I develop and employ computational, comparative and functional genomics approaches to study genome architecture, function and evolution. While I was a post-doc working on the human genome project it became clear to me that the genome era would not only influence the scope and type of questions that would be investigated in biology, it would require a paradigm shift in the way experimentation and data analysis were performed. I work with large and complex plant and animal genomes where we apply computational sequence analysis methods to assemble and annotate large genomes and transcriptomes, investigate within species and between species sequence variation, genome structure, gene structure, gene content, gene/genome organization and gene regulation. My research projects involve collecting primary genome annotation data in the form of genome sequences and catalogues of genes, developing methods and tools to leverage next generation sequence capacities, examining gene-expression, identifying targets of RNA and DNA binding proteins, analyzing alternatively spliced isoform expression, leveraging genomic data and approaches to address fundamental evolutionary questions concerning genome evolution, and examining the function and regulation of RNA processing.
Adam: my response continues...
So while it is true that mammals can regenerate individual tissues such as peripheral nerve and undergo compensatory hypertrophy there is no doubt that mammals have nowhere near the epimorphic abilities that salamanders do. In addition mammals tend to fibrose at...more
Dear Adam, you are, of course, correct in your comments as all animals on the planet can undergo some form of regeneration, known as physiological regeneration, to maintain homeostasis. The continual replacement of blood cells from the bone marrow, the continual replacement of epidermal cells fro...more
Hi Tim,
Classical genetics should be possible, but there are no well established lab lines not genotyping as of yet. Here are some links to some recent papers you may find interesting!
http://www.nature.com/nature/journal/v489/n7417/full/nature11499.html
http://onlinelibrary.wiley.com/doi...more
Hi Tim - thanks for you interest and your question.
So, we are really interested in doing a complete genome + annotation - and we are seeking support from additional funding sources to do this. For this competition we are requesting the materials to do a deep PacBio IsoSeq transcriptome. Our ra...more