Searching journal content for articles similar to Haerty and Golding 20 (6): 755.

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  1. Research: A novel quantitative trait locus implicates Msh3 in the propensity for genome-wide short tandem repeat expansions in mice
    • Mikhail O. Maksimov,
    • Cynthia Wu,
    • David G. Ashbrook,
    • Flavia Villani,
    • Vincenza Colonna,
    • Nima Mousavi,
    • Nichole Ma,
    • Lu Lu,
    • Jonathan K. Pritchard,
    • Alon Goren,
    • Robert W. Williams,
    • Abraham A. Palmer,
    • and Melissa Gymrek
    Genome Res. May 2023 33: 689-702; Published in Advance May 1, 2023, doi:10.1101/gr.277576.122
    ...microsatellite alterations at selected tetranucleotide repeats (EMAST) and to lower levels of MSI at dinucleotide repeats (Haugen et al. 2008; Campregher et al. 2012).Naturally occurring sequence variants in Msh3 have been shown to act as modifiers of the stability of CAG repeats in both mice and humans. Tomé et...
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  2. Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
    • Isabela Gerdes Gyuricza,
    • Joel M. Chick,
    • Gregory R. Keele,
    • Andrew G. Deighan,
    • Steven C. Munger,
    • Ron Korstanje,
    • Steven P. Gygi,
    • and Gary A. Churchill
    Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
    ...with age in mammalian tissues, including the heart (Bahar et al. 2006; Işıldak et al. 2020). Age-related dysregulation of transcripts is offset by selective translation, and post-transcriptional mechanisms become crucial for achieving cellular homeostasis (Gonskikh and Polacek 2017). The investigation...
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  3. Research: Genome-wide analysis of differential RNA editing in epilepsy
    • Prashant Kumar Srivastava,
    • Marta Bagnati,
    • Andree Delahaye-Duriez,
    • Jeong-Hun Ko,
    • Maxime Rotival,
    • Sarah R. Langley,
    • Kirill Shkura,
    • Manuela Mazzuferi,
    • Bénédicte Danis,
    • Jonathan van Eyll,
    • Patrik Foerch,
    • Jacques Behmoaras,
    • Rafal M. Kaminski,
    • Enrico Petretto,
    • and Michael R. Johnson
    Genome Res. March 2017 27: 440-450; doi:10.1101/gr.210740.116
    ...guanosine (i.e., A-to-G), and the conversion of cytosine to uracil (C-to-U) where uracil is translated as if it were thymine (C-to-T). These base-specific changes to RNA result from site-specific deamination of nucleotides catalyzed by ADARs (adenosine deaminases that act on RNA) and APOBEC1, the latter...
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  4. Method: Inferring the mode and strength of ongoing selection
    • Gustavo V. Barroso and
    • Kirk E. Lohmueller
    Genome Res. April 2023 33: 632-643; Published in Advance April 13, 2023, doi:10.1101/gr.276386.121
    ...(TIDES) that uses data from tens of thousands of family trios to make inferences about natural selection acting in a single generation. TIDES further improves on the state of the art by making no assumptions regarding demography, linkage, or dominance. We discuss how our method paves the way for studying...
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  5. Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
    • Ying Zhen,
    • Christian D. Huber,
    • Robert W. Davies,
    • and Kirk E. Lohmueller
    Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
    ...+ > 10−5) mutations along with the strength of selection acting on them. Weakly beneficial mutations are already accounted for in our model using the DFE from Huber et al. (2017) as they likely segregate as polymorphisms. We find that humans have a higher p+s+ than D. melanogaster, mirroring...
  6. Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
    • Stefan Oberlin,
    • Alexis Sarazin,
    • Clément Chevalier,
    • Olivier Voinnet,
    • and Arturo Marí-Ordóñez
    Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
    ...and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant s, and how such features impact their biology. Genome-wide transcript profiling revealed...
  7. Research: Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
    • Neelam Dabas Sen,
    • Fujun Zhou,
    • Nicholas T. Ingolia,
    • and Alan G. Hinnebusch
    Genome Res. August 2015 25: 1196-1205; Published in Advance June 29, 2015, doi:10.1101/gr.191601.115
    ...genes and -average length (79 nt) are shown. (B) Schematic showing 5′ UTR intervals assigned for calculating cumulative PARS scores. (C) Average PARS scores calculated for the indicated gene set for each 5′ UTR interval described in B. (*) P < 0.05. (D) Genome-wide changes in TE are negatively...
  8. Research: Genome-wide analysis of long noncoding RNA stability
    • Michael B. Clark,
    • Rebecca L. Johnston,
    • Mario Inostroza-Ponta,
    • Archa H. Fox,
    • Ellen Fortini,
    • Pablo Moscato,
    • Marcel E. Dinger,
    • and John S. Mattick
    Genome Res. May 2012 22: 885-898; Published in Advance March 9, 2012, doi:10.1101/gr.131037.111
    ...-coding transcripts. Significant difference calculated using a x2 test. Genome-wide analysis of lncRNA stability Genome Research 887 www..org that act in common biological pathways (same GO function) (Sharova et al. 2009) or proteins found within the same complexes (Friedel et al. 2009) often have similar stabilities...
  9. Research: Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability
    • Keiko Akagi,
    • Jingfeng Li,
    • Tatevik R. Broutian,
    • Hesed Padilla-Nash,
    • Weihong Xiao,
    • Bo Jiang,
    • James W. Rocco,
    • Theodoros N. Teknos,
    • Bhavna Kumar,
    • Danny Wangsa,
    • Dandan He,
    • Thomas Ried,
    • David E. Symer,
    • and Maura L. Gillison
    Genome Res. February 2014 24: 185-199; Published in Advance November 7, 2013, doi:10.1101/gr.164806.113
    ...Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability Keiko Akagi 1 , 2 , 3 , 10 , Jingfeng Li 1 , 2 , 3 , 10 , Tatevik R. Broutian 2 , 4 , Hesed Padilla-Nash 5 , Weihong Xiao 2 , 4...
  10. Research: Genome-wide detection of novel regulatory RNAs in E. coli
    • Rahul Raghavan,
    • Eduardo A. Groisman,
    • and Howard Ochman
    Genome Res. September 2011 21: 1487-1497; Published in Advance June 10, 2011, doi:10.1101/gr.119370.110
    ...Genome-wide detection of novel regulatory RNAs in E. coli Rahul Raghavan 1 , 2 , Eduardo A. Groisman 2 , 3 and Howard Ochman 1 , 2 , 4 1Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06516, USA...
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