Searching journal content for articles similar to Everett et al. 30 (3): 485.

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  1. Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
    • Kangli Wang,
    • Weikun Xia,
    • Yingli Gu,
    • Songpeng Zu,
    • Qian Yang,
    • Maria Luisa Amaral,
    • Yaozhi Wang,
    • Allen Wang,
    • Xiang-Dong Fu,
    • William C. Mobley,
    • and Bing Ren
    Genome Res. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
    ...; Late-down, late downregulated DEGs in aging. (G) Expression distribution of all nuclei in the oligodendrocytes subclass across ages for representative genes from the four age-associated DEG groups in panel F.Next, we performed age-associated differential expression analysis for each cell subclass...
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  2. Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
    • Benjamin D. Umans and
    • Yoav Gilad
    Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
    ...between genetic variants and environmental stressors is key to understanding the mechanisms underlying neurological diseases. In this study, we use human brain organoids to explore how varying oxygen levels expose context-dependent gene regulatory effects. By subjecting a genetically diverse panel of 21...
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  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
    ...deletions. Indels were then polarized into “true” insertions and deletions by comparison of each variant to the Drosophila simulans and Drosophila sechellia reference strains, which enabled inference of the ancestral state (see Methods) (Supplemental Fig. S10A,B). Polarization led to loss of ∼55% of indels...
  4. Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
    • Charlie George Barker,
    • Eirini Petsalaki,
    • Girolamo Giudice,
    • Julia Sero,
    • Emmanuel Nsa Ekpenyong,
    • Chris Bakal,
    • and Evangelia Petsalaki
    Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
    .... However, the exact regulatory systems that define these changes remain poorly characterized. In this study, we used a network-systems approach to integrate imaging data and RNA-seq expression data. Our workflow allowed the discovery of unbiased and context-specific gene expression signatures and cell...
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  5. Research: Transcriptional programs mediating neuronal toxicity and altered glial–neuronal signaling in a Drosophila knock-in tauopathy model
    • Hassan Bukhari,
    • Vanitha Nithianandam,
    • Rachel A. Battaglia,
    • Anthony Cicalo,
    • Souvarish Sarkar,
    • Aram Comjean,
    • Yanhui Hu,
    • Matthew J. Leventhal,
    • Xianjun Dong,
    • and Mel B. Feany
    Genome Res. April 2024 34: 590-605; Published in Advance April 10, 2024, doi:10.1101/gr.278576.123
    ...networks to explore further the biological pathways altered in Tau P251L knock-in brains compared with controls. We used the solution of the prize-collecting Steiner forest algorithm (Tuncbag et al. 2013) to map differentially expressed genes onto a network of physical protein interactions using Drosophila...
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  6. Research: Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements
    • Divya Selvaraju,
    • Filip Wierzbicki,
    • and Robert Kofler
    Genome Res. March 2024 34: 410-425; Published in Advance March 15, 2024, doi:10.1101/gr.278706.123
    ...to different Drosophila viruses but found similarly low numbers of reads aligning to viruses in all replicates (Supplemental Table S10).A recent landmark study by Moon et al. (2018) identified the gene lok (Chk2) as a crucial factor for triggering the ping-pong cycle against the P-element. We thus speculated...
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  7. Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
    • Wen Huang,
    • Andreas Massouras,
    • Yutaka Inoue,
    • Jason Peiffer,
    • Miquel Ràmia,
    • Aaron M. Tarone,
    • Lavanya Turlapati,
    • Thomas Zichner,
    • Dianhui Zhu,
    • Richard F. Lyman,
    • Michael M. Magwire,
    • Kerstin Blankenburg,
    • Mary Anna Carbone,
    • Kyle Chang,
    • Lisa L. Ellis,
    • Sonia Fernandez,
    • Yi Han,
    • Gareth Highnam,
    • Carl E. Hjelmen,
    • John R. Jack,
    • Mehwish Javaid,
    • Joy Jayaseelan,
    • Divya Kalra,
    • Sandy Lee,
    • Lora Lewis,
    • Mala Munidasa,
    • Fiona Ongeri,
    • Shohba Patel,
    • Lora Perales,
    • Agapito Perez,
    • LingLing Pu,
    • Stephanie M. Rollmann,
    • Robert Ruth,
    • Nehad Saada,
    • Crystal Warner,
    • Aneisa Williams,
    • Yuan-Qing Wu,
    • Akihiko Yamamoto,
    • Yiqing Zhang,
    • Yiming Zhu,
    • Robert R.H. Anholt,
    • Jan O. Korbel,
    • David Mittelman,
    • Donna M. Muzny,
    • Richard A. Gibbs,
    • Antonio Barbadilla,
    • J. Spencer Johnston,
    • Eric A. Stone,
    • Stephen Richards,
    • Bart Deplancke,
    • and Trudy F.C. Mackay
    Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
    ...Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines Wen Huang 1 , 10 , Andreas Massouras 2 , 3 , 10 , Yutaka Inoue 4 , Jason Peiffer 1 , Miquel Ràmia 5 , Aaron M. Tarone 6...
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  8. Research: Transposon accumulation at xenobiotic gene family loci in aphids
    • Tobias Baril,
    • Adam Pym,
    • Chris Bass,
    • and Alex Hayward
    Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
    ...examining the contribution of TEs to resistance evolution suggest that there can be an additive effect of successive TE insertions at focal host loci over time. For example, in the well-known case of the CYP gene CYP6G1 and DDT resistance in Drosophila, successive TE insertions are linked with an increasing...
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  9. Research: Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis
    • Arun B. Dutta,
    • Daniel S. Lank,
    • Roza K. Przanowska,
    • Piotr Przanowski,
    • Lixin Wang,
    • Bao Nguyen,
    • Ninad M. Walavalkar,
    • Fabiana M. Duarte,
    • and Michael J. Guertin
    Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
    ...be closer to repressed genes on average. To test this hypothesis, we first categorized genes as significantly activated, repressed, or unchanged for each pairwise comparison within the time course. For example, Klf5 (Fig. 3B, left panel) is one of a subset of 4225 genes immediately activated from 0 to 20...
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  10. Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
    • Marin Volarić,
    • Evelin Despot-Slade,
    • Damira Veseljak,
    • Brankica Mravinac,
    • and Nevenka Meštrović
    Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
    ...or short repeat arrays (Brajković et al. 2012; Kuhn et al. 2012; Feliciello et al. 2020). In Drosophila, an X-specific variant of 1.688 g/cm3 satDNA repeats dispersed in euchromatic regions have a role in dosage compensation through upregulation of X-linked genes in Drosophila males (Menon et al. 2014...
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