ArticlePLoS computational biology2007
A macaque's-eye view of human insertions and deletions: differences in mechanisms.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 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
38 citing papers in PubMed, 59 citations in OpenAlex.
- MuRaL-indel: a deep learning framework for building insertion and deletion mutation rate maps.Briefings in bioinformatics · 2026Article
- Mammalian mitochondrial DNA accumulates insertions and deletions with age in energetically demanding tissues.Molecular biology and evolution · 2026Article
- Assessing the impacts of various factors on circular RNA reliability.Life science alliance · 2023Article
- Study on the Association betweenGenes · 2023Article
- Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome.Genome research · 2021Article
- Divergent genome evolution caused by regional variation in DNA gain and loss between human and mouse.PLoS computational biology · 2018Article
- Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans.BMC evolutionary biology · 2017Article
- Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover.BioEssays : news and reviews in molecular, cellular and developmental biology · 2016Review
- Purifying Selection Maintains Dosage-Sensitive Genes during Degeneration of the Threespine Stickleback Y Chromosome.Molecular biology and evolution · 2015Article
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders.Journal of molecular evolution · 2015Article
- Coding sequence density estimation via topological pressure.Journal of mathematical biology · 2015Article
- Hellbender genome sequences shed light on genomic expansion at the base of crown salamanders.Genome biology and evolution · 2014Article
- Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate.Genome biology and evolution · 2014Article
- Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome.Molecular biology and evolution · 2014Article
- DeNovoGear: de novo indel and point mutation discovery and phasing.Nature methods · 2013Article
- Segmenting the human genome based on states of neutral genetic divergence.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- The impact of trans-regulation on the evolutionary rates of metazoan proteins.Nucleic acids research · 2013Article
- The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes.Genome research · 2013Article
- "Breaking news" from spermatids.Basic and clinical andrology · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Insertions and deletions (indels) cause numerous genetic diseases and lead to pronounced evolutionary differences among genomes. The macaque sequences provide an opportunity to gain insights into the mechanisms generating these mutations on a genome-wide scale by establishing the polarity of indels occurring in the human lineage since its divergence from the chimpanzee. Here we apply novel regression techniques and multiscale analyses to demonstrate an extensive regional indel rate variation stemming from local fluctuations in divergence, GC content, male and female recombination rates, proximity to telomeres, and other genomic factors. We find that both replication and, surprisingly, recombination are significantly associated with the occurrence of small indels. Intriguingly, the relative inputs of replication versus recombination differ between insertions and deletions, thus the two types of mutations are likely guided in part by distinct mechanisms. Namely, insertions are more strongly associated with factors linked to recombination, while deletions are mostly associated with replication-related features. Indel as a term misleadingly groups the two types of mutations together by their effect on a sequence alignment. However, here we establish that the correct identification of a small gap as an insertion or a deletion (by use of an outgroup) is crucial to determining its mechanism of origin. In addition to providing novel insights into insertion and deletion mutagenesis, these results will assist in gap penalty modeling and eventually lead to more reliable genomic alignments.
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Registered trials
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.