Author Archives: Jeff

Paper published on psychrophile alkane hydroxylases

Posted on December 16, 2014 by Jeff

We just published a paper in BMC Genomics on the occurrence of genes coding for alkane hydroxylases in the genomes of psychrophilic (cold loving) bacteria.  This paper does a couple of interesting things and fails to do several other interesting … Continue reading →

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DIAMOND – A game changer?

Posted on November 30, 2014 by Jeff

A very exciting paper was published in Nature Methods a couple weeks ago by Benjamin Buchfink and colleagues: Fast and Sensitive Protein Alignment Using DIAMOND.  The paper debuts the DIAMOND software, touted as a much-needed replacement for BLASTX.  BLASTX has … Continue reading →

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Basic computers for bioinformatics, revisited

Posted on November 16, 2014 by Jeff

I recently started a postdoc in a lab without any real computer infrastructure so I was in need of a system with a little more juice than my laptop.  While a graduate student at the UW I did everything except … Continue reading →

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Future of ice jobs at the UW

Posted on November 11, 2014 by Jeff

There are two great polar ecology jobs posted at the University of Washington right now.  It’s rare to find academic jobs specific to the polar regions so this will be a great opportunity for someone out there!  The new positions … Continue reading →

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In defense of observations

Posted on August 27, 2014 by Jeff

This week I’m at the biennial meeting of the International Society of Microbial Ecologists (ISME) in Seoul.  During lunch yesterday there was a special “bird’s eye view” talk given by Dr. James Prosser, a preeminent microbiologist from the University of … Continue reading →

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The history of sea ice microbial ecology

Posted on August 23, 2014 by Jeff

Doctoral dissertations typically include an introduction, a Chapter 1 that summarizes the work and the motivation for undertaking it.  Last week I submitted my dissertation to the UW and the introduction, which includes citations from some long-ago work on psychrophiles … Continue reading →

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Clustering metagenomic sequence reads

Posted on August 14, 2014 by Jeff

Another interesting paper caught my eye last week, Nielsen et al. in Nature Biotechnology; Identification and assembly of genomes and genetic elements in complex metagenomic samples without using a reference genome. First, a complaint: 53 authors, really?  There are more … Continue reading →

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Great modeling paper published

Posted on August 6, 2014 by Jeff

A very nice paper in the ISME Journal came across my Google Scholar alerts this week – Satellite remote sensing data can be used to model marine microbial metabolite turnover, by Larsen et al.  The author list includes some heavy … Continue reading →

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New website address!

Posted on July 22, 2014 by Jeff

Pending the (hopeful) defense of my dissertation on August 8th I’ll be starting a postdoc at the Lamont-Doherty Earth Observatory at Columbia University.  Since there’s generally a little downtime between turning in a thesis and defending it I’ve migrated this … Continue reading →

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Some thoughts on modeling

Posted on May 27, 2014 by Jeff

I’m not a modeler, but I played one once in grad school. Or at least that’s how I’m feeling at the moment. I’m currently working on the last chapter of my dissertation and it became necessary to explore the mechanisms … Continue reading →

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