Tuesday, January 27, 2009

Pseudomonas and Langille in the media

Ok, this is some serious self-promotion, but scientists (well PhD students anyway) don't get a chance to brag about their research being in the media very often. Plus, it is my blog, so why not?!

The actual science:
The research in question surrounded the sequencing of the Liverpool Epidemic Strain of Pseudomonas aeruginosa that was causing increased virulence in cystic fibrosis patients. One of the interesting things in the paper is that we identified several genes related to virulence (using STM) and that several of these genes were within genomic island and prophage regions. Of course virulence factors have been found within these types of regions before, but to have actual in-vivo (chronic rat lung infection model) experimental evidence that these genes are involved in virulence in an epidemic strain, really makes this research notable. The research was published in Genome Research and is open access.

The media coverage:
Lancet Infectious Diseases (sorry not OA).

Vancouver Sun

Ok, now for the fun stuff:
SFU News - Notice those sleepy eyes? That is what having a 2 month old will do to you!

The story even made some news on a non-English site:
Automatic translation results in me being referred to as "blue Gull", SFU as "West gate Philippines Sand University", and UBC as "Inferior poem University".

Wednesday, January 21, 2009

Looking for a bioinformatics expert?

What I have to offer:
  • A balanced background in both biology (BSc) and computer science (BCS)
  • Soon to be completed PhD
  • Extensive research experience in bioinformatics, genomics, phylogenetics/phylogenomics, evolution, and bacteria pathogenesis
  • Some previous research experience in medical imaging, ontology development, and metagenomics
  • An impressive publishing record (7 papers, 3 first authors, 2 more first authors under review)
  • Solid computational skills including Perl programming, database design (MySQL), parallel programming, and web design (PHP & JavaScript)
  • Good communication and social skills
  • More information
What I am looking for:
  • Post-doc or job (academic or industrial)
  • Preferably, a position where I have some significant manager or leadership responsibilities
  • Geographically interested in north eastern parts of North America (Ottawa down to New York), but would entertain positions elsewhere in N.A.
I didn't put any limitations on research interests, since I am open to many areas. However, anything having to due with the human microbiome project, human-bacteria interactions, or metagenomics would be of particular interest.

Please email me if you are interested or if you have suggestions on some good openings.

Wednesday, January 7, 2009

Airports & Interviews

Quick question: Why do people line up or huddle around an airport gate before they are called to board? The plane is not leaving until everyone has boarded, so why would you want to sit even longer in a cramped up airplane than is absolutely necessary?

I contemplated these questions and other airport mysteries (like who would pay a $38 service fee for changing Canadian to US currency) while recently sitting in airports for 7 hours and 5 hours on two separate trips.

Fortunately, both flights were worth while since one was a flight home where home made meals and warm fireplaces greeted my new family of 3 and the second was for a job that I am quite interested in at Boston. Luckily, another interview I had arranged did not require a flight so my sanity was slightly saved.

I would say that both interviews went fairly well, and overall I actually enjoyed the experience. Doing a PhD (or any large project I suppose), you tend to lose sight of the accomplishments that you have made along the way. Getting a chance to present my work to an audience that is genuinely interested (not just lab mates that have to be in attendance) does not happen that often and even though it can be a bit stressful, I usually find it rewarding.