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 Knowledge of where all the functional elements are located in a eukaryotic genome cannot by itself unleash an understanding of gene regulation as these elements operate in the context of chromatin, where DNA is wrapped around a core of eight histone proteins and packaged into higher order structures.
Functional elements might interchange between these chromatin contexts depending upon the temporal, spatial, and environmental state of the cell. Our research aims to provide a better understanding of where the functional elements reside in relation to nucleosomes.
Publications
 Interaction of Transcriptional Regulators with Specific Nucleosomes across the Saccharomyces Genome
R. Thomas Koerber, Ho Sung Rhee,, Cizhong Jiang and B. Franklin Pugh
Molecular Cell, Volume 35, Issue 6, 889-902, 24 September 2009
Download the data.
 A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome
Travis N. Mavrich, Ilya P. Ioshikhes, Bryan J. Venters, Cizhong Jiang, Lynn P. Tomsho, Ji Qi, Stephan C. Schuster, Istvan Albert, and B. Franklin Pugh
Genome Research, published online June 12, 2008
Download the sequencing data. Visit the website (now combined with the H2AZ data) displaying the nucleosome predictions. More information about GeneTrack a custom software tool written to address the storage, analysis and display needs of our project.
 Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome
Istvan Albert, Travis N. Mavrich, Lynn P. Tomsho, Ji Qi, Sara J. Zanton , Stephan C. Schuster, and B. Franklin Pugh
Nature 446, 572-576, (2007)
Download the sequencing data. Visit the website (now combined with the H3/H4 data) displaying the nucleosome predictions. More information about GeneTrack a custom software tool written to address the storage, analysis and display needs of our project.
 Nucleosome positions predicted by comparative genomics
Ilya P. Ioshikhes, Istvan Albert, Sara J. Zanton, and B. Franklin Pugh
Nature Genetics - 38 , 1210-1215 (2006)
Download the correlation data. Visit the website displaying the nucleosome predictions based on the dinucleotide correlation pattern.
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