Emily Rocke - Genome Sciences home page

I am a postdoctoral researcher in the Thomas lab in the Genome Sciences department at the University of Washington in Seattle. I have been learning biology and genetics techniques such as PCR (a technique used to duplicate large quantites of DNA sequence), DNA sequencing, and generally moving clear liquids around in pipettes. At the moment, I am carrying out a set of experiments to test the effect of specific regulatory sites in the nematode C. elegans.

I am also continuing my computational work on studying gene regulation and discovering regulatory sites. I am using large gene families in C. elegans such as some chemosensory gene families and the nuclear hormone receptor (nhr) genes. My primary research focus is to figure out how the 3-dimensional structure of DNA affects gene regulation. For example, as DNA winds around globs of protein called nucleosomes for storage, some sites on the DNA are more accessible than others, and some regulatory sites may be confined to these accessible regions in order to have an effect.

I did my Ph.D. work in the Computer Science and Engineering department, also at UW, with Martin Tompa. My graduate work focused on an algorithm for gapped motif discovery. A motif is an approximately repeating pattern in DNA or protein sequence, and a gapped motif is, loosely speaking, a motif in which alignment of the instances is helpful in seeing the strength of the pattern. As part of my work on motif discovery in protein sequences, I also developed a new method of scoring protein sequence alignments.

Curriculum Vitae

•   rocke-cv.pdf   rocke-cv.html

Papers

• New! Brief abstract of recent work on how 3-dimensional DNA structure affects a specific regulatory site in C. elegans:   Possible effect of chromatin structure on nhr family regulation, to be presented in a talk at the West coast worm meeting 2004. Preprint of a more detailed paper on this work will be available soon, on request.
• My Ph.D. dissertation:   thesis.pdf   thesis.ps
• A Hybrid Scoring Function for Protein Multiple Alignment, Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI) 2002.   pdf   ps
• Characterizing History Independent Data Structures.. Jason Hartline, Edwin Hong, Alexander Mohr, William Pentney, and Emily Rocke. International Society for Analysis, its Applications and Computation (ISAAC) 2002. © Springer-Verlag.   pdf   ps
• Using Suffix Trees for Gapped Motif Discovery. Proceedings of Combinatorial Pattern Matching (CPM) 2000. © Springer-Verlag, LNCS series.   pdf   ps
• An Algorithm for Finding Novel Gapped Motifs in DNA sequences. Emily Rocke and Martin Tompa. Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB) 1998.   pdf   ps

Contact info

Genome sciences, Thomas Lab
Health Sciences J-183
1705 NE Pacific St.
Seattle, WA 98195-7730

office: (206) 543-1435
fax: (206) 543-0754

ecrocke [at] gs.washington.edu