The communication of our research findings is a foundational pillar to our careers as scientists. One of the most common ways we scientists share information is by publishing papers in peer-reviewed journals. This primary method of information dissemination allows us to share our research findings both to our colleagues as well as the public at large. When preparing a manuscript for submission to a journal for peer review and subsequent publication, a lot of work goes into preparing a variety of documents. One of the important documents is a cover letter to the editor. This letter represents a significant hurdle for new and young researchers because it is often unclear what a cover letter should actually look like, and what information should be included. In this week's post I want to go over what a good cover letter could look like and how you can write your own. I say this is what it could look like because there is certainly a lot of room for interpretation and personal style, and there are many correct ways to do it. Here I am just going to cover one potential way to tackle the problem.
Sunday, December 11, 2016
Sunday, November 13, 2016
|Kicking off the IHMC meeting for 2016.|
This week I had the privilege of attending the 2016 International Human Microbiome Congress which was hosted in Houston, Texas in the United States. The goal of this recurring meeting is to get the worldwide human microbiome community together to discuss recent progress, current challenges, and future directions. In this post I want to give a summary of the meeting for anyone who could not attend.
Sunday, October 23, 2016
|Global online office hours will be held monthly|
through Google Chat.
Sunday, October 2, 2016
|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
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
|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
|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.