Searching journal content for articles similar to Löytynoja 32 (8): 1437.

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  1. Method: Short template switch events explain mutation clusters in the human genome
    • Ari Löytynoja and
    • Nick Goldman
    Genome Res. June 2017 27: 1039-1049; Published in Advance April 6, 2017, doi:10.1101/gr.214973.116
    ...Short template switch events explain mutation clusters in the human Ari Löytynoja1 and Nick Goldman2 1Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; 2European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton...
  2. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...—but for thousands of cells (Fig. 2B). Thus, cell-type clusters can be formed from single-cell data through the analysis of gene expression patterns just like in the previously mentioned short-read single-cell studies (Klein et al. 2015; Macosko et al. 2015; Zeisel et al. 2015).Alternative exon inclusion is usually...
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  3. Method: Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome
    • Jakob Skou Pedersen,
    • Eivind Valen,
    • Amhed M. Vargas Velazquez,
    • Brian J. Parker,
    • Morten Rasmussen,
    • Stinus Lindgreen,
    • Berit Lilje,
    • Desmond J. Tobin,
    • Theresa K. Kelly,
    • Søren Vang,
    • Robin Andersson,
    • Peter A. Jones,
    • Cindi A. Hoover,
    • Alexei Tikhonov,
    • Egor Prokhortchouk,
    • Edward M. Rubin,
    • Albin Sandelin,
    • M. Thomas P. Gilbert,
    • Anders Krogh,
    • Eske Willerslev,
    • and Ludovic Orlando
    Genome Res. March 2014 24: 454-466; Published in Advance December 3, 2013, doi:10.1101/gr.163592.113
    ...; Supplemental Fig. S2.8). Interestingly, phasograms also revealed a short-range periodicity of 10 bp, coinciding with the length of a turn of the DNA helix. This could reflect preferential shifts in nucleosome positioning every 10 bp (Brogaard et al. 2012) and/or preferential cleavage of the DNA backbone facing...
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  4. Methods: High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
    • Emily Hodges,
    • Andrew D. Smith,
    • Jude Kendall,
    • Zhenyu Xuan,
    • Kandasamy Ravi,
    • Michelle Rooks,
    • Michael Q. Zhang,
    • Kenny Ye,
    • Arindam Bhattacharjee,
    • Leonardo Brizuela,
    • W. Richard McCombie,
    • Michael Wigler,
    • Gregory J. Hannon,
    • and James B. Hicks
    Genome Res. September 2009 19: 1593-1605; Published in Advance July 6, 2009, doi:10.1101/gr.095190.109
    ...-CpG cytosines, none were identified as methylated in CHP-SKN-1 and two of the nearly 250,000 interrogated were called as methylated in MDAMB-231. Significant correlation between the methylation states of adjacent CpG sites and a high incidence of short-range comethylation has been reported previously (Eckhardt...
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