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  1. Resource: The Drosophila brain on cocaine at single-cell resolution
    • Brandon M. Baker,
    • Sneha S. Mokashi,
    • Vijay Shankar,
    • Jeffrey S. Hatfield,
    • Rachel C. Hannah,
    • Trudy F.C. Mackay,
    • and Robert R.H. Anholt
    Genome Res. October 2021 31: 1927-1937; Published in Advance May 25, 2021, doi:10.1101/gr.268037.120
    ...glia, act as the blood-brain barrier (DeSalvo et al. 2014; Kremer et al. 2017) and mediate the innate immune response (Kounatidis and Chtarbanova 2018). Genes associated with the blood-brain barrier in Drosophila are also up-regulated in response to cocaine. This includes ogre, which regulates gap...
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  2. 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
    ...of coordinately expressed genes ( Roy et al. 2002 ; Spellman and Rubin 2002 ; Lercher et al. 2003 ). Once established in populations, chromosomal inversions may play a role in the formation of new species ( Noor et al. 2001 ; Navarro and Barton 2003 ). Drosophila has been a model system for studying the evolution...
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  3. Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
    • Alexis Morrissey,
    • Jeffrey Shi,
    • Daniela Q. James,
    • and Shaun Mahony
    Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
    .... 2023; Sanchez et al. 2023; Zhao et al. 2023; Zheng et al. 2023). Although the training sets only included human samples, the test sets included data from human, mouse, Arabidopsis thaliana, Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae (Supplemental Table S2). We also...
  4. Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
    • Natan Belchikov,
    • Justine Hsu,
    • Xiang Jennie Li,
    • Julien Jarroux,
    • Wen Hu,
    • Anoushka Joglekar,
    • and Hagen U. Tilgner
    Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
    ...these associations in the human and Drosophila transcriptomes (Anvar et al. 2018; Alfonso-Gonzalez et al. 2023; Calvo-Roitberg et al. 2024). For instance, we found coordinated inclusion to be much more common with pairs of adjacent exons than with pairs of nonadjacent exons in mouse cerebellum (Gupta et al. 2018...
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  5. Research: Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
    • Andreas Schlattl,
    • Simon Anders,
    • Sebastian M. Waszak,
    • Wolfgang Huber,
    • and Jan O. Korbel
    Genome Res. December 2011 21: 2004-2013; Published in Advance August 23, 2011, doi:10.1101/gr.122614.111
    ...compensation in human cells may be less pronounced than in Drosophila melanogaster, where autosomal genes are typically partially compensated for dosage, with relative expression levels (heterozygous deletion vs. homozygous reference allele) of ;0.75 (Zhang et al. 2010). Other human cell types (i.e., non...
  6. PERSPECTIVE: Comparing the human and chimpanzee genomes: Searching for needles in a haystack
    • Ajit Varki and
    • Tasha K. Altheide
    Genome Res. December 2005 15: 1746-1758; doi:10.1101/gr.3737405
    ...these genomes while integrating these data with emerging knowledge about the corresponding “phenomes” and the relevant environmental influences. It is logical to tackle the genetic aspects via both genome-wide analyses and candidate gene studies. Genome-wide surveys could eliminate the majority of genomic...
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