Searching journal content for articles similar to Shlomi et al. 17 (11): 1626.

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  1. LETTER: The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
    • Gabriel Musso,
    • Michael Costanzo,
    • ManQin Huangfu,
    • Andrew M. Smith,
    • Jadine Paw,
    • Bryan-Joseph San Luis,
    • Charles Boone,
    • Guri Giaever,
    • Corey Nislow,
    • Andrew Emili,
    • and Zhaolei Zhang
    Genome Res. July 2008 18: 1092-1099; Published in Advance May 7, 2008, doi:10.1101/gr.076174.108
    ...The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast Gabriel Musso 1 , 2 , Michael Costanzo 1 , 2 , ManQin Huangfu 1 , 2 , Andrew M. Smith 1 , 2 , Jadine Paw 2 , Bryan-Joseph San Luis...
  2. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...high-order interactions. In contrast, boosting tree algorithms combine features through hierarchical conditional judgments. This mechanism inherently introduces multilevel conditional dependencies, enabling the model to automatically express nonlinear effects and potential higher-order interactions...
  3. Resource: Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq
    • Vincent M. Bruno,
    • Zhong Wang,
    • Sadie L. Marjani,
    • Ghia M. Euskirchen,
    • Jeffrey Martin,
    • Gavin Sherlock,
    • and Michael Snyder
    Genome Res. October 2010 20: 1451-1458; Published in Advance September 1, 2010, doi:10.1101/gr.109553.110
    ...Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq Vincent M. Bruno 1 , Zhong Wang 2 , Sadie L. Marjani 3 , Ghia M. Euskirchen 4 , Jeffrey Martin 2 , Gavin Sherlock 4 , 5...
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  4. Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    • Olga M. Sigalova,
    • Mattia Forneris,
    • Frosina Stojanovska,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Adam Rabinowitz,
    • Fayrouz Hammal,
    • Benoît Ballester,
    • Judith B. Zaugg,
    • and Eileen E.M. Furlong
    Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
    ...do so in a time point–specific manner, leading to significant allelic imbalance only at either 6–8 h or 10–12 h of embryogenesis. This is in keeping with our previous findings of condition-dependent eQTL during embryogenesis, in which the main variants (many in putative enhancers) impacted gene...
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  5. Research: Copy number variation alters local and global mutational tolerance
    • Grace Avecilla,
    • Pieter Spealman,
    • Julia Matthews,
    • Elodie Caudal,
    • Joseph Schacherer,
    • and David Gresham
    Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
    ...that affected fitness, 94% had condition-dependent effects. Research using mutation accumulation lines, wherein selection against deleterious mutations is relaxed by extreme bottlenecking (Katju and Bergthorsson 2019), has generated numerous estimates of CNV formation rates (Lynch et al. 2008; Liu and Zhang...
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  6. Method: Spatial Cellular Networks from omics data with SpaCeNet
    • Stefan Schrod,
    • Niklas Lück,
    • Robert Lohmayer,
    • Stefan Solbrig,
    • Dennis Völkl,
    • Tina Wipfler,
    • Katherine H. Shutta,
    • Marouen Ben Guebila,
    • Andreas Schäfer,
    • Tim Beißbarth,
    • Helena U. Zacharias,
    • Peter J. Oefner,
    • John Quackenbush,
    • and Michael Altenbuchinger
    Genome Res. September 2024 34: 1371-1383; Published in Advance September 4, 2024, doi:10.1101/gr.279125.124
    ...to a probabilistic model and edges between nodes represent conditional dependence between them, where the conditioning is on the remaining nodes in the network. The absence of edges defines a set of CI relations corresponding to direct pairwise independence between variables: for two variables X and Y that are CI...
  7. Research: The predicted RNA-binding protein regulome of axonal mRNAs
    • Raphaëlle Luisier,
    • Catia Andreassi,
    • Lisa Fournier,
    • and Antonella Riccio
    Genome Res. September 2023 33: 1497-1512; Published in Advance August 15, 2023, doi:10.1101/gr.277804.123
    ...with short 3′ UTR in NTF3-treated condition. Depending on the neurotrophin, 3′ UTR shifts targeted genes associated with distinct biological pathways: Whereas target genes related to cellular stress and DNA damage were overrepresented in response to NGF (Fig. 1I, top), target genes in neurons treated...
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  8. Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
    • Ulrich Omasits,
    • Adithi R. Varadarajan,
    • Michael Schmid,
    • Sandra Goetze,
    • Damianos Melidis,
    • Marc Bourqui,
    • Olga Nikolayeva,
    • Maxime Québatte,
    • Andrea Patrignani,
    • Christoph Dehio,
    • Juerg E. Frey,
    • Mark D. Robinson,
    • Bernd Wollscheid,
    • and Christian H. Ahrens
    Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
    ...Center Zurich, ETH & UZH Zurich, CH-8057 Zurich, Switzerland ↵6 These authors contributed equally to this work. Corresponding author: christian.ahrens@agroscope.admin.chAbstractAccurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing...
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  9. Research: Fitness benefits of loss of heterozygosity in Saccharomyces hybrids
    • Samuel M. Lancaster,
    • Celia Payen,
    • Caiti Smukowski Heil,
    • and Maitreya J. Dunham
    Genome Res. October 2019 29: 1685-1692; Published in Advance September 23, 2019, doi:10.1101/gr.245605.118
    ...Figure S5. Data from Supplemental Table S1. R2 = 0.00.View this table: In this window In a new window Table 2. Condition-dependent haploproficiency in hybrid yeastFitness effects of LOH are allele-specificIn our previous work, we found that loss of heterozygosity at the PHO84 locus was beneficial when...
  10. Method: Improved discovery of genetic interactions using CRISPRiSeq across multiple environments
    • Mia Jaffe,
    • Adam Dziulko,
    • Justin D. Smith,
    • Robert P. St.Onge,
    • Sasha F. Levy,
    • and Gavin Sherlock
    Genome Res. April 2019 29: 668-681; Published in Advance February 19, 2019, doi:10.1101/gr.246603.118
    ..., the 760 single CRISPRi strains carry gRNAs targeting 403 essential genes and 56 genes involved in respiration (Supplemental Table S1), spanning 97 GO-Slim Biological Process annotations (Hong et al. 2008), with up to five unique gRNAs per gene. In contrast to studies that use newly designed guide...
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