PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins (Q57696090)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17337525%20AND%20SRC:MED&resulttype=core&format=json

26 December 2019

title

PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins (English)

1 reference

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26 December 2019

1 reference

2

1 reference

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26 December 2019

3

Ralf Reski

1 reference

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26 December 2019

5

Stefan A Rensing

1 reference

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26 December 2019

author name string

Sandra Richardt

series ordinal

1

1 reference

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26 December 2019

Wolfgang Frank

series ordinal

4

1 reference

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26 December 2019

language of work or name

English

0 references

publication date

2 March 2007

1 reference

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26 December 2019

number of pages

15

1 reference

inferred from page(s)

published in

Plant Physiology

1 reference

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26 December 2019

volume

143

1 reference

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26 December 2019

issue

4

1 reference

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26 December 2019

page(s)

1452-1466

1 reference

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Creative Commons Attribution 4.0 International

26 December 2019

copyright license

start time

25 January 2021

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Transcription factor families in Arabidopsis: major progress and outstanding issues for future research

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Arabidopsis SPA proteins regulate photoperiodic flowering and interact with the floral inducer CONSTANS to regulate its stability.

2 November 2018

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DRTF: a database of rice transcription factors

2 November 2018

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Aprataxin forms a discrete branch in the HIT (histidine triad) superfamily of proteins with both DNA/RNA binding and nucleotide hydrolase activities

2 November 2018

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Evolutionary dynamics of prokaryotic transcriptional regulatory networks

2 November 2018

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Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity.

2 November 2018

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Grasses like mammals? Redundancy and compensatory regulation within the retinoblastoma protein family.

2 November 2018

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Analysis of the transcription factor WUSCHEL and its functional homologue in Antirrhinum reveals a potential mechanism for their roles in meristem maintenance

2 November 2018

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A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

2 November 2018

1 reference

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MSH2 is essential for the preservation of genome integrity and prevents homeologous recombination in the moss Physcomitrella patens

2 November 2018

1 reference

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Molecular evolution of the AP2 subfamily.

2 November 2018

1 reference

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Pfam: clans, web tools and services

2 November 2018

1 reference

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2 November 2018

The PROSITE database.

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WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Parameters determining the efficiency of gene targeting in the moss Physcomitrella patens

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Transcription factors in rice: a genome-wide comparative analysis between monocots and eudicots.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

COP1 - from plant photomorphogenesis to mammalian tumorigenesis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Transcription factor families have much higher expansion rates in plants than in animals.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Four distinct photoreceptors contribute to light-induced side branch formation in the moss Physcomitrella patens.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Evolution at two levels: on genes and form

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

InterProScan: protein domains identifier

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Isolation and characterization of new MIKC*-Type MADS-box genes from the moss Physcomitrella patens.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Evolutionary distance estimation and fidelity of pair wise sequence alignment

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The floral regulator LEAFY evolves by substitutions in the DNA binding domain.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

ProbCons: Probabilistic consistency-based multiple sequence alignment

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

ULTRAPETALA1 encodes a SAND domain putative transcriptional regulator that controls shoot and floral meristem activity in Arabidopsis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

MAFFT version 5: improvement in accuracy of multiple sequence alignment

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The PANTHER database of protein families, subfamilies, functions and pathways

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The apicoplast: a review of the derived plastid of apicomplexan parasites.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Differential expression on a daily basis of plastid sigma factor genes from the moss Physcomitrella patens. Regulatory interactions among PpSig5, the circadian clock, and blue light signaling mediated by cryptochromes.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

PhyloGenie: automated phylome generation and analysis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Targeted knockout in Physcomitrella reveals direct actions of phytochrome in the cytoplasm

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Loss of GH3 function does not affect phytochrome-mediated development in a moss, Physcomitrella patens.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

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

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Phototropins mediate blue and red light-induced chloroplast movements in Physcomitrella patens

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Aprataxin, a novel protein that protects against genotoxic stress

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The Jalview Java alignment editor

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

BLASTing proteomes, yielding phylogenies.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Transcription regulation and animal diversity

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Entrez: making use of its power

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

UV-B radiation arising from stratospheric ozone depletion influences the pigmentation of the Antarctic moss Andreaea regularis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Evolution of transcription factor function

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Plant-like traits associated with metabolism of Trypanosoma parasites

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The phylogenetic diversity of eukaryotic transcription

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Moss transcriptome and beyond

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The Bioperl toolkit: Perl modules for the life sciences

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Scoring residue conservation

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The role of lineage-specific gene family expansion in the evolution of eukaryotes

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

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

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

ATV: display and manipulation of annotated phylogenetic trees

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Transcription-associated protein families are primarily taxon-specific

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

A phylogenomic approach to microbial evolution

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Evolution of transcriptional regulation

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

EMBOSS: the European Molecular Biology Open Software Suite

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Activation tagging in Arabidopsis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

A short history of MADS-box genes in plants.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Structural organization and interactions of COP1, a light-regulated developmental switch

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Members of the YABBY gene family specify abaxial cell fate in Arabidopsis

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Arabidopsis STERILE APETALA, a multifunctional gene regulating inflorescence, flower, and ovule development

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Twilight zone of protein sequence alignments

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Role of WUSCHEL in regulating stem cell fate in the Arabidopsis shoot meristem.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Cluster analysis and display of genome-wide expression patterns

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Transcriptional regulators and the evolution of plant form.

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

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

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Molecular cloning of a small DNA binding protein with specificity for a tissue-specific negative element within the rps1 promoter

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The neighbor-joining method: a new method for reconstructing phylogenetic trees

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Recent changes in the GenBank On-line Service

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

The rapid generation of mutation data matrices from protein sequences

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea

2 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1851845

30 November 2018

Transcription in Archaea

1 reference

12 December 2020

DATF: a database of Arabidopsis transcription factors

1 reference

12 December 2020

CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B response in Arabidopsis

1 reference

12 December 2020

FACTORS DETERMINING THE ACCURACY OF CLADOGRAM ESTIMATION: EVALUATION USING COMPUTER SIMULATION

1 reference

12 December 2020

The origin and early evolution of plants on land

1 reference

COCI

https://opencitations.net/index/coci/api/v1/citations/10.1038/37918

15 July 2023

Identifiers

DOI

10.1104/PP.107.095760

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17337525%20AND%20SRC:MED&resulttype=core&format=json

26 December 2019

0 references

1 reference