Searching journal content for articles similar to Loomis et al. 23 (1): 121.

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  1. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...-length data provided phasing information that was corrected with the MiSeq data and resulted in the identification of 606 novel alleles out of the 1056 genes fully sequenced, which were not previously characterized (Albrecht et al. 2017).Like HLA sequences, 16S rDNA sequencing relies on an initial long...
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  2. Research: Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate
    • Wilfried M. Guiblet,
    • Marzia A. Cremona,
    • Monika Cechova,
    • Robert S. Harris,
    • Iva Kejnovská,
    • Eduard Kejnovsky,
    • Kristin Eckert,
    • Francesca Chiaromonte,
    • and Kateryna D. Makova
    Genome Res. December 2018 28: 1767-1778; Published in Advance November 6, 2018, doi:10.1101/gr.241257.118
    ...effect of non-B DNA on the fidelity of DNA synthesis. With a -wide analysis of data generated by a sequencing instrument, we substantially expanded prior knowledge of this phenomenon gained by examination of plasmid constructs, disease-associated genes, and human genetic diversity (Zhao et al. 2010...
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  3. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    ...either the repeat and/or some of its flanking sequences for numerous repeat-expandable genes, including CANVAS, SCA31, SCA37, BAFME1, 2, 3, 4, 6, 7, and DBQD. This is likely due to the inability of the methods used to handle the repeat. For example, the XYLT1 CGG repeat and its flanking sequences could...
  4. Method: Detection of long repeat expansions from PCR-free whole-genome sequence data
    • Egor Dolzhenko,
    • Joke J.F.A. van Vugt,
    • Richard J. Shaw,
    • Mitchell A. Bekritsky,
    • Marka van Blitterswijk,
    • Giuseppe Narzisi,
    • Subramanian S. Ajay,
    • Vani Rajan,
    • Bryan R. Lajoie,
    • Nathan H. Johnson,
    • Zoya Kingsbury,
    • Sean J. Humphray,
    • Raymond D. Schellevis,
    • William J. Brands,
    • Matt Baker,
    • Rosa Rademakers,
    • Maarten Kooyman,
    • Gijs H.P. Tazelaar,
    • Michael A. van Es,
    • Russell McLaughlin,
    • William Sproviero,
    • Aleksey Shatunov,
    • Ashley Jones,
    • Ahmad Al Khleifat,
    • Alan Pittman,
    • Sarah Morgan,
    • Orla Hardiman,
    • Ammar Al-Chalabi,
    • Chris Shaw,
    • Bradley Smith,
    • Edmund J. Neo,
    • Karen Morrison,
    • Pamela J. Shaw,
    • Catherine Reeves,
    • Lara Winterkorn,
    • Nancy S. Wexler,
    • The US–Venezuela Collaborative Research Group,
    • David E. Housman,
    • Christopher W. Ng,
    • Alina L. Li,
    • Ryan J. Taft,
    • Leonard H. van den Berg,
    • David R. Bentley,
    • Jan H. Veldink,
    • and Michael A. Eberle
    Genome Res. November 2017 27: 1895-1903; Published in Advance September 8, 2017, doi:10.1101/gr.225672.117
    ..., Cambridge, Massachusetts 02139, USA Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole- sequencing (WGS) data. A solution to this problem is an important step toward integrating...
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  5. Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
    • Manuel Tardaguila,
    • Lorena de la Fuente,
    • Cristina Marti,
    • Cécile Pereira,
    • Francisco Jose Pardo-Palacios,
    • Hector del Risco,
    • Marc Ferrell,
    • Maravillas Mellado,
    • Marissa Macchietto,
    • Kenneth Verheggen,
    • Mariola Edelmann,
    • Iakes Ezkurdia,
    • Jesus Vazquez,
    • Michael Tress,
    • Ali Mortazavi,
    • Lennart Martens,
    • Susana Rodriguez-Navarro,
    • Victoria Moreno-Manzano,
    • and Ana Conesa
    Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
    ..., Spain; 10Gene Expression and mRNA Metabolism Laboratory, CIPF, 46012 Valencia, Spain ↵11 Joint first authorship. Corresponding author: aconesa@ufl.edu, aconesa@cipf.esAbstractHigh-throughput sequencing of full-length transcripts using long reads has paved the way for the discovery of thousands of novel...
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  6. LETTER: CpG Methylation Modifies the Genetic Stability of Cloned Repeat Sequences
    • Kerrie Nichol and
    • and Christopher E. Pearson
    Genome Res. August 1, 2002 12: 1246-1256; Published in Advance July 19, 2002, doi:10.1101/gr.74502
    ...unsequenceable because they are unclonable, at least stably. Many of these sequences are composed of repeat sequences. In an attempt to facilitate stable maintenance of cloned repeat tracts, we have considered CpG methylation as a factor that may contribute to repeat stability. Alterations in CpG methylation...
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