Searching journal content for articles similar to Fujimoto et al. 30 (3): 334.

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  1. 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
    ...C. elegans whole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency Bettina Meier 1 , 6 , Susanna L. Cooke 2 , 6 , Joerg Weiss 1 , Aymeric P. Bailly 1 , 3 , Ludmil B. Alexandrov...
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  2. Research: Whole genome sequencing of matched primary and metastatic acral melanomas
    • Samra Turajlic,
    • Simon J. Furney,
    • Maryou B. Lambros,
    • Costas Mitsopoulos,
    • Iwanka Kozarewa,
    • Felipe C. Geyer,
    • Alan MacKay,
    • Jarle Hakas,
    • Marketa Zvelebil,
    • Christopher J. Lord,
    • Alan Ashworth,
    • Meirion Thomas,
    • Gordon Stamp,
    • James Larkin,
    • Jorge S. Reis-Filho,
    • and Richard Marais
    Genome Res. February 2012 22: 196-207; Published in Advance December 19, 2011, doi:10.1101/gr.125591.111
    ...Whole genome sequencing of matched primary and metastatic acral melanomas Samra Turajlic 1 , 8 , Simon J. Furney 1 , 8 , Maryou B. Lambros 2 , Costas Mitsopoulos 3 , Iwanka Kozarewa 4 , Felipe C. Geyer 2 , Alan MacKay 2...
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  3. Research: Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites
    • Neekesh V. Dharia,
    • David Plouffe,
    • Selina E.R. Bopp,
    • Gonzalo E. González-Páez,
    • Carmen Lucas,
    • Carola Salas,
    • Valeria Soberon,
    • Badry Bursulaya,
    • Tadeusz J. Kochel,
    • David J. Bacon,
    • and Elizabeth A. Winzeler
    Genome Res. November 2010 20: 1534-1544; Published in Advance September 9, 2010, doi:10.1101/gr.105163.110
    ...1;Dharia et al. 2009). First, 10–15mg of whole genomic DNA from parasites grown in leukocyte-depleted red cells from each Peruvian isolate was fragmented with DNase I, end-labeled, and hybridized to a tiling microarray that covers ;90% of coding regions, which comprise 53% of the and 60...
  4. Method: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
    • Keisha D. Carlson,
    • Peter H. Sudmant,
    • Maximilian O. Press,
    • Evan E. Eichler,
    • Jay Shendure,
    • and Christine Queitsch
    Genome Res. May 2015 25: 750-761; Published in Advance February 6, 2015, doi:10.1101/gr.182212.114
    ...known as microsatellite instability (MSI), has a long history as a biomarker for certain colorectal cancers, more recently also for endometrial cancers (Boland et al. 1998; Kim et al. 2013). In fact, a recent study used exome sequencing data (∼20× coverage, 100 bp reads) (cf. Supplemental Fig. 1...
  5. Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
    • Kohei Hagiwara,
    • Andrew Thrasher,
    • Nadezhda V. Terekhanova,
    • and Jinghui Zhang
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
    ...novo indel detection because DNA-based indel detection is known to have a limited sensitivity of 40%–50% (Fig. 1, application workflow; Alioto et al. 2015; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020). We also evaluated the effectiveness of this approach for mutations rated...
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  6. Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
    • Nick Riddiford,
    • Katarzyna Siudeja,
    • Marius van den Beek,
    • Benjamin Boumard,
    • and Allison J. Bardin
    Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
    ...; The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium 2020). These initiating mutations are thought to arise in normal cells and can therefore provide key insights into the mutational processes at play in precancerous states. Large-scale sequencing projects have detailed the mutational burdens...
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  7. Method: lobSTR: A short tandem repeat profiler for personal genomes
    • Melissa Gymrek,
    • David Golan,
    • Saharon Rosset,
    • and Yaniv Erlich
    Genome Res. June 2012 22: 1154-1162; Published in Advance April 20, 2012, doi:10.1101/gr.135780.111
    ...individual, by tracing Mendelian inheritance patterns in STR alleles in whole-genome sequencing of a HapMap trio, and by comparing lobSTR results to traditional molecular techniques. Encouraged by the speed and accuracy of lobSTR, we used the algorithm to conduct a comprehensive survey of STR variations...
  8. ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
    • Stephen Richards,
    • Yue Liu,
    • Brian R. Bettencourt,
    • Pavel Hradecky,
    • Stan Letovsky,
    • Rasmus Nielsen,
    • Kevin Thornton,
    • Melissa J. Hubisz,
    • Rui Chen,
    • Richard P. Meisel,
    • Olivier Couronne,
    • Sujun Hua,
    • Mark A. Smith,
    • Peili Zhang,
    • Jing Liu,
    • Harmen J. Bussemaker,
    • Marinus F. van Batenburg,
    • Sally L. Howells,
    • Steven E. Scherer,
    • Erica Sodergren,
    • Beverly B. Matthews,
    • Madeline A. Crosby,
    • Andrew J. Schroeder,
    • Daniel Ortiz-Barrientos,
    • Catharine M. Rives,
    • Michael L. Metzker,
    • Donna M. Muzny,
    • Graham Scott,
    • David Steffen,
    • David A. Wheeler,
    • Kim C. Worley,
    • Paul Havlak,
    • K. James Durbin,
    • Amy Egan,
    • Rachel Gill,
    • Jennifer Hume,
    • Margaret B. Morgan,
    • George Miner,
    • Cerissa Hamilton,
    • Yanmei Huang,
    • Lenée Waldron,
    • Daniel Verduzco,
    • Kerstin P. Clerc-Blankenburg,
    • Inna Dubchak,
    • Mohamed A.F. Noor,
    • Wyatt Anderson,
    • Kevin P. White,
    • Andrew G. Clark,
    • Stephen W. Schaeffer,
    • William Gelbart,
    • George M. Weinstock,
    • and Richard A. Gibbs
    Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
    ....genome.org. The annotated whole genome project has been deposited into DDBJ/EMBL/GenBank under the project accession AADE00000000. The version described in this paper is the first version, AADE01000000. The sequences of the proximal and distal Arrowhead breakpoints have been deposited in GenBank with accession nos. AY...
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