GC3 biology in corn, rice, sorghum and other grasses (Q21267226)

1043108578

19 August 2022

Tatiana V. Tatarinova

Tatiana V Tatarinova

1

Tatiana V

Tatarinova

1 reference

19 August 2022

John B Bouck

3

John B

Bouck

1 reference

1043108578

19 August 2022

Kenneth A Feldmann

series ordinal

4

author given names

Kenneth A

author last names

Feldmann

1 reference

1043108578

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

19 August 2022

language of work or name

English

0 references

publication date

2010

0 references

published in

BMC Genomics

0 references

volume

11

0 references

issue

1

0 references

page(s)

308

0 references

cites work

1 reference

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Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters

19 March 2017

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The TIGR Plant Transcript Assemblies database

19 March 2017

1 reference

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GC-compositional strand bias around transcription start sites in plants and fungi

19 March 2017

1 reference

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Genome wide analysis of Arabidopsis core promoters

19 March 2017

1 reference

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GC-content evolution in mammalian genomes: the biased gene conversion hypothesis

19 March 2017

1 reference

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Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine

19 March 2017

1 reference

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The Sorghum bicolor genome and the diversification of grasses

19 March 2017

1 reference

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Can GC content at third-codon positions be used as a proxy for isochore composition?

19 March 2017

1 reference

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Isochores and the evolutionary genomics of vertebrates

19 March 2017

1 reference

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Warm-blooded isochore structure in Nile crocodile and turtle

19 March 2017

1 reference

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An approach to the organization of eukaryotic genomes at a macromolecular level

19 March 2017

1 reference

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Isochores exhibit evidence of genes interacting with the large-scale genomic environment

19 March 2017

1 reference

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Chromosome bands, their chromatin flavors, and their functional features

19 March 2017

1 reference

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The isochore patterns of invertebrate genomes

19 March 2017

1 reference

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Developmental programming of CpG island methylation profiles in the human genome

12 September 2017

1 reference

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Insights into corn genes derived from large-scale cDNA sequencing

12 September 2017

1 reference

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Osiris: an integrated promoter database for Oryza sativa L.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Rapidly regulated genes are intron poor.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Links between core promoter and basic gene features influence gene expression

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Insights into the Musa genome: syntenic relationships to rice and between Musa species

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Rapid divergence of codon usage patterns within the rice genome

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

The TIGR Rice Genome Annotation Resource: improvements and new features

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Codon usage between genomes is constrained by genome-wide mutational processes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Isochores and tissue-specificity

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Biased gene conversion: implications for genome and sex evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Vanishing GC-rich isochores in mammalian genomes.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

The impact of polyploidy on grass genome evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Selection for short introns in highly expressed genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Compositional gradients in Gramineae genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Colinearity and gene density in grass genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Two classes of genes in plants

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Chargaff difference analysis of the bithorax complex of Drosophila melanogaster

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Codon usage and gene function are related in sequences of Arabidopsis thaliana

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Compositional differences within and between eukaryotic genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Statistical analysis of vertebrate sequences reveals that long genes are scarce in GC-rich isochores.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Codon usage in bacteria: correlation with gene expressivity

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Molecular basis of base substitution hotspots in Escherichia coli

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

The signature of selection mediated by expression on human genes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Gradients in nucleotide and codon usage along Escherichia coli genes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Compositional compartmentalization and compositional patterns in the nuclear genomes of plants

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

The isochore organization and the compositional distribution of homologous coding sequences in the nuclear genome of plants

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Gene distribution and isochore organization in the nuclear genome of plants

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

On the possible effects of homeostatic shifts in human embryonic development

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Deletion polymorphism in wheat chromosome regions with contrasting recombination rates

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Effect of CWG methylation on expression of plant genes

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Correlation of chi orientation with transcription indicates a fundamental relationship between recombination and transcription.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

The distribution of genes in the human genome

30 May 2018

1 reference

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Genome-wide discovery of cis-elements in promoter sequences using gene expression

30 May 2018

1 reference

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GC level and expression of human coding sequences

29 November 2018

1 reference

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Different functional classes of genes are characterized by different compositional properties

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Codon usage in higher plants, green algae, and cyanobacteria.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Synonymous codon usage and gene function are strongly related in Oryza sativa

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Duplication and DNA segmental loss in the rice genome: implications for diploidization

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Mutational bias affects protein evolution in flowering plants

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Skew in CG content near the transcription start site in Arabidopsis thaliana.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Covariation of GC content and the silent site substitution rate in rodents: implications for methodology and for the evolution of isochores.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

The covariation between TpA deficiency, CpG deficiency, and G C content of human isochores is due to a mathematical artifact.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

Codon usages in different gene classes of the Escherichia coli genome

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2895627

The correlation between GC3 and hydropathy in human genes

29 November 2018

1 reference

12 December 2020

Human coding and noncoding DNA: compositional correlations

1 reference

12 December 2020

Epialleles via DNA methylation: consequences for plant evolution

1 reference

12 December 2020

In plants, highly expressed genes are the least compact

1 reference

12 December 2020

Comparative genomics of grasses promises a bountiful harvest

1 reference

12 December 2020

Recombination and mammalian genome evolution

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2164-11-308

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2164-11-308

1 reference

9 September 2019

Fatcat ID

release_b2sp4xkgsves7e6radqelwhvni

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/b2sp4xkgsves7e6radqelwhvni

24 November 2022

mapped directly with Wikidata item

1 reference

1 reference

PubMed publication ID

20470436

1 reference