ArticleBMC bioinformatics2012
NRE: a tool for exploring neutral loci in the human genome.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Variation and selection at predicted G-quadruplexes across the human pangenome.bioRxiv : the preprint server for biology · 2026Article
- Relaxation of selective constraint on the sweet-taste receptor gene TAS1R2 in lorisiform primates.Scientific reports · 2025Article
- A Protocol to Extract a Specific Genomic Region from a Public Whole-Genome Database and Modify Analytical Bin Length for Population Genetic Studies.Methods and protocols · 2024Article
- Reduction of bitter taste receptor gene family in folivorous colobine primates relative to omnivorous cercopithecine primates.Primates; journal of primatology · 2024Article
- Human subsistence and signatures of selection on chemosensory genes.Communications biology · 2023Article
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- The genetic prehistory of the Andean highlands 7000 years BP though European contact.Science advances · 2018Article
- The Role of Phylogenetically Conserved Elements in Shaping Patterns of Human Genomic Diversity.Molecular biology and evolution · 2018Article
- Modeling SNP array ascertainment with Approximate Bayesian Computation for demographic inference.Scientific reports · 2018Article
- Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories.G3 (Bethesda, Md.) · 2017Article
- Variable Autosomal and X Divergence Near and Far from Genes Affects Estimates of Male Mutation Bias in Great Apes.Genome biology and evolution · 2016Article
- The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence.BMC evolutionary biology · 2016Article
- Explosive genetic evidence for explosive human population growth.Current opinion in genetics & development · 2016Review
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- Methods and models for unravelling human evolutionary history.Nature reviews. Genetics · 2015Review
- Aberrant Time to Most Recent Common Ancestor as a Signature of Natural Selection.Molecular biology and evolution · 2015Article
- Morphological and population genomic evidence that human faces have evolved to signal individual identity.Nature communications · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundAnalyzing regions of the genome where genetic variation is free from the confounding effects of natural selection is essential for many population genetic studies. Several recent studies in humans have stressed the large effect of natural selection at linked neutral sites and have shown that the choice of putatively neutral regions can have a marked effect on estimates of demographic history.
resultsNRE (Neutral Region Explorer) provides a mechanism for the easy extraction and analysis of nearly neutral regions from the human genome. It can combine many genomic filters, including filters for selection, recombination rate, genetic distance to the nearest gene, percent overlap with annotated regions, and user-provided loci. The program implements a two-step filtering process for greater versatility, allowing users to compile a basic set of neutrality criteria, explore their effect, and use this knowledge to refine filtering. Results can be instantly downloaded in standard formats, along with summary and ranking statistics, or exported to genome browsers such as those from the 1000 Genomes and UCSC. The applicability and value of NRE are demonstrated through an example in the estimation of the ratio of chromosome X-to-autosomal effective population size using different strategies for the selection of neutral regions.
conclusionsThe combined features of NRE make possible the sort of flexible, rigorous mining and analysis of neutral loci increasingly demanded by population genetic studies. NRE is available at http://nre.cb.bscb.cornell.edu.
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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.