Searching journal content for articles similar to Carvalho et al. 36 (1): 71.

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  1. Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
    • Harsh G. Shukla,
    • Mahul Chakraborty,
    • and J.J. Emerson
    Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
    ...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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  2. Resource: The Release 6 reference sequence of the Drosophila melanogaster genome
    • Roger A. Hoskins,
    • Joseph W. Carlson,
    • Kenneth H. Wan,
    • Soo Park,
    • Ivonne Mendez,
    • Samuel E. Galle,
    • Benjamin W. Booth,
    • Barret D. Pfeiffer,
    • Reed A. George,
    • Robert Svirskas,
    • Martin Krzywinski,
    • Jacqueline Schein,
    • Maria Carmela Accardo,
    • Elisabetta Damia,
    • Giovanni Messina,
    • María Méndez-Lago,
    • Beatriz de Pablos,
    • Olga V. Demakova,
    • Evgeniya N. Andreyeva,
    • Lidiya V. Boldyreva,
    • Marco Marra,
    • A. Bernardo Carvalho,
    • Patrizio Dimitri,
    • Alfredo Villasante,
    • Igor F. Zhimulev,
    • Gerald M. Rubin,
    • Gary H. Karpen,
    • and Susan E. Celniker
    Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
    ...reads. [Supplemental material is available for this article.] The sequence of the fruit fly Drosophila melanogaster was first reported in 2000 (Adams et al. 2000). This sequence assembly, designated Release 1, represented the single-copy fraction of the in 116.2megabases (Mb) of sequence in 134...
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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
    ...), and Drosophila mauritiana is from Garrigan et al. (2014).Here we use high-coverage long-read sequencing to assemble sim-complex s de novo, permitting us to resolve repetitive regions that have, until now, evaded scrutiny. These assemblies are comparable in completeness and contiguity to the latest release...
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  4. Method: Improved assembly of noisy long reads by k-mer validation
    • Antonio Bernardo Carvalho,
    • Eduardo G. Dupim,
    • and Gabriel Goldstein
    Genome Res. December 2016 26: 1710-1720; Published in Advance October 7, 2016, doi:10.1101/gr.209247.116
    ...of cesium chloride centrifugation for theDrosophila sample, whichmay have selected against AT-rich regions such as exons flanked by massive AT-rich satellite blocks (they will have a smaller buoyant density). A more worrisome possibility is that PacBio sequencing has some intrinsic, strong bias (e...
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