ArticleGenome research2000
Assessment of compositional heterogeneity within and between eukaryotic genomes.
Article in Genome research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 149 citations in OpenAlex.
- Compositional Structure of the Genome: A Review.Biology · 2023Review
- Slaying (Yet Again) the Brain-Eating Zombie Called the "Isochore Theory": A Segmentation Algorithm Used to "Confirm" the Existence of Isochores Creates "Isochores" Where None Exist.International journal of molecular sciences · 2022Article
- Nanodosimetric Calculations of Radiation-Induced DNA Damage in a New Nucleus Geometrical Model Based on the Isochore Theory.International journal of molecular sciences · 2022Article
- BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences.Bioinformatics (Oxford, England) · 2021Article
- Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster.Genome biology and evolution · 2019Article
- Functional conservation of sequence determinants at rapidly evolving regulatory regions across mammals.PLoS computational biology · 2018Article
- Identification of Human Lineage-Specific Transcriptional Coregulators Enabled by a Glossary of Binding Modules and Tunable Genomic Backgrounds.Cell systems · 2017Article
- The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview.Journal of molecular evolution · 2017Review
- The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.Journal of molecular evolution · 2016Review
- New insights into the interplay between codon bias determinants in plants.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.Genome biology and evolution · 2015Article
- A comparative study and a phylogenetic exploration of the compositional architectures of mammalian nuclear genomes.PLoS computational biology · 2014Article
- The genome sequence of a widespread apex predator, the golden eagle (Aquila chrysaetos).PloS one · 2014Article
- Human-specific CpG "beacons" identify loci associated with human-specific traits and disease.Epigenetics · 2012Article
- Normal and compound poisson approximations for pattern occurrences in NGS reads.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- Organizational heterogeneity of vertebrate genomes.PloS one · 2012Article
- Mutation bias is the driving force of codon usage in the Gallus gallus genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2011Article
- Article
- Modeling compositional dynamics based on GC and purine contents of protein-coding sequences.Biology direct · 2010Article
- Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses.PloS one · 2010Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Using large amounts of long genomic sequences, we studied the compositional patterns of eukaryotic genomes. We developed a simple measure, the compositional heterogeneity (or variability) index, to compare the differences in compositional heterogeneity between long genomic sequences. The index measures the average difference in GC content between two adjacent windows normalized by the standard error expected under the assumption of random distribution of nucleotides in a window. We report the following findings: (1) The extent of the compositional heterogeneity in a genomic sequence strongly correlates with its GC content in all multicellular eukaryotes studied regardless of genome size. (2) The human genome appears to be highly compositionally heterogeneous both within and between individual chromosomes; the heterogeneity goes much beyond the predictions of the isochore model. (3) All genomes of multicellular eukaryotes examined in this study are compositionally heterogeneous, although they also contain compositionally uniform segments, or isochores. (4) The true uniqueness of the human (or mammalian) genome is the presence of very high GC regions, which exhibit unusually high compositional heterogeneity and contain few long homogeneous segments (isochores). In general, GC-poor isochores tend to be longer than GC-rich ones. These findings indicate that the genomes of multicellular organisms are much more heterogeneous in nucleotide composition than depicted by the isochore model and so lead to a looser definition of isochores.
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Registered trials
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