Searching journal content for articles similar to Kaplow et al. 25 (6): 907.

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  1. Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
    • Bo Yan,
    • Duan Wang,
    • Romualdas Vaisvila,
    • Zhiyi Sun,
    • and Laurence Ettwiller
    Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
    ...to read methylation and sequence from the same original DNA molecule, our method identifies both the methylation state and variants at the single-molecule level. This allows phasing of the methylation state with heterogeneous SNPs directly on the read, enabling the identification of differentially...
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  2. Method: Whole-genome bisulfite sequencing with improved accuracy and cost
    • Masako Suzuki,
    • Will Liao,
    • Frank Wos,
    • Andrew D. Johnston,
    • Justin DeGrazia,
    • Jennifer Ishii,
    • Toby Bloom,
    • Michael C. Zody,
    • Soren Germer,
    • and John M. Greally
    Genome Res. September 2018 28: 1364-1371; Published in Advance August 9, 2018, doi:10.1101/gr.232587.117
    ...Genet 41: 178–186. ↵Jeltsch A. 2006. Molecular enzymology of mammalian DNA methyltransferases. Curr Top Microbiol Immunol 301: 203–225. ↵Kaplow IM, MacIsaac JL, Mah SM, McEwen LM, Kobor MS, Fraser HB. 2015. A pooling-based approach to mapping genetic variants associated with DNA methylation. Genome Res...
  3. Method: De novo mutation rates at the single-mutation resolution in a human HBB gene region associated with adaptation and genetic disease
    • Daniel Melamed,
    • Yuval Nov,
    • Assaf Malik,
    • Michael B. Yakass,
    • Evgeni Bolotin,
    • Revital Shemer,
    • Edem K. Hiadzi,
    • Karl L. Skorecki,
    • and Adi Livnat
    Genome Res. March 2022 32: 488-498; Published in Advance January 14, 2022, doi:10.1101/gr.276103.121
    ...of encountering any particular target mutation of interest is miniscule, rendering it impractical to measure rates of target mutations using such studies.To overcome this barrier, we have developed a method that enables identifying and counting, with high accuracy, ultrarare genetic variants of choice...
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  4. Method: A comprehensively molecular haplotype-resolved genome of a European individual
    • Eun-Kyung Suk,
    • Gayle K. McEwen,
    • Jorge Duitama,
    • Katja Nowick,
    • Sabrina Schulz,
    • Stefanie Palczewski,
    • Stefan Schreiber,
    • Dustin T. Holloway,
    • Stephen McLaughlin,
    • Heather Peckham,
    • Clarence Lee,
    • Thomas Huebsch,
    • and Margret R. Hoehe
    Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
    .... To this end we haplotype-resolved a European individual, ‘‘Max Planck One’’ (MP1), to an extremely high degree of completeness, exceeding previous efforts in terms of both numbers of variants and length of contigs phased (Levy et al. 2007; Kitzman et al. 2011). We applied a fosmid pool-based next generation...
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  5. Methods: Rapid inexpensive genome-wide association using pooled whole blood
    • Jamie E. Craig,
    • Alex W. Hewitt,
    • Amy E. McMellon,
    • Anjali K. Henders,
    • Lingjun Ma,
    • Leanne Wallace,
    • Shiwani Sharma,
    • Kathryn P. Burdon,
    • Peter M. Visscher,
    • Grant W. Montgomery,
    • and Stuart MacGregor
    Genome Res. November 2009 19: 2075-2080; Published in Advance October 3, 2009, doi:10.1101/gr.094680.109
    ...the power of pooling-based GWA studies. Additionally, copy number variants are difficult to quantify, and cannot be currently analyzed. Further development of this POB methodology could be directly applied to diverse fields, such as animal trait mapping, or be transferable to other array-based technologies...
  6. Methods: Targeted screening of cis-regulatory variation in human haplotypes
    • Dominique J. Verlaan,
    • Bing Ge,
    • Elin Grundberg,
    • Rose Hoberman,
    • Kevin C.L. Lam,
    • Vonda Koka,
    • Joana Dias,
    • Scott Gurd,
    • Nicolas W. Martin,
    • Hans Mallmin,
    • Olof Nilsson,
    • Eef Harmsen,
    • Ken Dewar,
    • Tony Kwan,
    • and Tomi Pastinen
    Genome Res. January 2009 19: 118-127; Published in Advance October 29, 2008, doi:10.1101/gr.084798.108
    ...to assess AE, which maximizes the information content per gene. Linkage disequilibrium (LD) between the causal variants and intragenic SNPs can lead to AE biased toward one allele. Secondly, we measured allelic expression in pooled DNA and RNA, which allows for the enrichment of heritable variation...
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