Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals (Q31058303)

11 August 2017

Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals (English)

1 reference

11 August 2017

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1 reference

1 reference

6

Erika Lindquist

0 references

Shinichi Sunagawa

3

Shinichi Sunagawa

0 references

Till Bayer

Till Bayer

1

0 references

Manuel Aranda

Manuel Aranda

2

0 references

Christian R. Voolstra

Christian R Voolstra

8

0 references

Mary Alice Coffroth

7

Mary Alice Coffroth

1 reference

11 August 2017

Lauren K Yum

4

1 reference

11 August 2017

Michael K Desalvo

5

1 reference

11 August 2017

Mónica Medina

9

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11 August 2017

language of work or name

English

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publication date

18 April 2012

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11 August 2017

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11 August 2017

7

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11 August 2017

4

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11 August 2017

e35269

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Creative Commons CC0 License

11 August 2017

start time

18 April 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

describes a project that uses

MIRA

MIRA

1 reference

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

cites work

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Identification of fast-evolving genes in the scleractinian coral Acropora using comparative EST analysis

21 June 2018

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Differential sensitivity of coral larvae to natural levels of ultraviolet radiation during the onset of larval competence

21 June 2018

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Rapid evolution of coral proteins responsible for interaction with the environment

21 June 2018

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HMMER web server: interactive sequence similarity searching

21 June 2018

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MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

21 June 2018

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Unexpected complexity of the reef-building coral Acropora millepora transcription factor network

21 June 2018

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Protein synthesis is the primary target of reactive oxygen species in the photoinhibition of photosystem II.

21 June 2018

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The Apicomplexan AP2 family: integral factors regulating Plasmodium development

21 June 2018

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Synonymous but not the same: the causes and consequences of codon bias

21 June 2018

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Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data.

21 June 2018

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Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Search and clustering orders of magnitude faster than BLAST

21 June 2018

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

21 June 2018

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Evolutionary analysis of orthologous cDNA sequences from cultured and symbiotic dinoflagellate symbionts of reef-building corals (Dinophyceae: Symbiodinium).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai'i

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

BioMart Central Portal--unified access to biological data

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

In silico analysis of nickel containing superoxide dismutase evolution and regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

21 June 2018

Selection on Codon Bias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

PlasmoDB: a functional genomic database for malaria parasites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Differential gene expression during thermal stress and bleaching in the Caribbean coral Montastraea faveolata

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Horizontal gene transfer in eukaryotic evolution

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Early evolution of histone genes: prevalence of an 'orphon' H1 lineage in protostomes and birth-and-death process in the H2A family.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Nucleosome organization in the Drosophila genome.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

DBD--taxonomically broad transcription factor predictions: new content and functionality

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

The Pfam protein families database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

The many faces of chromatin assembly factor 1.

21 June 2018

1 reference

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BEAST: Bayesian evolutionary analysis by sampling trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

KAAS: an automatic genome annotation and pathway reconstruction server

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Spliced leader RNA trans-splicing in dinoflagellates

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Protein glutathionylation and oxidative stress

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Catalase characterization and implication in bleaching of a symbiotic sea anemone.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Plant thioredoxins are key actors in the oxidative stress response

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Towards a functional dissection of thioredoxin networks in plant cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis"

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Histones in functional diversification. Core histone variants

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Gene expression in Florida red tide dinoflagellate Karenia brevis: analysis of an expressed sequence tag library and development of DNA microarray

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Insights into a dinoflagellate genome through expressed sequence tag analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Lateral gene transfer in eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

"Species" radiations of symbiotic dinoflagellates in the Atlantic and Indo-Pacific since the Miocene-Pliocene transition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Dinoflagellate chloroplasts--where have all the genes gone?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Plasmodium biology: genomic gleanings

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Phylogenomics of the nucleosome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Studies of marine planktonic diatoms. I. Cyclotella nana Hustedt, and Detonula confervacea (cleve) Gran

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Scaling laws in the functional content of genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

MrBayes 3: Bayesian phylogenetic inference under mixed models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Molecular chaperones, stress proteins and redox homeostasis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Histone H3 variants specify modes of chromatin assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

SSAHA: a fast search method for large DNA databases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

InterProScan--an integration platform for the signature-recognition methods in InterPro

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

The evolution of isochores

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Chromosome separation and segregation in dinoflagellates and bacteria may depend on liquid crystalline states

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Lineage-specific loss and divergence of functionally linked genes in eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

EMBOSS: the European Molecular Biology Open Software Suite

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

KEGG: kyoto encyclopedia of genes and genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Protein disulfide isomerase as a regulator of chloroplast translational activation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

A codon-based model of nucleotide substitution for protein-coding DNA sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

The 'effective number of codons' used in a gene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

Chromatins of low-protein content: special features of their compaction and condensation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3329448

The host transcriptome remains unaltered during the establishment of coral-algal symbioses.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Development and heat stress-induced transcriptomic changes during embryogenesis of the scleractinian coral Acropora palmata.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Coral host transcriptomic states are correlated with Symbiodinium genotypes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Genomic survey of candidate stress-response genes in the estuarine anemone Nematostella vectensis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Single gene circles in dinoflagellate chloroplast genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Plastid genes in a non-photosynthetic dinoflagellate.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Histone chaperones ASF1 and NAP1 differentially modulate removal of active histone marks by LID-RPD3 complexes during NOTCH silencing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

INVESTIGATING THE BIODIVERSITY, ECOLOGY, AND PHYLOGENY OF ENDOSYMBIOTIC DINOFLAGELLATES IN THE GENUS SYMBIODINIUM USING THE ITS REGION: IN SEARCH OF A "SPECIES" LEVEL MARKER

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Development of a coral cDNA array to examine gene expression profiles in Montastraea faveolata exposed to environmental stress

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Comparative Genomic Study of the Thioredoxin Family in Photosynthetic Organisms with Emphasis on Populus trichocarpa

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0035269

Profiling differential gene expression of symbiotic and aposymbiotic corals using a high coverage gene expression profiling (HiCEP) analysis

21 January 2018

1 reference

12 December 2020

Dynamics of actin evolution in dinoflagellates

1 reference

12 December 2020

Genomic understanding of dinoflagellates

1 reference

12 December 2020

Novel regulators in photosynthetic redox control of plant metabolism and gene expression

1 reference

12 December 2020

Light-regulated transcription of genes encoding peridinin chlorophyll a proteins and the major intrinsic light-harvesting complex proteins in the dinoflagellate amphidinium carterae hulburt (Dinophycae). Changes In cytosine methylation accompany pho

1 reference

12 December 2020

Hydroxymethyluracil in eukaryote DNA: a natural feature of the pyrrophyta (dinoflagellates)

1 reference

12 December 2020

A molecular genetic classification of zooxanthellae and the evolution of animal-algal symbioses

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0035269

Identifiers

DOI

1 reference

11 August 2017

0 references

1 reference

11 August 2017

PubMed publication ID

22529998

1 reference