Sunday, December 11, 2016

How to Write a Manuscript Submission Cover Letter

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, November 13, 2016

Summary of the 2016 International Human Microbiome Congress

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

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.

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.

Sunday, April 3, 2016

The Illumina Error Profile for Metagenomic Sequencing

Microbiology, and especially microbial ecology, has become increasingly dependent on advanced DNA and RNA sequencing technologies. This is most evident with the increasing popularity of the human microbiome and its various impacts on human health. While using DNA sequencing sometimes appears relatively simple (a result of the great efforts made to simplify the user experience), it is actually still a very complicated technique that requires a lot of thought and skill. One aspect that genomic scientists (whether focusing on human or microbial DNA) must always consider is the bias introduced by the sequencing platform itself. This week I want to focus on a recently published manuscript that describes the  sequencing error profile associated with some of the most popular Illumina platforms.

Sunday, March 20, 2016

My Experience Sharing Protocols in the New "" Environment

Scientists publish methods in their manuscripts, but these summaries can fail to capture the technical details involved in the described processes. Many scientists get around this by by making the actual step-by-step protocols freely available to the public. There are a variety of avenues for accomplishing this. Some scientists publish their protocols with their manuscripts, some post them in public archives, and others publish them on their lab websites. There are advantages and disadvantages to these approaches, and most of us are always learning about new and improved resources to facilitate the sharing process. I recently learned about the online resource, which is a surprisingly robust and free resource for sharing experimental protocols.

Sunday, March 6, 2016

Helping Both Humans and Dogs: A Recent Study of Canine Atopic Dermatitis

Example of canine Atopic Dermatitis, as seen
in the manuscript we are discussing.
Atopic dermatitis (AD), which is also referred to as Eczema, is a very common dermatological disease, especially in children. It is estimated that AD affects 10% of children. The disease presents as dry, scaly, itchy skin. Atopic dermatitis can be especially problematic when the victim (often a child) itches the skin extensively, thereby increasing susceptibility to skin infections. Treatment of the disease ranges from controlling the itchy skin with soothing topical medication to bathing the patient in dilute bleach (the bleach bath technique).

Sunday, February 14, 2016

Methods Matter: Getting Started with the Skin Microbiome

Your choice of sequencing approach matters. Think
about your goals and the methodological caveats
before starting your experiments.
The field of microbiome research has been hugely popular in the past few years. It has forced us to rethink our approaches to various medical practices, and has captured the imaginations of both amateur and professional scientists. With this popularity has come an influx of scientists trying to incorporate the microbiome into their own research. It is of course great that people want to get into the field, but unfortunately it is deceptively difficult for newcomers who are not always aware of how best to get started. This has led to the execution of poorly designed studies that could have been improved by more methodological resources in the literature. To this end, my colleague (and lab mate) led a research project to evaluate the differences between sequencing methods of the skin microbiome, a consideration that is often overlooked by newcomers to the field. This week I want to briefly hit the highlights of the paper and suggest that you read it if you are interested in starting any skin microbiome work.

Sunday, February 7, 2016

The Open Metagenome Toolkit Project

Almost two years ago I started collecting some scripts that I wrote for my own microbial metagenomic analyses. These are some relatively simple Perl and Python scripts that do some common tasks that are required when studying bacterial or viral metagenomes. This collection of scripts if called the Open Metagenome Toolkit. I recently added a few more scripts that I think are helpful, including a script to translate nucleotide sequences and a script to calculate the average lengths of reads. This week our post is about the Open Metagenome Toolkit because it is a cool opportunity for collaborative programming in our microbiome community.

Sunday, January 24, 2016

Recent Study Reveals Role for Bacterial Viruses in Microbiome Evolution

The microbiome is a complex community of bacteria,
viruses, and other microbes.
Microbial communities are fierce battlegrounds between bacteria and other microbes competing for limited resources. One method some bacteria use to kill their competitors is the production of bacteriocins. Bacteriocins are protein toxins produced by bacteria to limit the growth of related bacteria, thereby providing a competitive advantage to the bacteriocin-producing bacteria. This dynamic is important to our health because it can impact bacterial infections and overall microbiome composition. The group of Nedialkova et al recently added a whole new level of insight into bacteriocins and microbial ecology by linking bacteriocin production to the presence of bacteriophages (bacterial viruses).

Sunday, January 17, 2016

A Primer on Linear Regression and its Associated Misconceptions

Welcome to the new year and the first Prophage blog post for 2016! This is already looking like it will be a great year for science and blogging. But enough with the pleasantries, let's dive into some science.