ArticleGenome research2022
Automated annotation of human centromeres with HORmon.
Article in Genome research, 2022. 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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18 citing papers in PubMed, 33 citations in OpenAlex.
- AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.Bioinformatics (Oxford, England) · 2026Article
- Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer.Genome research · 2026Article
- Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs.Genome biology · 2026Article
- RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.Molecular ecology resources · 2025Article
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- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- Novel Cascade Alpha Satellite HORs in Orangutan Chromosome 13 Assembly: Discovery of the 59mer HOR-The largest Unit in Primates-And the Missing Triplet 45/27/18 HOR in Human T2T-CHM13v2.0 Assembly.International journal of molecular sciences · 2024Article
- Precise identification of cascading alpha satellite higher order repeats in T2T-CHM13 assembly of human chromosome 3.Croatian medical journal · 2024Article
- Article
- Novel Concept of Alpha Satellite Cascading Higher-Order Repeats (HORs) and Precise Identification of 15mer and 20mer Cascading HORs in Complete T2T-CHM13 Assembly of Human Chromosome 15.International journal of molecular sciences · 2024Article
- Efficient genome monomer higher-order structure annotation and identification using the GRMhor algorithm.Bioinformatics advances · 2024Article
- Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes.American journal of human genetics · 2023Review
- Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv.Nucleic acids research · 2023Article
- Characterization of large-scale genomic differences in the first complete human genome.Genome biology · 2023Article
- Article
- HiCAT: a tool for automatic annotation of centromere structure.Genome biology · 2023Article
- Review
- In-Depth Satellitome Analyses of 37 Drosophila Species Illuminate Repetitive DNA Evolution in the Drosophila Genus.Genome biology and evolution · 2022Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in long-read sequencing opened a possibility to address the long-standing questions about the architecture and evolution of human centromeres. They also emphasized the need for centromere annotation (partitioning human centromeres into monomers and higher-order repeats [HORs]). Although there was a half-century-long series of semi-manual studies of centromere architecture, a rigorous centromere annotation algorithm is still lacking. Moreover, an automated centromere annotation is a prerequisite for studies of genetic diseases associated with centromeres and evolutionary studies of centromeres across multiple species. Although the monomer decomposition (transforming a centromere into a monocentromere written in the monomer alphabet) and the HOR decomposition (representing a monocentromere in the alphabet of HORs) are currently viewed as two separate problems, we show that they should be integrated into a single framework in such a way that HOR (monomer) inference affects monomer (HOR) inference. We thus developed the HORmon algorithm that integrates the monomer/HOR inference and automatically generates the human monomers/HORs that are largely consistent with the previous semi-manual inference.
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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.