I'm a Genomics Scientist at the Stowers Institute. I work with people to apply genomics methodologies to a variety of biological problems. I help people design and execute experiments. Most of my time is spent analyzing and interpreting data. I have experience designing and building microarrays for a variety of purposes. More recently I have been developing analysis routines for high volume sequence data (Illumina).
In the past I directed the microarray group at the Stowers Institute.
Current projects of interest:
Developing ChIP Seq methods for flatworm, and using UCSC assembly hubs to view the flatowrm genome.
Interactive Collaboration Network Map for the Stowers Institute - dynamically illustrates connections between people and groups based on co-publication (2012).
Design of a novel microarray for zebrafish based on VEGA40 (January 2011).
Design of novel microarrays for Schmidtea mediterranea (November 2010, March 2011).
MEEBO Chip - development of a Mouse Exonic Evidence Based Open-source long (70-mer) oligo set to represent the mouse genome, in collaboration with Ash Alizadeh and Max Diehn (2003).
Experimental Comparative Genomics Sea Urchin DNA microarray - a small project to scan the Sea Urchin genome (what's known of it to date) and design probes based on homology to highly characterized genes from other organisms.
S. pombe genome set (9000 70-mer probes for interrogating fission yeast).
Genomic Tiling array for S. cerevisiae. Consists of 70-mers designed for 250 base resolution coverage of intergenic regions of yeast. When used in conjunction with Operon's expression set one can construct a tiling array for most of the genome, good for ChIP chip and CGH.
Iterative Gene Group analysis - Understand genomic data by iterating through groups of genes to see how they are dispersed in a data set. Genes are put into groups for reasons. When the data highlights certain groups as showing activity in the data, those reasons are handed back to you.
Novel microarray for Nematostella (44k genes)
Using systematic gene synthesis to construct libraries of known mutations.
qPCR primer sets for model organism genomes:
- qPCR primer sets for all yeast genes: gff_file for browser tracks | S. cerevisiae qPCR Primers (2008). These primer sets were derived with uPrimer, and are unverified. But it's a start.
- qPCR primer sets for all S. pombe genes. S. pombe qPCR Primers (2009). Unverified.
- qPCR primer sets for all c. elegans genes. C. elegans qPCR Primers (2008). Unverified.
- qPCR primer sets for all zebrafish genes.
Common Microarray Protocols
- Post-processing of DNA microarrays printed with long oligos (70mers) - Shampoo Method
- Flourescent Probe preparation by amino-allyl Reverse Transcription.
- Total RNA prep from Yeast
- Zymo Columns for Probe cleanup
- Purification of mRNA with OliogoTex beads
- Examination of RNA with Agilent BioAnalyzer
I can be reached at cws at stowers . org