ArticlePloS one2008
Systems biology of the clock in Neurospora crassa.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
59 citing papers in PubMed, 107 citations in OpenAlex.
- Article
- A daily cycle of White Collar Complex dephosphorylation sustains circadian rhythmicity inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Phase Separation-Regulated Fungal Growth, Sexual Development, Adaptation and Synthetic Biology Applications.Journal of fungi (Basel, Switzerland) · 2025Review
- MINE: maximally informative next experiment-toward a new GWAS experimental design and methodology.G3 (Bethesda, Md.) · 2025Article
- Light-Regulated Gene Expression Patterns During Conidial Formation inCurrent issues in molecular biology · 2025Article
- MINE: a new way to design genetics experiments for discovery.Briefings in bioinformatics · 2025Article
- Origin of the clock inFrontiers in molecular biosciences · 2025Review
- The clock in growing hyphae and their synchronization in Neurospora crassa.Communications biology · 2024Article
- Light Stress in Yeasts: Signaling and Responses in Creatures of the Night.International journal of molecular sciences · 2023Review
- The macroscopic limit to synchronization of cellular clocks in single cells of Neurospora crassa.Scientific reports · 2022Article
- Characterizing the gene-environment interaction underlying natural morphological variation in Neurospora crassa conidiophores using high-throughput phenomics and transcriptomics.G3 (Bethesda, Md.) · 2022Article
- High-throughput Growth Measurements of Yeast Exposed to Visible Light.Bio-protocol · 2022Article
- The Resonance and Adaptation ofJournal of fungi (Basel, Switzerland) · 2021Article
- Circadian Interactomics: How Research Into Protein-Protein Interactions Beyond the Core Clock Has Influenced the Model of Circadian Timekeeping.Journal of biological rhythms · 2021Review
- A global search for novel transcription factors impacting the Neurospora crassa circadian clock.G3 (Bethesda, Md.) · 2021Article
- Entrainment Is NOT Synchronization: An Important Distinction and Its Implications.Journal of biological rhythms · 2021Article
- Identifying a stochastic clock network with light entrainment for single cells of Neurospora crassa.Scientific reports · 2020Article
- Circadian misalignment on submarines and other non-24-h environments - from research to application.Military Medical Research · 2020Review
- What is Phase in Cellular Clocks?The Yale journal of biology and medicine · 2019Article
- Ensemble methods for stochastic networks with special reference to the biological clock of Neurospora crassa.PloS one · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A model-driven discovery process, Computing Life, is used to identify an ensemble of genetic networks that describe the biological clock. A clock mechanism involving the genes white-collar-1 and white-collar-2 (wc-1 and wc-2) that encode a transcriptional activator (as well as a blue-light receptor) and an oscillator frequency (frq) that encodes a cyclin that deactivates the activator is used to guide this discovery process through three cycles of microarray experiments. Central to this discovery process is a new methodology for the rational design of a Maximally Informative Next Experiment (MINE), based on the genetic network ensemble. In each experimentation cycle, the MINE approach is used to select the most informative new experiment in order to mine for clock-controlled genes, the outputs of the clock. As much as 25% of the N. crassa transcriptome appears to be under clock-control. Clock outputs include genes with products in DNA metabolism, ribosome biogenesis in RNA metabolism, cell cycle, protein metabolism, transport, carbon metabolism, isoprenoid (including carotenoid) biosynthesis, development, and varied signaling processes. Genes under the transcription factor complex WCC ( = WC-1/WC-2) control were resolved into four classes, circadian only (612 genes), light-responsive only (396), both circadian and light-responsive (328), and neither circadian nor light-responsive (987). In each of three cycles of microarray experiments data support that wc-1 and wc-2 are auto-regulated by WCC. Among 11,000 N. crassa genes a total of 295 genes, including a large fraction of phosphatases/kinases, appear to be under the immediate control of the FRQ oscillator as validated by 4 independent microarray experiments. Ribosomal RNA processing and assembly rather than its transcription appears to be under clock control, suggesting a new mechanism for the post-transcriptional control of clock-controlled genes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.