@article{honeycutt_gibson_2004, title={Use of regression methods to identify motifs that modulate germline transcription in Drosophila melanogaster}, volume={83}, ISSN={["1469-5073"]}, DOI={10.1017/S0016672304006780}, abstractNote={Identification of cis-regulatory motifs has been difficult due to the short and variable length of the sequences that bind transcription factors. Using both sequence and microarray expression data, we present a method for identifying cis-regulatory motifs that uses regression trees to refine results from simple linear regression of expression levels on motif counts. Analysis of expression patterns from two separate datasets for genes showing significant differences in expression between the sexes in Drosophila melanogaster resulted in a model that identified known binding sites upstream of genes that are differentially expressed in the germline. We obtained a strong result for motif TCGATA, part of the larger, characterized binding site of dGATAb protein. We also identified an uncharacterized motif that is positively associated with sex-biased expression and was assembled from smaller motifs grouped by our model. A regression tree model provides a grouping of independent variables into multiple linear models, an advantage over a single multivariate model. In our case, this grouping of motifs suggests binding sites for cooperating factors in sex-specific expression, as well as a way of combining smaller motifs into larger binding sites.}, number={3}, journal={GENETICS RESEARCH}, author={Honeycutt, E and Gibson, G}, year={2004}, month={Jun}, pages={177–188} }
 @article{gibson_honeycutt_2002, title={The evolution of developmental regulatory pathways}, volume={12}, ISSN={["1879-0380"]}, DOI={10.1016/S0959-437X(02)00352-0}, abstractNote={Evolutionary analysis of the content of developmental regulatory pathways has been advanced by the publication of pairs of complete genome sequences from representative taxonomic groups. Annotation of the fission yeast, rice, and mouse genomes confirms that most regulatory families are shared among eukaryotes but also shows that certain gene families have restricted distributions. Theoretical advances in the past few years include development of the theory of scale-free networks, which provides a new framework in which to consider the connectivity and evolution of regulatory systems, and introduction of algorithms that use comparative data to enhance detection of transcriptional regulatory motifs.}, number={6}, journal={CURRENT OPINION IN GENETICS & DEVELOPMENT}, author={Gibson, G and Honeycutt, E}, year={2002}, month={Dec}, pages={695–700} }