Searching journal content for articles similar to Li et al. 21 (6): 940.

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  1. Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
    • Taishan Hu,
    • Timothy L. Mosbruger,
    • Nikolaos G. Tairis,
    • Amalia Dinou,
    • Pushkala Jayaraman,
    • Mahdi Sarmady,
    • Kingham Brewster,
    • Yang Li,
    • Tristan J. Hayeck,
    • Jamie L. Duke,
    • and Dimitri S. Monos
    Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
    ...discrepancies occur when the depth of coverage across a given region is too low for variant calling, read correction, or assembly. Low complexity region discrepancies occur in homopolymers or simple repeats. These regions commonly cause sequencing errors and often have low coverage due to either capture...
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  2. Method: Genome skimming with nanopore sequencing precisely determines global and transposon DNA methylation in vertebrates
    • Christopher Faulk
    Genome Res. June 2023 33: 948-956; Published in Advance July 13, 2023, doi:10.1101/gr.277743.123
    ...-pass or low-coverage sequencing, is defined as shallow sequencing down to 0.05× coverage of a (Li et al. 2021). Here I determined that just 0.01× coverage is sufficient to achieve high precision in global DNA methylation assessment in vertebrate s. Genome skimming has been used for diverse purposes, including...
  3. Research: Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes
    • Fan Zhang,
    • Hongzhang Xue,
    • Xiaorui Dong,
    • Min Li,
    • Xiaoming Zheng,
    • Zhikang Li,
    • Jianlong Xu,
    • Wensheng Wang,
    • and Chaochun Wei
    Genome Res. May 2022 32: 853-863; Published in Advance April 8, 2022, doi:10.1101/gr.276015.121
    ...Long-read sequencing of 111 rice s reveals significantly larger pan-s Fan Zhang1,2,7, Hongzhang Xue3,7, Xiaorui Dong3, Min Li2, Xiaoming Zheng1, Zhikang Li1,2, Jianlong Xu1,4, Wensheng Wang1,2,5 and Chaochun Wei3,6 1Institute of Crop Sciences/National Key Facility for Crop Gene Resources...
  4. Research: Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays
    • Jeremiah H. Li,
    • Chase A. Mazur,
    • Tomaz Berisa,
    • and Joseph K. Pickrell
    Genome Res. April 2021 31: 529-537; Published in Advance February 3, 2021, doi:10.1101/gr.266486.120
    ...(Wetterstrand 2019). Specifically, low-coverage shotgun whole- sequencing followed by imputation has been utilized for a number of problems in statistical and population genetics, from providing the backbone for graph- based pans in sorghum to trait mapping in human pharmacogenetics (Cai et al. 2015a; Liu et al...
  5. Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
    • Sergey Aganezov,
    • Sara Goodwin,
    • Rachel M. Sherman,
    • Fritz J. Sedlazeck,
    • Gayatri Arun,
    • Sonam Bhatia,
    • Isac Lee,
    • Melanie Kirsche,
    • Robert Wappel,
    • Melissa Kramer,
    • Karen Kostroff,
    • David L. Spector,
    • Winston Timp,
    • W. Richard McCombie,
    • and Michael C. Schatz
    Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
    ...-molecule long-read sequencing is possible even at relatively low coverage levels of 25×–30× average read depth, with very similar results achievable with either ONT or PacBio long reads.View larger version: In this window In a new window Figure 3. Structural variation inference on down-sampled long-read data...
  6. Method: Revealing the genetic structure of a trait by sequencing a population under selection
    • Leopold Parts,
    • Francisco A. Cubillos,
    • Jonas Warringer,
    • Kanika Jain,
    • Francisco Salinas,
    • Suzannah J. Bumpstead,
    • Mikael Molin,
    • Amin Zia,
    • Jared T. Simpson,
    • Michael A. Quail,
    • Alan Moses,
    • Edward J. Louis,
    • Richard Durbin,
    • and Gianni Liti
    Genome Res. July 2011 21: 1131-1138; Published in Advance March 21, 2011, doi:10.1101/gr.116731.110
    ...mating, and is likely due to the considerable variation in recombination rates along the , with about half of the events concentrated in recombination hotspots (discussed in SupplementalMaterial SI). We further sequenced two segregants from the F6 pool at low coverage (Supplemental Material SI...
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  7. Resource: A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines
    • Liming Liang,
    • Nilesh Morar,
    • Anna L. Dixon,
    • G. Mark Lathrop,
    • Goncalo R. Abecasis,
    • Miriam F. Moffatt,
    • and William O.C. Cookson
    Genome Res. April 2013 23: 716-726; Published in Advance January 23, 2013, doi:10.1101/gr.142521.112
    .....org probably because microarray-based genotyping is still more reliable than the low-coverage, next-generation sequencing used in the 1000 Genomes Project pilot 1 study. At the non-HapMap sites, 1000G imputation still achieved high quality, but the reduction of imputation accuracy was more noticeable. For rare...
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  8. Method: Association studies for next-generation sequencing
    • Li Luo,
    • Eric Boerwinkle,
    • and Momiao Xiong
    Genome Res. July 2011 21: 1099-1108; Published in Advance April 26, 2011, doi:10.1101/gr.115998.110
    ...to the stochastic placement of sequence reads across the , some regionsmay not be sampled at all or only at low coverage. The rates ofmissing data for next-generation sequencing platforms are often high (i.e., >20%). Ignoring missing data can introduce biases in association studies. Because rare variants...
  9. Resource: Accurate detection and genotyping of SNPs utilizing population sequencing data
    • Vikas Bansal,
    • Olivier Harismendy,
    • Ryan Tewhey,
    • Sarah S. Murray,
    • Nicholas J. Schork,
    • Eric J. Topol,
    • and Kelly A. Frazer
    Genome Res. April 2010 20: 537-545; Published in Advance February 11, 2010, doi:10.1101/gr.100040.109
    ...that represent artifacts of systematic sequencing errors. Additionally, once a SNP has been identified in an individual, relaxed criteria can be used to assign genotypes (detect SNPs at low coverage) in other individuals. Population sequence data can be used for SNP detection even in the absence of accurate base...
  10. Method: Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    • Nadin Rohland and
    • David Reich
    Genome Res. May 2012 22: 939-946; Published in Advance January 20, 2012, doi:10.1101/gr.128124.111
    ..., Boehnke M, Abecasis G. 2011. Low coverage sequencing: Implications for the design of complex trait association studies. Genome Res 21: 940–951. Lundin S, Stranneheim H, Pettersson E, Klevebring D, Lundeberg J. 2010. Increased throughput by parallelization of library preparation for massive sequencing. PLo...
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