ArticleNature biotechnology2013
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.
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 170 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
170 citing papers in PubMed, 326 citations in OpenAlex.
- Sequential-GAM constructs the single-cell geometric 3D genome structure.Nucleic acids research · 2026Article
- Strand-seq and the future of personalized genomics.Nature genetics · 2026Review
- HaploC-tools reveal haplotype-specific chromosome conformation and chromatin states.Nature communications · 2026Article
- Haplotype-resolved reconstruction and functional interrogation of cancer karyotypes.Cell systems · 2026Article
- A chromosome-level, haplotype-resolved genome assembly for the barn owl, Tyto alba.GigaScience · 2026Article
- CiFi: accurate long-read chromosome conformation capture with low-input requirements.Nature communications · 2025Article
- Review
- Mosquito sex determination: recent advances and applications.Current opinion in insect science · 2025Review
- Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding.Genome research · 2025Article
- Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D.Nature structural & molecular biology · 2025Article
- Active regulatory elements recruit cohesin to establish cell specific chromatin domains.Scientific reports · 2025Article
- Analysis of 30 chromosome-level Drosophila genome assemblies reveals dynamic evolution of centromeric satellite repeats.Genome biology · 2025Article
- CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Genome assembly in the telomere-to-telomere era.Nature reviews. Genetics · 2024Review
- hictk: blazing fast toolkit to work with .hic and .cool files.Bioinformatics (Oxford, England) · 2024Article
- Phased nanopore assembly with Shasta and modular graph phasing with GFAse.Genome research · 2024Article
- GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences.Journal of molecular evolution · 2024Article
- Haplotype-resolved 3D chromatin architecture of the hybrid pig.Genome research · 2024Article
- BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.Nucleic acids research · 2023Article
110 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Rapid advances in high-throughput sequencing facilitate variant discovery and genotyping, but linking variants into a single haplotype remains challenging. Here we demonstrate HaploSeq, an approach for assembling chromosome-scale haplotypes by exploiting the existence of 'chromosome territories'. We use proximity ligation and sequencing to show that alleles on homologous chromosomes occupy distinct territories, and therefore this experimental protocol preferentially recovers physically linked DNA variants on a homolog. Computational analysis of such data sets allows for accurate (∼99.5%) reconstruction of chromosome-spanning haplotypes for ∼95% of alleles in hybrid mouse cells with 30× sequencing coverage. To resolve haplotypes for a human genome, which has a low density of variants, we coupled HaploSeq with local conditional phasing to obtain haplotypes for ∼81% of alleles with ∼98% accuracy from just 17× sequencing. Whereas methods based on proximity ligation were originally designed to investigate spatial organization of genomes, our results lend support for their use as a general tool for haplotyping.
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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.