@article {320,
	title = {Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.},
	journal = {Genome Biol},
	volume = {14},
	year = {2013},
	month = {2013},
	pages = {R85},
	abstract = {<p>WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory protein coding genes. The algorithm is applicable to systems with tens of thousands of genes, while accounting for critical aspects of biological networks, including self-loops, large hubs, and target rearrangements. We validate WaRSwap on a newly inferred regulatory network from Arabidopsis thaliana, and compare outcomes on published Drosophila and human networks. Specifically, sustained input switches are among the few over-represented circuits across this diverse set of eukaryotes.</p>},
	keywords = {Algorithms, Animals, Arabidopsis, Computational Biology, Drosophila melanogaster, Gene Expression Regulation, Gene Regulatory Networks, Humans, MicroRNAs, Molecular Sequence Annotation, Nucleic Acid Conformation, Software, Transcription Factors},
	issn = {1474-760X},
	doi = {10.1186/gb-2013-14-8-r85},
	author = {Megraw, Molly and Mukherjee, Sayan and Ohler, Uwe}
}
@article {322,
	title = {A stele-enriched gene regulatory network in the Arabidopsis root.},
	journal = {Mol Syst Biol},
	volume = {7},
	year = {2011},
	month = {2011 Jan 18},
	pages = {459},
	abstract = {<p>Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65\% of the TFs, but morphological phenotypes were associated with only 16\%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered.</p>},
	keywords = {Arabidopsis, Arabidopsis Proteins, Gene Expression Profiling, Gene Regulatory Networks, MicroRNAs, Plant Roots, Reproducibility of Results, Systems Biology, Transcription Factors, Two-Hybrid System Techniques},
	issn = {1744-4292},
	doi = {10.1038/msb.2010.114},
	author = {Brady, Siobhan M and Zhang, Lifang and Megraw, Molly and Martinez, Natalia J and Jiang, Eric and Yi, Charles S and Liu, Weilin and Zeng, Anna and Taylor-Teeples, Mallorie and Kim, Dahae and Ahnert, Sebastian and Ohler, Uwe and Ware, Doreen and Walhout, Albertha J M and Benfey, Philip N}
}
