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.

Sunday, May 22, 2016

Piggybacking Instead of Killing: New Insights Into Virus Community Dynamics

The human microbiome is an important component of human health and disease. It is an ecosystem of microbes that exists in and on humans, and can affect disease states through disturbances in composition, diversity, metabolism, etc. Understanding the human microbiome will not only allow us to better understand human health, but it will also allow us to treat medical conditions in new and effective ways (e.g. Fecal Microbiota Transplants).

Sunday, May 15, 2016

Real Time Code Correction with Linters

If you are a regular around here, or if you even took a look at the date since the last post, you may have noticed a gap. As tends to happen in the blog world, I took a hiatus to focus on other projects and research. This was actually very productive and I am excited for you to see the fruits of those labors in the coming months. So thanks for sticking with us and joining in the return of Prophage activity.