Ronald W. Davis

Honors and Awards

• Distinguished Alumni Award, California Institute of Technology (2007)
• Recipient of, Dickson Prize in Medicine, University of Pittsburgh (2005-2004)
• Lifetime Achievement Award, Genetics Society of America (2004)
• Herbert A. Sober Award, ASBMB/IUBMB (2004)
• Senior Scholar Award in Global Infectious Disease, Ellison Medical Foundation (2002)

Postdoctoral Advisees

Michael Akhras,  Patrick Flaherty,  Colin Harvey,  Maureen Hillenmeyer,  Janine Mok,  Alexander Morgan,  Erik Pettersson,  Junhee Seok,  Judith Zaugg,  Yuping Zhang

Internet Links

• Genome Technology Center

Current Research Interests

We are using Saccharomyces cerevisiae and Human to conduct whole genome analysis projects. The yeast genome sequence has approximately 6,000 genes. We have made a set of haploid and diploid strains (21,000) containing a complete deletion of each gene. In order to facilitate whole genome analysis each deletion is molecularly tagged with a unique 20-mer DNA sequence. This sequence acts as a molecular bar code and makes it easy to identify the presence of each deletion. The mixture of all such tag strains then allows for the analysis of the entire genome with the manipulation of a single culture. During growth under a variety of conditions the loss of a tag indicates the loss of a deletion from the population. The concentration of each tag is determined by PCR amplification of the tags and hybridization to an Affymetrix DNA chip that contains the complement to all of the DNA sequence tags. This approach is being applied to other microorganisms.

We have identified a number of wild isolates of yeast that grow at much higher temperatures than is typical for Saccharomyces cerevisiae and are pathogenic and can kill a mouse. Microarrays have been used to map complex genetic traits such as virulence traits in pathogenic Saccharomyces cerevisiae using hybridization to detect single nucleotide polymorphisms. We have developed a new technology termed Recipical Hemizygosity Scanning that allows the determination of the contribution to the phenotype of all pair wise alleles for the whole genome from 2 independent strains. Using this technology we can map and quantitate all of the alleles in the genome for any complex quantitative trait in a single tube assay. These technologies will allow us to explore allelic contributions in complex mixed culture real environments and to investigate ecology at the genome level.

We are conducting a whole genome analysis (transcriptome and proteome) from blood of Human trauma patients. In this large clinical study we are establishing the standards for clinical genomics. We have developed 2 new technologies, "Molecular Inversion Probes" (MIP) for massive multiplex analysis of SNP and DNA content in Human and, "Mismatch Repair Detection" for discovery of rare Human polymorphisms. Both technologies are being applied to numerous clinical investigations.

Clinical Trials

• Effect of Celecoxib on Perioperative Inflammatory Response in Colon Cancer Terminated

Publications

• A Rapid, Cost-Effective Method of Assembly and Purification of Synthetic DNA Probes >100 bp. Jensen MA, Jauregui L, Davis RW. PLoS One. 2012; 7 (4): e34373
• High-throughput, high-fidelity HLA genotyping with deep sequencing. Wang C, Krishnakumar S, Wilhelmy J, Babrzadeh F, Stepanyan L, Su LF, Levinson D, Fernandez-Viña MA, Davis RW, Davis MM, Mindrinos M. Proc Natl Acad Sci U S A. 2012
• Improvement in cell capture throughput using parallel bioactivated microfluidic channels. Javanmard M, Babrzadeh F, Nyrén P, Davis RW. Biomed Microdevices. 2012
• JETTA: Junction and Exon Toolkits for Transcriptome Analysis. Seok J, Xu W, Gao H, Davis RW, Xiao W. Bioinformatics. 2012
• Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research. Seok J, Xu W, Jiang H, Davis RW, Xiao W. PLoS One. 2012; 7 (2): e31440