Submitted by Eoin Brodie on
This project builds on a bioinformatics workflow we have developed to distill microbial genomes (including those assembled from metagenomes) into a suite of functional traits (genes, pathways, whole genome properties) that represent the lifestyle of microbes in complex natural systems. The SPUR project will involve the analysis of existing genomes from public databases and a number of projects to explore patterns of trait distribution and trait-linkage. We have developed simplified trait-based models of microbial metabolism, and these computational models can use the information derived from genomes to create simulations of how different features of microbes will impact their fitness (ability to compete) under a range of conditions.
There are opportunities for two undergraduates to contribute to this work:
- From the bioinformatics side for example working on methods to reduce the complexity of thousands of genomes to a reduced set of 'hypothetical organisms' that capture most of the important features of microbes and exploring patterns of those features/traits across ecosystems; or
- Exploring using computational models, how microbial traits interact to affect how microbes compete and cooperate under different environmental conditions.
If you enjoy ecology, coding and environmental/biological sciences these should be fun, challenging and rewarding projects. The questions you will ask are open for discussion, if you are passionate about a specific group of microbes, an ecosystem process or a particular global change phenomenon etc, let's chat and work those into your project.
Finally, you will work within an inclusive, respectful, multi-disciplinary team that spans UCB and Berkeley Lab so you will get an insight into research in a National Laboratory as well as a university setting. These projects and the training you will receive can be accomplished mostly remotely if necessary but some team meetings will be beneficial and will help you expand your network and experience a team science environment. Our goal is to train you and help you get a publication from this work.
We look forward to hearing from you.
There are a few possible roles here - roughly breaking down into:
- Bioinformatics and statistical exploration of microbial trait distributions and trait-linkage from isolate or metagenome-assembled genomes,
- Using trait-based models to explore how microbial traits influence their fitness across a range of conditions.
In both cases you will work directly with either a postdoc or a research scientist.
A wide variety of backgrounds could be helpful for this work
- some experience with coding, like Python, R, Java, Matlab, C++, or Julia is needed - you don't need to be an expert, you just to understand the basics and be able to learn the syntax.
- After that interest/expertise in microbiology, ecology, biogeochemistry, biochemistry, biophysics, molecular biology, statistics, or math would be helpful.