As the advancement of genomic sequencing technologies has steadily increased the amount of publicly available genomics data, methods for generating meaningful insights from this data have also proliferated. The sub-field of biological data science tasked with developing these methods is known as ‘bioinformatics.’ MRIGlobal’s Applied Biology & Bioinformatics team leads and supports projects across the fields of infectious disease diagnostics, biosurveillance, and microbial forensics.
“It is an extraordinary time to be working in bioinformatics method development,” said Joe Russell, Ph.D., MRIGlobal Principal Scientist and Group Lead for the Applied Biology & Bioinformatics team. “The confluence of exponentially increasing genomics data across many different domains and emerging machine learning approaches to scale traditional statistical techniques in novel ways has produced extremely fertile ground for creative applications.”
Infectious disease diagnostics
Infectious diseases, under evolutionary pressures, often gain, lose, or alter segments of their genomes to accommodate new biological niches. For example, there have been multiple variants of the SARS-CoV-2 virus that cause COVID-19. Leveraging creative bioinformatics method development to minimize the lag time between a pathogen making a functionally important genotype-to-phenotype alteration and the implementation of appropriate public health responses is a foundational goal for our bioinformatics team.
Researchers across the world are developing increasingly sophisticated methods for infectious disease detection and diagnostics to predict, prevent, and mitigate the risk infectious diseases pose to human health. MRIGlobal seeks to play a critical role in this global group of collaborative researchers, providing high quality, customer-focused bioinformatics leadership to improve biosurveillance efforts and human health. As an example, MRIGlobal researchers have recently published a set of novel feature-engineering algorithms for identifying genomic motifs that are highly explanatory for, or even predictive of, phenotypes-of-concern in RNA viruses. This approach significantly improves our ability to characterize the functional threat profile of a novel virus encountered through surveillance efforts, as well as providing promising targets for vaccines and therapeutics. “We’re constantly thinking of new ways to discover hidden information that is encoded in the sequences of these viral genomes,” said Phil Davis, Senior Scientist with the Applied Biology & Bioinformatics group. “We’ve made a lot of progress, but I think we’ve just scratched the surface of what’s possible.”
Biosurveillance is an application where bioinformatics can be leveraged to detect, monitor, and characterize national security health threats in both human and animal populations, as well as environmental samples. MRIGlobal has worked on an array of applied biosurveillance programs that required creative bioinformatics development. An example is the DTRA-funded ‘Sample-2-Sequence’ (S2S) program. MRIGlobal was contracted to develop an end-to-end metagenomics-based biosurveillance workflow. It was designed to be incorporated into austere DoD laboratories worldwide. A key portion of this development was a method to taxonomically classify microbial sequencing reads within a ‘push-button’ graphical user interface that could be adopted with minimal training by non-experts. The result was the PanGIA metagenomics taxonomy classification tool. “PanGIA offers an extremely intuitive analysis environment for metagenomics data,” said Dr. Russell. “We’ve developed PanGIA to accommodate all sequencing technologies, including real-time sequencing using nanopore platforms. It is open-source, easily installable, with flexible databases, uniquely-informative confidence scores on a per-taxon basis, and deployable on commodity computer hardware. We think it offers a significant departure from the complex, expert-only tools that characterize many of the open-source options to date and will add a lot of value to routine analyses conducted by clinicians and public health practitioners.”
MRIGlobal researchers have linked PanGIA with our ultra-portable molecular biosurveillance platform, Mercury Lab. GPUs embedded in Mercury Lab allow real-time basecalling of nanopore sequencing data, and PanGIA comes pre-installed for real-time classification of microbially-derived sequencing reads directly on Mercury Lab’s computational architecture. “Moving these technologies from the laboratory out into the field is only recently possible,” added Russell. “However, the ability to support high-level bioinformatics as close to the point of sampling as possible will radically improve the pound-for-pound information content of emerging biosurveillance ecosystems.
The field of microbial forensics analyzes evidence associated with bioterrorism acts, bio-crime, or inadvertent microorganism/toxin release. This field is a combination of the practices of epidemiology with the characterization of microbes and microbial-related evidence. This is an important application of bioinformatics.
MRIGlobal has been the lead bioinformatics performer for several DoD microbial forensics initiatives over the past two decades. This has involved the iterative development and validation of operational analysis workflows that provide continuous capability while actively incorporating new and emerging techniques. The goal of these programs have included staying ahead of potential adversaries’ abilities to use biology for harmful actions, and creative use of biological information for more nuanced intelligence gathering. With the rapid rise of synthetic biology and genome-editing technologies, this mission-space has grown increasingly complex. MRIGlobal researchers are using a combination of machine learning, novel assay development, and novel hardware development to address the needs of USG partners charged with keeping our nation safe from biological threats. Our clients are smart leaders with deadly-serious missions. MRIGlobal’s bioinformatics team prides itself on consistently providing new and creative methods to help our customers fulfill their duties.
MRIGlobal is mission-ready for project work.
Our facilities maintain current registration, permits, and unique access to work with many biological agents. These include infectious disease agents from United States Department of Health and Human Services (including Centers for Disease Control and Prevention), United States Department of Agriculture, universities, and hospitals.
MRIGlobal possesses an extensive culture collection of well-characterized pathogens, and access to additional strains and clinical samples of interest through an existing network of laboratories worldwide.
Getting started with MRIGlobal
Contact MRIGlobal and get started with trusted genomics and bioinformatics services.
As a not-for-profit contract research organization, we have proven ourselves as an objective partner driven to make our clients’ products more successful. We specialize in defense, human health, pharmaceutical sciences, in-vitro diagnostics, energy and environment, agriculture, and global health.
To learn more about our work or how we can help you, contact us today. If you are part of an agency, business, or academic institution seeking assistance with a project, use our Project Quote Tool to get started.
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