Category Archives: Research

Recently congress recommended that NASA create an Ocean Worlds Exploration Program whose primary goal is “to discover extant life on another world using a mix of Discovery, New Frontiers, and flagship class missions”.  Pretty awesome.  In February I was invited … Continue reading →

I use phylogenetic placement, namely the program pplacer, in a lot of my publications.  It is also a core part of of the paprica metabolic inference pipeline.  As a result I field a lot questions from people trying to integrate … Continue reading →

I’m happy to report that one of the appendices in my dissertation was just published in the journal Polar Biology.  The paper, titled Wind-driven distribution of bacteria in coastal Antarctica: evidence from the Ross Sea region, was a long time … Continue reading →

I’m really excited (and relieved) to report that my review on the taxonomy and function of sea ice microbial communities was recently published in the journal Elementa.  The review is part of a series on biological exchange processes at the … Continue reading →

Apparently not very well.  A couple weeks ago I came across a really cool paper by some current and former students at the University of Washington School of Oceanography and the UW School of Aquatic and Fisheries Science.  The authors … Continue reading →

I’m going to keep draining the pool analogy until it’s dry… I’m going to miss the biological oceanography journal club at LDEO tomorrow in order to attend the Sequencing the Urban Genome symposium at the NY Academy of Sciences.  It’s … Continue reading →

For an ongoing project I needed to predict the metabolic pathways that are present in a metagenome.  This is actually something that I’ve been interested in trying to do for a while, as metabolic pathways can tell us much more … Continue reading →

Answer: Both! For this week’s LDEO biological oceanography journal club  we discussed a very interesting paper recently published in Nature Communications by Pablo Serret et al., titled Both respiration and photosynthesis determine the scaling of plankon metabolism in the oligotrophic … Continue reading →

We’re starting a summer biological oceanography journal club at LDEO and the inaugural paper is by Lechtenfield et al. (2015), published just a couple of months ago in Nature Communications.  Titled Marine sequestration of carbon in bacterial metabolites, the paper … Continue reading →

In a couple chapters of my dissertation I made use of protein flexibility values calculated with the ProtParam module in Biopython (Bio.SeqUtils.ProtParam).  The flexibility function makes use of amino acid β-factors as reported by Vihinen et al. (1994).  We were … Continue reading →