Searching journal content for articles similar to Gregory and Hebert 9 (4): 317.

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  1. Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
    • Kehan Lang,
    • Chenyang Jia,
    • Siyu Li,
    • Yi Guo,
    • Dingjun Hu,
    • and Shengquan Chen
    Genome Res. March 26, 2026 ; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
    ...types for three key oligodendrocyte lineage genes: OLIG2, CNP, and FA2H. (E,F) Pseudotime dynamics of CNP and FA2H gene expression and promoter-proximal DNA methylation along the oligodendrocyte lineage trajectory. (G) Pseudotime-based module scores of two biological processes: oligodendrocyte...
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  2. Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
    • Marin Volarić,
    • Evelin Despot-Slade,
    • Damira Veseljak,
    • Brankica Mravinac,
    • and Nevenka Meštrović
    Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
    ...; Joshi and Meller 2017). The euchromatic counterpart of (peri)centromeric DNA in the beetle T. castaneum modulates the local chromatin environment upon heat stress changing the expression of neighboring genes (Feliciello et al. 2015). Although there is clear evidence that satDNAs exist outside the (peri...
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  3. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...as regulators of the function by modulating DNA methylation levels in cis, which ultimately can represent the molecular mechanisms underlying phenotypic variation and disease.MethodsDescription of the cohortsFor this work, we used DNA methylation and PCR-free WGS data sets from individuals collected by the PCGC...
  4. Research: Delayed DNA replication in haploid human embryonic stem cells
    • Matthew M. Edwards,
    • Michael V. Zuccaro,
    • Ido Sagi,
    • Qiliang Ding,
    • Dan Vershkov,
    • Nissim Benvenisty,
    • Dieter Egli,
    • and Amnon Koren
    Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
    ...address: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA Corresponding author: koren@cornell.eduAbstractHaploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication...
  5. Resource: A genome-wide interactome of DNA-associated proteins in the human liver
    • Ryne C. Ramaker,
    • Daniel Savic,
    • Andrew A. Hardigan,
    • Kimberly Newberry,
    • Gregory M. Cooper,
    • Richard M. Myers,
    • and Sara J. Cooper
    Genome Res. November 2017 27: 1950-1960; Published in Advance October 11, 2017, doi:10.1101/gr.222083.117
    ...not necessarily reside solely in the canonical DNA sequence motif (Reddy et al. 2012b; Deplancke et al. 2016; Tehranchi et al. 2016). Consequently, to systematically examine evolutionary conservation at base pairs most critical for DAP binding, we applied a previously described method (Lee 2016) to train 10-mer...
  6. Research: DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation
    • Joseph C. Siefert,
    • Constantin Georgescu,
    • Jonathan D. Wren,
    • Amnon Koren,
    • and Christopher L. Sansam
    Genome Res. August 2017 27: 1406-1416; Published in Advance May 16, 2017, doi:10.1101/gr.218602.116
    ...regionswas not related to their proximity to genes in general (Fig. 6C). As transcriptional enhancers are often DNA demethylated during development, we also analyzed the replication timing and enrichment of differentially methylated regions (DMRs) that were demethylated between 6 and 24 hpf (Lee et al. 2015...
  7. Research: Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4
    • Kate Liddiard,
    • Brian Ruis,
    • Taylor Takasugi,
    • Adam Harvey,
    • Kevin E. Ashelford,
    • Eric A. Hendrickson,
    • and Duncan M. Baird
    Genome Res. May 2016 26: 588-600; Published in Advance March 3, 2016, doi:10.1101/gr.200840.115
    ...a predisposition for the ultimate fusion ligation. We next investigated junction-proximal sequence context and discovered a unique and significant enhancement (sixfold over WT; P≤ 0.001) in the incidence of non-B DNA structures (Cer et al. 2013) within 500 bp of LIG3−/−:LIG4−/− inter-chromosomal fusion junctions...
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  8. Research: Age-associated DNA methylation in pediatric populations
    • Reid S. Alisch,
    • Benjamin G. Barwick,
    • Pankaj Chopra,
    • Leila K. Myrick,
    • Glen A. Satten,
    • Karen N. Conneely,
    • and Stephen T. Warren
    Genome Res. April 2012 22: 623-632; Published in Advance February 1, 2012, doi:10.1101/gr.125187.111
    ...for population stratification. Together, these data provide a more complete understanding of the link between DNAm and age, showing a much stronger relationship in children than in adults, which ultimately will reveal more about the role of DNAm in health and disease. Methods DNA methylation profiling Five...
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  9. Research: C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency
    • Bettina Meier,
    • Susanna L. Cooke,
    • Joerg Weiss,
    • Aymeric P. Bailly,
    • Ludmil B. Alexandrov,
    • John Marshall,
    • Keiran Raine,
    • Mark Maddison,
    • Elizabeth Anderson,
    • Michael R. Stratton,
    • Anton Gartner,
    • and Peter J. Campbell
    Genome Res. October 2014 24: 1624-1636; Published in Advance July 16, 2014, doi:10.1101/gr.175547.114
    ..., in general, though, the DNA repair community largely relies on toxicity assays that score for reduced survival to study consequences of carcinogen exposure and/or loss of repair fidelity. These assays and assays that rely on single locus reporter systems lack the genomic breadth to characterize a full...
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  10. Research: A DNA hypermethylation module for the stem/progenitor cell signature of cancer
    • Hariharan Easwaran,
    • Sarah E. Johnstone,
    • Leander Van Neste,
    • Joyce Ohm,
    • Tim Mosbruger,
    • Qiuju Wang,
    • Martin J. Aryee,
    • Patrick Joyce,
    • Nita Ahuja,
    • Dan Weisenberger,
    • Eric Collisson,
    • Jingchun Zhu,
    • Srinivasan Yegnasubramanian,
    • William Matsui,
    • and Stephen B. Baylin
    Genome Res. May 2012 22: 837-849; Published in Advance March 5, 2012, doi:10.1101/gr.131169.111
    ...A DNA hypermethylation module for the stem/progenitor cell signature of cancer Hariharan Easwaran 1 , 7 , Sarah E. Johnstone 1 , 7 , Leander Van Neste 2 , Joyce Ohm 3 , Tim Mosbruger 1 , Qiuju Wang 1 , Martin J. Aryee 1...
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