(Q45094649)

9 December 2017

title

Dissecting plant genomes with the PLAZA comparative genomics platform (English)

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9 December 2017

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9 December 2017

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9 December 2017

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9 December 2017

Sebastian Proost

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author name string

Elisabeth Wischnitzki

series ordinal

3

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9 December 2017

Sara Movahedi

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4

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9 December 2017

Christopher Scheerlinck

series ordinal

5

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9 December 2017

language of work or name

English

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publication date

23 December 2011

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9 December 2017

number of pages

11

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based on heuristic

inferred from page(s)

published in

Plant Physiology

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9 December 2017

volume

158

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9 December 2017

issue

2

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9 December 2017

page(s)

590-600

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The NCBI Taxonomy database

9 December 2017

cites work

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3 November 2018

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3 November 2018

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3 November 2018

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The Medicago genome provides insight into the evolution of rhizobial symbioses

3 November 2018

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Orthology prediction methods: a quality assessment using curated protein families

3 November 2018

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The genome of the extremophile crucifer Thellungiella parvula

3 November 2018

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De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

3 November 2018

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Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice.

3 November 2018

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The Selaginella genome identifies genetic changes associated with the evolution of vascular plants

3 November 2018

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The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

3 November 2018

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3 November 2018

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A greedy, graph-based algorithm for the alignment of multiple homologous gene lists

3 November 2018

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The genome of woodland strawberry (Fragaria vesca)

3 November 2018

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The genome of Theobroma cacao

3 November 2018

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MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

3 November 2018

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Gene clusters for secondary metabolic pathways: an emerging theme in plant biology

3 November 2018

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GreenPhylDB v2.0: comparative and functional genomics in plants.

3 November 2018

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The genome of the domesticated apple (Malus × domestica Borkh.)

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Draft genome sequence of the oilseed species Ricinus communis

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Genomic analysis of organismal complexity in the multicellular green alga Volvox carteri

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The next generation becomes the now generation

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Genome sequencing and analysis of the model grass Brachypodium distachyon

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Genome sequence of the palaeopolyploid soybean

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The B73 Maize Genome: Complexity, Diversity, and Dynamics

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Ensembl Genomes: extending Ensembl across the taxonomic space

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The flowering world: a tale of duplications

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

3 November 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Circos: an information aesthetic for comparative genomics

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The Sorghum bicolor genome and the diversification of grasses

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Large-scale assignment of orthology: back to phylogenetics?

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

InterPro: the integrative protein signature database

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Evolution of genome architecture

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The quest for orthologs: finding the corresponding gene across genomes

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Reconciliation with non-binary species trees.

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Genome structure of the legume, Lotus japonicus

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Gene Ontology annotation quality analysis in model eukaryotes

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Next-generation sequencing transforms today's biology

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

eggNOG: automated construction and annotation of orthologous groups of genes

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Assessing performance of orthology detection strategies applied to eukaryotic genomes

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Identifying clusters of functionally related genes in genomes

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The TIGR Rice Genome Annotation Resource: improvements and new features

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Orthologs, paralogs, and evolutionary genomics

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Genetic structure and diversity in Oryza sativa L

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Nuclear DNA amounts in angiosperms: progress, problems and prospects.

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

The evolutionary dynamics of eukaryotic gene order

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

MUSCLE: multiple sequence alignment with high accuracy and high throughput

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Gene structure conservation aids similarity based gene prediction

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

An efficient algorithm for large-scale detection of protein families

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

A simple algorithm to infer gene duplication and speciation events on a gene tree.

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Gene ontology: tool for the unification of biology

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Measuring genome evolution

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

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

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

Distinguishing Homologous from Analogous Proteins

3 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3271752

3 November 2018

Identifiers

DOI

10.1104/PP.111.189514

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9 December 2017

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