Department of Energy Awards $1M to CU Denver-Led Team for Computational Biology

September 18, 2020
DNA and hand artistic image

The U.S. Department of Energy (DOE) announced $5 million in funding for six new research projects in computational biology, $1,049,639 of which goes to Chris Miller, associate professor in CU Denver’s Department of Integrative Biology, and his collaborators—Farnoush Banaei-Kashani from CU Denver, Kelly Wrighton from CSU, and Chris Henry from DOE.

Miller’s project, titled Finding the Missing Pieces: Filling Gaps that Impede the Translation of Omics Data into Models, seeks to develop novel computational biology approaches and software to better understand microbial genomes relevant to the environment. According to Miller, there are parallels to studying the human microbiome in many challenges we see today—climate change, bioenergy-relevant systems, and more.

Computational Biology Research in Ohio’s Wetlands

Take, for example, a freshwater wetland system in Ohio. Miller and his colleagues studied this model for years because microbes in the soil of freshwater wetlands naturally emit the greenhouse gas methane. All that said, we know relatively little about the controls on this microbial process or how changing climate or land-use practices might affect emissions.

Old Woman Creek National Estuarine Research Reserve
Miller’s Ohio Wetlands study location—Old Woman Creek National Estuarine Research Reserve

“There are thousands of different types of microbes (bacteria, fungi, etc.) living in even just a pinch of this soil,” Miller said. “But we have no clue how to grow and study most of them in the lab, so DNA sequencing and computation give us the ability to extract DNA directly from soil, sequence the bits of genome we recover, and then computationally try to piece the original genomes back together.”

The reason this matters? Miller notes by following this process, we are able to actually predict which proteins those genomes encode and infer what the microbes might be doing in the environment.

New Discoveries

“In some of these complex soils, we are discovering novel organisms—lots of them—and the genes we are sequencing often look nothing like scientists have characterized in the lab before,” Miller said. “New computational approaches are needed to infer microbial biochemistry and metabolism from the DNA so we can better understand and predict microbial roles in the larger ecosystems.”

Mud coring equitment
One of the coring instruments Miller and his team use to pull up columns of muck to section off for DNA sequencing. “Slices of these cores are the sorts of samples we use DNA sequencing and genome inference for in order to understand methane emissions,” Miller said.

By developing new algorithms and software for analyzing microbial genomes recovered from the environment, Miller and his team will develop and scale new computational methods to infer functions for genes. This will be integrated into a DOE computational biology system called KBase so scientists all over the world can utilize their methods to more efficiently figure out what proteins and genomes are doing in their systems of interest.

“This project is exciting because it is foundational to answering so many different kinds of questions,” said Miller. “Biology is increasingly ‘Big Data’ science, and we need to make sure we have the computational tools to keep up with the data generation … Our collaborators on this project are world-class, and I feel grateful that CU Denver students and I will have the chance to work with and learn from this team to advance the science.”

Related Research: Genetic Adaptation to Climate Change Is Swift in Crop Pests

Awards were selected based on competitive peer review under a DOE Funding Opportunity Announcement issued by the Office of Biological and Environmental Research (BER) within DOE’s Office of Science. Total funding is $5 million in Fiscal Year 2020 dollars, for projects up to three years in duration.

A list of projects can be found on the BER homepage under the heading, “What’s New.”