Latest Publications:
Resistance to Germline RNAi in a Caenorhabditis elegans Wild Isolate Exhibits Complexity and Non-Additivity - G3

Design and Construction of Recombinant Inbred Lines - Methods in Molecular Biology
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Drosophila Sequence Specific Transcription Factor Binding Site Matrices
Various groups have been kind enough to compile lists of binding sites and matrices for a large and growing number of transcription factors in Drosophila. I am in the process of pulling many of them together for personal uses and would like to share them with the community. Its not clear to me how to cite curators of curators of experimentalists so if you would like to publish work using these matrices please do your best to cite as completely as possible. Certainly a reference to just me is not sufficient! I will attempt to include as much information as possible about where the data came from and when and if I manipulated it in any way. Please feel free to email me with questions or comments, dpollard@socrates.berkeley.edu.
DNAse I Footprinted Sites
Casey Bergman has compiled an extensive database of DNAse I footprinted sites, www.flyreg.org. I ran MEME on each set of footprints using a range of fixed widths (6-18). Some of the factors had footprints that were shorter than some of the fixed widths I was trying so I treated these cases in both of two ways: (1) I excluded all footprints shorted than the fixed width, or (2) I added flanking sequence to both sides of the footprint equal to the difference in length of the footprint and the fixed width. I then selected my choice of the best matrices for each factor. These selections can be browsed or downloaded as a tar archive or a single flat file.
More matrices from other sources will be posted soon.