ReviewMethods in molecular biology (Clifton, N.J.)2012
Methods to detect selection on noncoding DNA.
Review in Methods in molecular biology (Clifton, N.J.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed, 36 citations in OpenAlex.
- Ancestral chromatin state constrains the functional landscape of bivalent domains in mammalian spermatogenesis.bioRxiv : the preprint server for biology · 2026Article
- Detecting signals of adaptive evolution in grape plastomes with a focus on the Cretaceous-Palaeogene (K/Pg) transition.Annals of botany · 2022Article
- Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis.Development (Cambridge, England) · 2022Article
- KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences.Genomics, proteomics & bioinformatics · 2022Article
- Diversification and Functional Evolution of HOX Proteins.Frontiers in cell and developmental biology · 2022Review
- Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective.Frontiers in genetics · 2021Review
- Robust inference of positive selection on regulatory sequences in the human brain.Science advances · 2020Article
- Monarch Butterfly Migration Moving into the Genetic Era.Trends in genetics : TIG · 2020Review
- Parallel molecular evolution and adaptation in viruses.Current opinion in virology · 2019Review
- Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.GigaScience · 2019Article
- DNA barcoding and TLC as tools to properly identify natural populations of the Mexican medicinal species Galphimia glauca Cav.PloS one · 2019Article
- Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.PloS one · 2017Article
- Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.BMC evolutionary biology · 2015Article
- Article
- Inferring positive selection in humans from genomic data.Investigative genetics · 2015Article
- Natural selection on coding and noncoding DNA sequences is associated with virulence genes in a plant pathogenic fungus.Genome biology and evolution · 2014Article
- Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora.PLoS genetics · 2014Article
- A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers.Molecular biology and evolution · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Vast tracts of noncoding DNA contain elements that regulate gene expression in higher eukaryotes. Describing these regulatory elements and understanding how they evolve represent major challenges for biologists. Advances in the ability to survey genome-scale DNA sequence data are providing unprecedented opportunities to use evolutionary models and computational tools to identify functionally important elements and the mode of selection acting on them in multiple species. This chapter reviews some of the current methods that have been developed and applied on noncoding DNA, what they have shown us, and how they are limited. Results of several recent studies reveal that a significantly larger fraction of noncoding DNA in eukaryotic organisms is likely to be functional than previously believed, implying that the functional annotation of most noncoding DNA in these organisms is largely incomplete. In Drosophila, recent studies have further suggested that a large fraction of noncoding DNA divergence observed between species may be the product of recurrent adaptive substitution. Similar studies in humans have revealed a more complex pattern, with signatures of recurrent positive selection being largely concentrated in conserved noncoding DNA elements. Understanding these patterns and the extent to which they generalize to other organisms awaits the analysis of forthcoming genome-scale polymorphism and divergence data from more species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.