Searching journal content for articles similar to Mi et al. 13 (9): 2118.

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  1. Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
    • Lianne B Cohen,
    • Tamara Hadzic,
    • Caitlin Sauer,
    • Julia R Gibbs,
    • and Zeba Wunderlich
    Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
    ...of how animals fight 32 infections. 33 Key words 34 Drosophila immunity/Immune-responsive enhancer/STARR-seq 35 36 Running Title 37 Genome-wide survey of fly immune enhancers 38 39 Introduction 40 When encountering pathogenic microbes, animals must regulate an effective immune response 41 to survive...
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  2. Perspective: Functional assays in Drosophila facilitate classification of variants of uncertain significance associated with rare diseases
    • Jung-Wan Mok,
    • Shelley B. Gibson,
    • Haley A. Dostalik,
    • and Shinya Yamamoto
    Genome Res. July 2025 35: 1473-1484; Published in Advance June 4, 2025, doi:10.1101/gr.278291.123
    ...and functional classification of VUS. To compile a list of papers published using Drosophila melanogaster as a model organism to study rare disease genes and variants between January 2020 and April 2024, we first performed manual inspections of all abstracts published in the following journals where many new...
  3. Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
    • Satyam P. Srivastav,
    • Cédric Feschotte,
    • and Andrew G. Clark
    Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
    ...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
  4. Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
    • Daniel Siqueira de Oliveira,
    • Anaïs Larue,
    • William Vilas Boas Nunes,
    • Francois Sabot,
    • Alejandra Bodelón,
    • María Pilar García Guerreiro,
    • Cristina Vieira,
    • and Claudia Marcia Aparecida Carareto
    Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
    ...-derived sequences (Lipatov et al. 2005). A recent transcriptome-wide study identified 327 genes in Drosophila melanogaster that generate chimeric transcripts across different populations (Oliveira et al. 2023). Among all genes, 76 generate chimeric transcripts from TE insertions that were present in one strain...
  5. Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
    • Paras Verma,
    • Deeksha Thakur,
    • Deepanshi Awasthi,
    • and Shashi Bhushan Pandit
    Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
    ...remains limited owing to dearth of subsequent proteogenomic consequences. To coalesce the genomic information embedded in exons with isoform sequences, we present an innovative framework, “Exon Nomenclature And Classification of Transcripts” (ENACT). This centralizes exonic loci such that protein sequence...
  6. Resource: The developmental proteome of Drosophila melanogaster
    • Nuria Casas-Vila,
    • Alina Bluhm,
    • Sergi Sayols,
    • Nadja Dinges,
    • Mario Dejung,
    • Tina Altenhein,
    • Dennis Kappei,
    • Benjamin Altenhein,
    • Jean-Yves Roignant,
    • and Falk Butter
    Genome Res. July 2017 27: 1273-1285; Published in Advance April 5, 2017, doi:10.1101/gr.213694.116
    ..., National University of Singapore, Singapore 117599; 7Institute of Zoology, University of Cologne, 50674 Cologne, Germany Drosophila melanogaster is a widely used genetic model organism in developmental biology. While this model organism has been intensively studied at the RNA level, a comprehensive...
  7. Research: Genome-wide analysis of promoter architecture in Drosophila melanogaster
    • Roger A. Hoskins,
    • Jane M. Landolin,
    • James B. Brown,
    • Jeremy E. Sandler,
    • Hazuki Takahashi,
    • Timo Lassmann,
    • Charles Yu,
    • Benjamin W. Booth,
    • Dayu Zhang,
    • Kenneth H. Wan,
    • Li Yang,
    • Nathan Boley,
    • Justen Andrews,
    • Thomas C. Kaufman,
    • Brenton R. Graveley,
    • Peter J. Bickel,
    • Piero Carninci,
    • Joseph W. Carlson,
    • and Susan E. Celniker
    Genome Res. February 2011 21: 182-192; Published in Advance December 22, 2010, doi:10.1101/gr.112466.110
    ...Genome-wide analysis of promoter architecture in Drosophila melanogaster Roger A. Hoskins 1 , 7 , Jane M. Landolin 1 , 7 , James B. Brown 2 , 7 , Jeremy E. Sandler 1 , Hazuki Takahashi 3 , Timo Lassmann 3 , Charles Yu...
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  8. Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
    • Jonathan S. Brammeld,
    • Mia Petljak,
    • Inigo Martincorena,
    • Steven P. Williams,
    • Luz Garcia Alonso,
    • Alba Dalmases,
    • Beatriz Bellosillo,
    • Carla Daniela Robles-Espinoza,
    • Stacey Price,
    • Syd Barthorpe,
    • Patrick Tarpey,
    • Constantine Alifrangis,
    • Graham Bignell,
    • Joana Vidal,
    • Jamie Young,
    • Lucy Stebbings,
    • Kathryn Beal,
    • Michael R. Stratton,
    • Julio Saez-Rodriguez,
    • Mathew Garnett,
    • Clara Montagut,
    • Francesco Iorio,
    • and Ultan McDermott
    Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
    ...Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer and identification of drug resistance mutations Jonathan S. Brammeld,1 Mia Petljak,1 Inigo Martincorena,1 Steven P. Williams,1 Luz Garcia Alonso,2 Alba Dalmases,3 Beatriz Bellosillo,3 Carla Daniela Robles-Espinoza,4...
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  9. Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
    • Tsung-Cheng Chang,
    • Mihaela Pertea,
    • Sungyul Lee,
    • Steven L. Salzberg,
    • and Joshua T. Mendell
    Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115
    .... Notably, the clustering of thesemiRNAs and even their order in the cluster is conserved between mammals and Drosophila, suggesting that their coordinated regulation has been subject to strong evolutionary selection (Roush and Slack 2008). Our assemblies confirmed the existence of a previously annotated...
  10. Research: Genome-wide map of regulatory interactions in the human genome
    • Nastaran Heidari,
    • Douglas H. Phanstiel,
    • Chao He,
    • Fabian Grubert,
    • Fereshteh Jahanbani,
    • Maya Kasowski,
    • Michael Q. Zhang,
    • and Michael P. Snyder
    Genome Res. December 2014 24: 1905-1917; Published in Advance September 16, 2014, doi:10.1101/gr.176586.114
    ...Genome-wide map of regulatory interactions in the human genome Nastaran Heidari 1 , 5 , Douglas H. Phanstiel 1 , 5 , Chao He 2 , Fabian Grubert 1 , Fereshteh Jahanbani 1 , Maya Kasowski 1 , 3 , Michael Q...
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