“Our goal is to gain a more rigorous understanding of animal transcription networks. The BDTNP has developed methods to produce and quantitatively analyze data for transcription factors’ in vitro and in vivo DNA binding specificities, the expression patterns of factors and their target genes, and the accessibility of DNA in chromatin. Studying all of these components of the network together is, we believe, an essential step towards our eventual goal of deriving predictive computational models of animal transcription system wide.”

“Since we try to work at the edge of what is possible, our research can change rapidly in unexpected ways. At the moment, I see Next-Generation sequencing as being a source of vast new data sets, a major leap from microarray technology in both the information content and the complexity of analysis.”

“My research will most probably continue in the area of even earlier detection of cancer using DNA methylation markers. For colorectal cancer this means detecting the disease at a pre-cancerous stage known as an advanced adenoma. Detection of pre-cancerous disease will require improvements both in the tumor markers used and in the isolation and preparation of DNA from blood samples.”

“What I can say is that structural changes, and in particular CNVs, may indeed be responsible for a lot of sporadic disease given the fact that locus specific mutation rates for CNV mutations can be 100 to 10,000 times more frequent than locus specific mutation rates for single base pair changes or SNPs (single nucleotide polymorphisms). It may also be that the nervous system in particular is more susceptible to copy number changes than other biochemical pathways, or networks of interacting proteins in different physiological systems, within the body.”

“Larger studies and extensive clinical validation will help to identify miRNAs that have true diagnostic value. From our experience and published reports, microRNA profiles have appeared to be more useful in terms of their diagnostic value than messenger RNA profiles. The fact that miRNAs are stable in FFPE (formalin-fixed paraffin embedded) tissue samples opens up a wider array of available diagnostic specimens for such validations. Poor stability of messenger RNA in FFPE samples and the ability to amplify it has been an issue for doing such kinds of transcriptomic studies. Being able to go back to older archived tissues from patients with known clinical outcomes obviously allows you to do the kinds of studies that are needed to validate the diagnostic and predictive value of a particular profile. Recent advances in technology for detection of microRNA have pushed the ability to detect levels from even a single cell so even samples with limited material are possible to evaluate now.”