ArticleGenome research2016
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 461 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
461 citing papers in PubMed, 870 citations in OpenAlex.
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- Chromosome-level genome assemblies of Brownlowia tersa and Brownlowia argentata (Brownlowioideae: Malvaceae).Scientific data · 2026Article
- Recurrent evolution of cryptic triploids in cultivated enset increases yield.PLoS genetics · 2026Article
- Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model.Communications biology · 2026Article
- A highly contiguous chromosome-level genome assembly of the Chilean jack mackerel Trachurus murphyi.Scientific data · 2026Article
- Ecological and genomic signatures of the convergent evolution of planktivory in fossil and living reef fishes over deep time.Nature communications · 2026Article
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- Whole genome sequence analysis supports the genomic mosaicism of the endangered Hawaiian duck (Anas wyvilliana).Scientific reports · 2026Article
- Assembling telomere-to-telomere genomes of Fusarium oxysporum f. sp. lactucae provides a roadmap for studying genome and phenotype evolution.BMC genomics · 2026Article
- Benchmarking Hi-C scaffolders using reference genomes and de novo assemblies.Genome biology · 2026Article
- The Evolution and Origin of Allotetraploid Aegilops geniculata Revealed by the Homoeolog-Resolved Genome Assembly.Plant biotechnology journal · 2026Article
- A chromosome-scale genome of Sarracenia purpurea reveals a significant expansion of plant defense and stress response gene families following paleopolyploidization.The plant genome · 2026Article
- Chromosome-level genome of the bank vole (Clethrionomys glareolus): a resource for eco-evo-disease research.Scientific data · 2026Article
- Genome report: de novo genome assembly of the greater Bermuda land snail, Poecilozonites bermudensis (Mollusca: Gastropoda), confirms ancestral genome duplication.G3 (Bethesda, Md.) · 2026Article
- The Neijiang pig T2T genome reveals domestication history and germplasm traits of Southwest Chinese local breeds.Communications biology · 2026Article
- NOD-like receptor repertoire in the chromosome-level genome of the demospongeFrontiers in immunology · 2026Article
- A pangenome and pantranscriptome of hexaploid oat.Nature · 2026Article
- Article
401 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 4 institutions in 1 country.
Funding
Abstract
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can address this problem, dramatically increasing the scaffold contiguity of assemblies. Here, we describe a simpler approach ("Chicago") based on in vitro reconstituted chromatin. We generated two Chicago data sets with human DNA and developed a statistical model and a new software pipeline ("HiRise") that can identify poor quality joins and produce accurate, long-range sequence scaffolds. We used these to construct a highly accurate de novo assembly and scaffolding of a human genome with scaffold N50 of 20 Mbp. We also demonstrated the utility of Chicago for improving existing assemblies by reassembling and scaffolding the genome of the American alligator. With a single library and one lane of Illumina HiSeq sequencing, we increased the scaffold N50 of the American alligator from 508 kbp to 10 Mbp.
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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.