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author:("Yu, qihai")
1.  Systems Biology of the Clock in Neurospora crassa 
PLoS ONE  2008;3(8):e3105.
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.
doi:10.1371/journal.pone.0003105
PMCID: PMC2518617  PMID: 18769678
2.  Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network 
PLoS Computational Biology  2007;3(8):e171.
Hypoxia induces the expression of genes that alter metabolism through the hypoxia-inducible factor (HIF). A theoretical model based on differential equations of the hypoxia response network has been previously proposed in which a sharp response to changes in oxygen concentration was observed but not quantitatively explained. That model consisted of reactions involving 23 molecular species among which the concentrations of HIF and oxygen were linked through a complex set of reactions. In this paper, we analyze this previous model using a combination of mathematical tools to draw out the key components of the network and explain quantitatively how they contribute to the sharp oxygen response. We find that the switch-like behavior is due to pathway-switching wherein HIF degrades rapidly under normoxia in one pathway, while the other pathway accumulates HIF to trigger downstream genes under hypoxia. The analytic technique is potentially useful in studying larger biomedical networks.
Author Summary
A complex biomolecular network utilizes different pathways to perform different functions. However, the interactions within the network are typically so complicated that the pathway structure is usually hidden. By some mathematical techniques, the pathways can be identified and possibly decoupled, whereby the insightful details of the network can be exposed. As an example, we study in this paper the hypoxia response network that manifests a dramatic switch-like behavior for certain sets of rate constants: a slight change of the oxygen concentration close to a critical value will lead to distinct reaction patterns. By a technique called extreme pathway analysis, the network is decoupled into three major and some minor pathways. Flux distribution among these pathways can thus be measured by integrating the ordinary differential equations for any given set of rate constants. For the sets of rate constants where the switch-like behavior is observed, we found that such a behavior is due to the switching of flux between two of the three major pathways.
doi:10.1371/journal.pcbi.0030171
PMCID: PMC1963493  PMID: 17784783

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