contact me at damian.kao "at" gmail.com
I am a postdoctoral researcher in Aziz Aboobaker's lab at the University of Nottingham. Our broad research topic is regeneration. Specifically, we use the freshwater flat worm (Schmidtea mediterranea) as our model organism to study the mechanism underlying regeneration. We tackle the complexities of our research with a combination of molecular experiments and next generation sequencing.
My undergraduate degree was in genetics and I've held lab technician jobs in a couple of Drosophila labs. My benchwork experience mainly consist of molecular cloning work, animal dissections, and embryo injections. When I joined the Aboobaker lab, I had the choice to analyze a large amount of RNA-seq data. Given my experience with programming and web development, I felt it was a great opportunity to get into the bioinformatics field.
My work now consists mainly of analyzing the large amount of sequencing data produced at different regenerating conditions. Processing and analyzing the data is a constant learning process as new technologies/methodologies come out every week. However, coupling the massive amount of sequencing data with biological knowledge is a far more daunting task. I hope to be able to further develop my biological knowledge and effectively bridge the gap between informatics and biological theory.
My secondary interest lies in data visualization and communication. With the exponentially rising amount of sequencing data, it is becoming more important to be able to tame this deluge of information and display it in an accessible way. I feel the traditional tables/figures or supplemental excel files that researchers commonly find in publications are just not good enough for conveying the data. There is a gold mine of information that most publications are only showing a few facets of. To that end, I am currently working on a way to use client-side browser technology to display large amounts of biological information such as NGS data.
Much of the difficulty with phylogenetic tree visualization (and with data visualization more generally) is that we all too often constrain ourselves to the “paper paradigm”—the practice of displaying data in ways that are optimized for printing on paper. Many applications fail to take full advantage of the freedom that a computer display gives us over printed sheets; we read and write documents and browse web pages that are constrained to be optimal for printing, but fail to realize that such documents are unlikely to be optimal for visualization on a digital device. Of course, the paper paradigm of visualization seems most natural to us, but is this only because we are too familiar with the paper format? Society is undergoing a rapid transition in terms of its use of computing devices. Computers have enabled us to generate and store large amounts of data that would not have been possible using paper. We now need to take the next step with a transition to data visualization that is optimized for interactive displays rather than printed paper."
― J. Rosindell1, L. J. Harmon. doi:10.1371/journal.pbio.1001406
I started this personal blog as a way to organize my research. Similar to a lab journal for a benchtop biologist, this blog serves as a way to document my progress.
I also strongly believe that science should be accessible. Rational thinking, discussion of ideas, and curiosity should be encouraged and not be relegated to esotericism. I refer to this quote by Neil deGrasse Tyson:
“I would teach how science works as much as I would teach what science knows. I would assert (given that essentially, everyone will learn to read) that science literacy is the most important kind of literacy they can take into the 21st century. I would undervalue grades based on knowing things and find ways to reward curiosity. In the end, it's the people who are curious who change the world.”
― Neil deGrasse Tyson
- KAO D, FELIX D, and ABOOBAKER A. The planarian regeneration transcriptome reveals a shared but temporally shifted regulatory program between opposing head and tail scenarios. BMC Genomics 2013, 14:797. doi:10.1186/1471-2164-14-797
- ABOOBAKER AA and KAO D. A lack of commitment for over 500 million years: conserved animal stem cell pluripotency. EMBO Journal (in press)
- SOLANA J, KAO D, MIHAYLOVA Y, JABER-HIJAZI F, MALLA S, WILSON R and ABOOBAKER A, 2012. Defining The Molecular Profile Of Planarian Pluripotent Stem Cells Using A Combinatorial RNA-Seq, RNAi And Irradiation Approach.Genome Biology. 13(3), R19 (In Press.)
- BLYTHE, MJ, KAO, D, MALLA, S, ROWSELL, J, WILSON, R, EVANS, D, JOWETT, J, HALL, A, LEMAY, V, LAM, S and ABOOBAKER, AA, 2010. A Dual Platform Approach To Transcript Discovery For The Planarian Schmidtea Mediterranea To Establish Rnaseq For Stem Cell And Regeneration Biology Plos One. 5(12)