In my first post on this topic, I defined bioinformatics and summarized some of the work done here at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine, and our bioinformatics department. Now, I’d like to describe some of the bioinformatics projects and share the career transition tips from our bioinformatics department here.
Examples of bioinformatics research projects
IGS is one of three NIH-funded Genome Sequencing Centers for Infectious Disease. In this capacity, IGS works on projects that involve sequencing dozens or even hundreds of strains or species of microorganisms. The ability to compare the genomes of hundreds of strains of a particular species allows researchers to identify particular genes or gene families that are associated with particular phenotypes of the individual strains, such as increased ability to cause disease. This information can then be used to help in vaccine or drug development. Here is a short video highlighting some of IGS’ bioinformatics projects.
Each human body plays host to millions of microorganisms. There are 10 times as many microbial cells in each human body than there are human cells. There is abundant evidence that changes in the composition of these microbial communities are correlated with human health and disease.
The NIH, as part of an international effort, has undertaken the Human Microbiome Project (HMP) to characterize these communities of organisms. Samples are taken from human body sites most populated with microorganisms (gut, mouth, nasal passages, skin, urogenital tract) and the entire complement of DNA from the site is collected and sequenced. This is called a “metagenome”, the genome of a community of organisms.
Analyzing metagenomic data is quite challenging since many (perhaps most) of the organisms in the sample are unknown. Thus metagenomics has opened an entire new category of bioinformatics challenges and is a particularly active area of current bioinformatics work. IGS is the Data Analysis and Coordination Center for the HMP and as such, we are responsible for providing the research community with tools and resources that allow them to make effective use of the massive amounts of data generated by this project. Here is a short video describing the DACC for the HMP.
Careers in bioinformatics
When bioinformatics was a newer field, it was easier to get jobs and internships with little or no programming experience, if the person had a strong science or microbiology background. Today, it’s harder to get entry-level jobs in bioinformatics if you have no programming experience. Employers expect bioinformatics job candidates to have bioinformatics exposure or programming experience before being hired.
Yet, as the field has grown, there are more resources available such as open-source tools, new textbooks, and web-based organizations that have information about their tools online. A motivated microbiologist can now get more background information about bioinformatics work than was available a few years ago. It is a rapidly growing field that values strong microbiology research backgrounds and many new job opportunities are available.
Beginning Perl for Bioinformatics – James Tisdall
· GMOD site – http://gmod.org/wiki/Overview#What_is_a_GMOD.3F
· Intro video to bioinformatics from Dr. Owen White, Director of Bioinformatics at IGS
· Video about careers in bioinformatics, again from Dr. White.