Searching journal content for articles similar to Sun et al. 31 (9): 1590.

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  1. Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
    • Shelley Reich,
    • Tobias Loschko,
    • Julie Jung,
    • Samantha Nestel,
    • Ralf J. Sommer,
    • and Michael S. Werner
    Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
    ...expectations for when differential gene expression should matter. Here, we collated existing data into a gene-regulatory network (GRN) and performed developmental transcriptomics across different environmental conditions, genetic backgrounds, and mutants to assess the regulatory logic of mouth-form plasticity...
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  2. Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
    • Marina Athanasouli,
    • Tobias Loschko,
    • and Christian Rödelsperger
    Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
    ...and differential transcriptomic responses of coexpression modules in the nematode. Analysis of the interactome identifies several intestinal modules as the primary response layer to diverse microbiota and reveals a number of broadly conserved metabolic interactions. In summary, our study establishes a multiomic...
  3. Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
    • Alejandro Ceron-Noriega,
    • Miguel V. Almeida,
    • Michal Levin,
    • and Falk Butter
    Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
    ...and completeness of our chosen transcriptome assembly approach. We thus generated 74 million paired-end RNA-seq reads of 79-base length from a nonsynchronized C. elegans culture containing all developmental stages ranging from embryos to adult worms. The RNA-seq reads were quality controlled and either used...
  4. Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
    • Neel Prabh and
    • Christian Rödelsperger
    Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
    ...sequence in Drosophila (Zile et al. 2020; Li et al. 2021). Recent studies using deep transcriptomics and ribosome-profiling identified thousands of species-specific sequences with evidence of transcription and translation that form the raw material for incipient de novo gene formation (Ruiz-Orera et al...
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