ArticleNature biotechnology2013
High-throughput genome scaffolding from in vivo DNA interaction frequency.
Article in Nature biotechnology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers.
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Who cites it
118 citing papers in PubMed.
- Evaluation of acute myeloid leukemia using genomic proximity mapping-based next generation cytogenomics.Haematologica · 2026Article
- Benchmarking Hi-C scaffolders using reference genomes and de novo assemblies.Genome biology · 2026Article
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- Genome evolution and diversity of wild and cultivated rice species.Nature communications · 2024Article
- Review
- A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes.Nucleic acids research · 2024Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Crosslinking intensity modulates the reliability and sensitivity of chromatin conformation detection at different structural levels.Communications biology · 2024Article
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
- Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.Cell · 2024Article
- hictk: blazing fast toolkit to work with .hic and .cool files.Bioinformatics (Oxford, England) · 2024Article
- Evaluation of Acute Myeloid Leukemia Genomes using Genomic Proximity Mapping.medRxiv : the preprint server for health sciences · 2024Article
- Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing.Scientific reports · 2024Article
- Are cereal grasses a single genetic system?Nature plants · 2024Article
- GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences.Journal of molecular evolution · 2024Article
- Chromosome-scale assembly of the streamlined picoeukaryoteMicrobial genomics · 2024Article
- Orchestrating chromosome conformation capture analysis with Bioconductor.Nature communications · 2024Article
- A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes.Communications biology · 2023Article
58 more citing papers are in PubMed but not listed here.
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Abstract
Despite advances in DNA sequencing technology, assembly of complex genomes remains a major challenge, particularly for genomes sequenced using short reads, which yield highly fragmented assemblies. Here we show that genome-wide in vivo chromatin interaction frequency data, which are measurable with chromosome conformation capture-based experiments, can be used as genomic distance proxies to accurately position individual contigs without requiring any sequence overlap. We also use these data to construct approximate genome scaffolds de novo. Applying our approach to incomplete regions of the human genome, we predict the positions of 65 previously unplaced contigs, in agreement with alternative methods in 26/31 cases attempted in common. Our approach can theoretically bridge any gap size and should be applicable to any species for which global chromatin interaction data can be generated.
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