Sunday, October 23, 2016

Global Online Office Hours

Global online office hours will be held monthly
through Google Chat.
Interest in the microbiome has continued to skyrocket. It seems like there is a new microbiome commercialization strategy everyday, and more and more scientists are looking to incorporate the microbiome into their research programs. It is certainly an exciting time for the microbiome. Unfortunately the increased demand has been met with a somewhat insufficient supply of information and resources. Of course there are some excellent resources out there, but a lot of people don't have access to a "microbiome researcher" to answer their questions. Sometimes this means newcomers to the field make some crucial mistakes because they are forced to "go it alone". In an effort to generate even more unique resources for all of the microbiome folks out there, I decided to hold Global Online Office Hours.

Sunday, October 2, 2016

A New Look At Irritable Bowel Disease and Viruses: The Core Human "Phageome"

An illustration of the core protein clusters (PCs; groups
of similar genes) found in the photic and aphotic zones
of the ocean. This new study applies a similar approach
using phage genomes instead of genes. Source
Ongoing research has continued to implicate the microbiome in a variety of human diseases. We often hear about this in the context of bacterial communities. Certain bacterial communities appear to be associated with health, and disrupting these communities seems to be associated with disease. To better understand these bacterial communities, we sometimes group the shared members together as the "core bacterial community" that is associated with health or disease. In some ways these core bacteria are considered important to the system because they are found in every instance of health or disease. But what about the core phages (bacterial viruses) of these communities? A few weeks ago Manrique et al published a study that began addressing this question.

Sunday, September 18, 2016

How to Detect Circular Virus Genomes from Metagenomes

Many virus genomes are circular, like the olympic rings.
When analyzing virus metagenomic data, we often find it helpful to identify contigs that represent complete circular genomes [1,2]. In addition to offering biological information, this is used as a quality control technique to evaluate whether the sequencing efforts were robust enough to allow for complete genome assembly. This approach has the advantage of reference independence because it does not require aligning reads to a reference genome to evaluate sequence completion.

Saturday, August 27, 2016

Improving Human Virome Studies: Updates to Virus Classification

The proposed phage proteomic tree by Rohwer and Edwards.
Taxonomy is an important aspect of microbiome research. Whether we are studying communities of bacteria, viruses, or other microbes, there are benefits to labeling microbes. Taxonomic names immediately give us information about their relationships to each other, such as similar bacteria being grouped into the same genus. Taxonomic identities also provide some information about an organism's functionality and/or clinical pathology. For example, by mentioning that a bacteria is a member of the genus Staphylococcus, you might think that it is a round, gram-positive bacterium that might inhabit the skin and is otherwise related to other members of that genus (including genomic relationships). In the end, the practice does what it aims to do, which is classify organisms in an informative way.

Sunday, July 31, 2016

Antibiotics, Birth, and the Microbiome: A Personal Experience

The new addition to our family!
Well July has shaped up to be an incredible month. In addition to working on some cool projects whose results you will be seeing in the near future, my wife delivered our first child. Her name is Clara and we are very excited to be welcoming her into our family. Unfortunately the road to delivery was a little bumpy (although not nearly as bad as it could have been). One aspect of the process that stood out to me was the use of antibiotics during delivery. I thought this was interesting because we hear so much about the microbiome differences between vaginal and c-section births, but not much about antibiotic treatment. This week I wanted to share my experience with you, both to shed some light on what can happen during delivery, and to provide my own thoughts on the subject.

Sunday, June 26, 2016

The Up-And-Coming Bioinformatics Language: A First Look At Julia

Programming is a dynamic field that transitions from one language to another over the years. A classic example is the transition to Perl, which then transitioned into Python. The R language has also exploded in recent years, and all of these languages are used heavily in bioinformatics. Instead of focusing on the current state of bioinformatics, I want to focus this post on where we could be going in the future. More specifically, I want to discuss an up-and-coming programming language named Julia, which has potential for use in bioinformatics.

Sunday, June 12, 2016

Tips For Getting The Optimal Postdoc

So you've been in grad school for a while, you've published some cool papers, and you are ready to graduate with your PhD and take the next step in your career. For many, this means pursuing a postdoc. But how do you get started, and what should you be thinking about? Since I was in this position only a short time ago, I felt I would share my thoughts on the process, hoping that it helps any readers getting ready for that same next step.