Searching journal content for articles similar to Yuille et al. 14 (10b): 2015.

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  1. Perspective: Why community consultation matters in genomic research benefit-sharing models
    • Sarah LeBaron von Baeyer,
    • Rebecca Crocker,
    • Rindra Rakotoarivony,
    • Jean Freddy Ranaivoarisoa,
    • Germain Jules Spiral,
    • Stephane Castel,
    • Andrew Farnum,
    • Holly Vance,
    • Noah Collins,
    • Keolu Fox,
    • and Kaja Wasik
    Genome Res. January 2024 34: 1-6; Published in Advance January 31, 2024, doi:10.1101/gr.278308.123
    ...areas to address through benefit-sharing distribution. Each participant was presented with a list of the previously identified five key priority areas and was asked to select the most important one. Regional differences were observed among the 257 responses, with participants from the west coast more...
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  2. Perspective: Moving beyond Bermuda: sharing data to build a medical information commons
    • Robert Cook-Deegan and
    • Amy L. McGuire
    Genome Res. June 2017 27: 897-901; Published in Advance April 3, 2017, doi:10.1101/gr.216911.116
    ..., WalthamMC, et al. 2003. Sharing publication-related data and materials: responsibilities of authorship in the life sciences. Plant Physiol 132: 19–24. Cochrane AL. 1972. Effectiveness and efficiency: random reflections on health services. Nuffield Provincial Hospitals Trust, London, UK. Collins FS, Varmus...
  3. Research: Disclosing pathogenic genetic variants to research participants: Quantifying an emerging ethical responsibility
    • Christopher A. Cassa,
    • Sarah K. Savage,
    • Patrick L. Taylor,
    • Robert C. Green,
    • Amy L. McGuire,
    • and Kenneth D. Mandl
    Genome Res. March 2012 22: 421-428; Published in Advance December 6, 2011, doi:10.1101/gr.127845.111
    ...Disclosing pathogenic genetic variants to research participants: Quantifying an emerging ethical responsibility Christopher A. Cassa 1 , 2 , 3 , 9 , Sarah K. Savage 3 , Patrick L. Taylor 4 , Robert C. Green 2 , 5 , 6 , Amy L. McGuire 7...
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  4. Insight/Outlook: Ethical and practical challenges of sharing data from genome-wide association studies: The eMERGE Consortium experience
    • Amy L. McGuire,
    • Melissa Basford,
    • Lynn G. Dressler,
    • Stephanie M. Fullerton,
    • Barbara A. Koenig,
    • Rongling Li,
    • Cathy A. McCarty,
    • Erin Ramos,
    • Maureen E. Smith,
    • Carol P. Somkin,
    • Carol Waudby,
    • Wendy A. Wolf,
    • and Ellen Wright Clayton
    Genome Res. July 2011 21: 1001-1007; Published in Advance June 1, 2011, doi:10.1101/gr.120329.111
    ...Specimens collected over time, using multiple consents, with evolving revisions Lack of consistency across consortium sites in IRB determination for need for re-contact and new consent for GWAS, federal data sharing Balancing compliance with NIH GWAS data-sharing policy with site-specific responsibility...
  5. Resource: A systems view on DNA damage response kinetics in Tetrahymena
    • Emily Nischwitz,
    • Vivien Schoonenberg,
    • Rachel Mullner,
    • Albert Fradera-Sola,
    • Susanne Zimbelmann,
    • Joshua J Smith,
    • and Falk Butter
    Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
    ...Systems Biology of Signal Transduction, German Cancer 15 Research Center (DKFZ), 69120 Heidelberg, Germany 16 8 These authors contributed equally. Either author can be listed first. 17 * Correspondence: falk.butter@fli.de (FB) 18 19 Abstract 20 A tightly regulated DNA damage response is critical...
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  6. Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
    • Irene Mei,
    • Susanne Nichterwitz,
    • Melanie Leboeuf,
    • Jik Nijssen,
    • Isadora Lenoel,
    • Dirk Repsilber,
    • Christian S. Lobsiger,
    • and Eva Hedlund
    Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
    ...upregulate both detrimental and regenerative responses to ALS and share pathway activation, indicating that breakdown occurs through similar mechanisms across vulnerable neurons, albeit with distinct timing. Meta-analysis across four rodent mutant Sod1 MN transcriptome data sets identify a shared...
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  7. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...in ATAC-seq peaks were also 185 significantly enriched among regions gaining H3K27ac. These shared terms included 186 hallmark antiviral processes such as “interferon-mediated signalling pathway” and “response 187 to type I interferon” and “regulation of receptor signalling pathway via JAK...
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  8. Method: Unified integration of spatial transcriptomics across platforms with LLOKI
    • Ellie Haber,
    • Ajinkya Deshpande,
    • Jian Ma,
    • and Spencer Krieger
    Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
    ...panels, data sparsity, and technical variability. Here, we introduce LLOKI, a novel framework for integrating imaging-based ST data from diverse platforms without requiring shared gene panels. LLOKI addresses ST integration through two key alignment tasks: feature alignment across technologies and batch...
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  9. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ...structure and the complex genetic architecture they reveal.To address these limitations, estimates of pairwise haplotypes shared identical-by-descent, or identity-by-descent (IBD), offer a more precise approach for detecting recent fine-scale population structure in large genomic data sets (Shemirani et al...
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  10. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...response, is highlighted in red.To facilitate comparison, we combined the two pans and categorized each gene family based on its presence or absence across all strains into six distinct groups: Shared core gene families are present in all strains of both species, whereas species-unique core gene families...
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