Areas Paul McMurdie is Knowledgeable in:
I am most interested in problems that utilize microbes for the production of energy or commodity chemicals, or for the destruction of hazardous compounds that threaten human health or the environment. I am also interested in new DNA sequencing technology, its applications and challenges, especially related computational and statistical challenges.
Techniques Paul McMurdie Uses:
Extensive literature reviews, numerical simulations / modeling, algorithm development, combinatoric molecular reactions, brute-force screening, brute-force computation, trial-and-error, magnets, hot glue, duct tape.
Paul McMurdie's Problem Solving Skills:
- graphic display of complex data
- Drupal database construction
- bioinformatics and genome assembly, Next-Gen sequencing, bacterial genetics
- microbiology techniques, anaerobic cell culture, unusual bacterial metabolism
- Statistical programming / data mining - R language
- molecular biology, assay development, PCR, probe design, cloning
Paul McMurdie's Problem Solving Experience:
- I helped design and test a qPCR assay for measuring the specific concentration of a particular gene in samples that contained dirt, microbes, and toxic compounds.
- I helped test/troubleshoot a novel cell-sorting technique applied to very small (0.2 - 0.5 micrometer diameter) bacterial cells using a custom microfluidics device with integrated laser trap and on-chip chemistries. I also helped design and build an unrelated microfluidics device for fragmenting and sorting bacterial filaments.
- I developed a custom web-based bacterial strain database for my former lab based on Drupal / MySQL. They interact with the database exclusively using web browsers and currently track ~1000 bacterial strains from >100 experiments and 20 researchers, past and present.
- I developed a custom workflow of tools for bacterial genome annotation and comparative genomics. The result of that analysis is now published in a peer-reviewd, open-access genetics journal.
- I designed a system to detect and study a gene delivery system in an unusual bacterium (publication pending).
- I developed heuristic algorithms to sort DNA sequences from multiple organisms, and as well as the proceeding lab work required to finish ("close") sequencing the genome of interest. One such complete genome is now available in GenBank and another is in preparation.