 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20040540

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Differential expression of two clusters of mouse histone genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20040540

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20040540

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1105/TPC.109.071506

1 reference

3 September 2017

0 references

1 reference