Searching journal content for articles similar to Shukla et al. 35 (9): 2023.

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  1. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...technologies fail in the same regions of the D. melanogaster Y ChromosomeKim et al. (2024) recently published an extensive ONT sequencing data set of many Drosophila species, including a 400× coverage of the reference D. melanogaster strain (iso-1). The D. melanogaster data set was generated using ONT Q20+ (10...
  2. Resource: CGC1, a new reference genome for Caenorhabditis elegans
    • Kazuki Ichikawa,
    • Massa J. Shoura,
    • Karen L. Artiles,
    • Dae-Eun Jeong,
    • Chie Owa,
    • Haruka Kobayashi,
    • Yoshihiko Suzuki,
    • Manami Kanamori,
    • Yu Toyoshima,
    • Yuichi Iino,
    • Ann E. Rougvie,
    • Lamia Wahba,
    • Andrew Z. Fire,
    • Erich M. Schwarz,
    • and Shinichi Morishita
    Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
    ...into exons or introns of protein-coding genes; a fourth instance may be termination of mRNAs from adjacent genes. The possibility remains that TRs are specifically transcribed into ncRNAs (Subirana and Messeguer 2021), as is known to occur for some loci in the Drosophila melanogaster (Biswas et al. 2024...
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  3. Research: Evolution of genome structure in the Drosophila simulans species complex
    • Mahul Chakraborty,
    • Ching-Ho Chang,
    • Danielle E. Khost,
    • Jeffrey Vedanayagam,
    • Jeffrey R. Adrion,
    • Yi Liao,
    • Kristi L. Montooth,
    • Colin D. Meiklejohn,
    • Amanda M. Larracuente,
    • and J.J. Emerson
    Genome Res. March 2021 31: 380-396; Published in Advance February 9, 2021, doi:10.1101/gr.263442.120
    ...1997).Previous assemblies were biased toward unique sequences, neglecting repetitive regions (Drosophila12 Genomes Consortium 2007; Bhutkar et al. 2008; Garrigan et al. 2012; Hu et al. 2013). However, these regions harbor extensive hidden genetic variation relevant to evolution and organismal...
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  4. Research: Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders
    • Heather Fairfield,
    • Anuj Srivastava,
    • Guruprasad Ananda,
    • Rangjiao Liu,
    • Martin Kircher,
    • Anuradha Lakshminarayana,
    • Belinda S. Harris,
    • Son Yong Karst,
    • Louise A. Dionne,
    • Coleen C. Kane,
    • Michelle Curtain,
    • Melissa L. Berry,
    • Patricia F. Ward-Bailey,
    • Ian Greenstein,
    • Candice Byers,
    • Anne Czechanski,
    • Jocelyn Sharp,
    • Kristina Palmer,
    • Polyxeni Gudis,
    • Whitney Martin,
    • Abby Tadenev,
    • Laurent Bogdanik,
    • C. Herbert Pratt,
    • Bo Chang,
    • David G. Schroeder,
    • Gregory A. Cox,
    • Paul Cliften,
    • Jeffrey Milbrandt,
    • Stephen Murray,
    • Robert Burgess,
    • David E. Bergstrom,
    • Leah Rae Donahue,
    • Hanan Hamamy,
    • Amira Masri,
    • Federico A. Santoni,
    • Periklis Makrythanasis,
    • Stylianos E. Antonarakis,
    • Jay Shendure,
    • and Laura G. Reinholdt
    Genome Res. July 2015 25: 948-957; Published in Advance April 27, 2015, doi:10.1101/gr.186882.114
    ...that at least one category of exome-recalcitrant mutation might be larger copy number variations or structural rearrangements. Alternatively, exome-recalcitrant mutations may simply be regulatory mutations that reside outside of the exome or are coding mutations occurring in poorly annotated regions. To explore...
  5. Method: Paired-end sequencing of Fosmid libraries by Illumina
    • Louise J.S. Williams,
    • Diana G. Tabbaa,
    • Na Li,
    • Aaron M. Berlin,
    • Terrance P. Shea,
    • Iain MacCallum,
    • Michael S. Lawrence,
    • Yotam Drier,
    • Gad Getz,
    • Sarah K. Young,
    • David B. Jaffe,
    • Chad Nusbaum,
    • and Andreas Gnirke
    Genome Res. November 2012 22: 2241-2249; Published in Advance July 16, 2012, doi:10.1101/gr.138925.112
    ..., incorrectly spaced and chimeric artifacts sufficiently low, to enable applications such as mapping of structural variation and scaffolding of de novo assemblies. We demonstrate the power of Fosill to map genome rearrangements in a cancer cell line and identified three fusion genes that were corroborated...
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