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In conclusion, we put forward a stochastic approach to model the Boolean and continuous dynamics of an experimentally-based GRN, and thus, take Waddington's Epigenetic Landscapes into a specific biological framework: Flower organ specification in Arabidopsis thaliana.
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According to our results, this protocol, here referred to as Rd.HMM, detects fine structural details on the folding patterns, that seem to be tightly linked to the fitness of a structural framework for a specific biological function.
This provided a meaningful framework for the specific biological activities that are involved in pollination-induced corolla senescence in petunias.
Similarly the 1,238 RMP specific genes are likely to provide the biological framework that separates the rodent from primate malaria.
We have developed a framework to formally couple Bayesian network learning and experimental feedback to model a specific biological response in yeast.
Despite its long history, H2A-specific clipping is nothing near a coherent biological framework.
In our framework, subnetworks do not have any specific biological meaning and are allowed to overlap.
Hereafter, we will describe specific study designs to further test the above-proposed biological framework of oxidative-stress-induced alterations in FA and 1-C cycle metabolism.
Using the Gene Ontology (GO) framework, we can statistically test for over- or under-representation of specific biological processes, molecular functions, and cellular components.
FunPat is an R package that integrates gene selection, clustering and functional annotations into a single analysis framework, providing clusters of DE genes associated to temporal patterns and specific biological terms.
However, a major limitation in this framework is their unknown mode of action, and the lack of a specific biological target.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com