Advancing Infectious Disease Genomics with AWS at Emory

Dr. Timothy Read’s laboratory at Emory University is a leader in the field of infectious disease genomics, with a long-standing focus on understanding bacterial pathogen evolution and developing genomic tools for clinical diagnostics. With a career including appointments at  The Institute for Genomic Research and the Naval Medical Research Center, Dr. Read has built a research program that integrates cutting-edge sequencing technologies with computational biology to explore how pathogens evolve, spread, and acquire virulence.

The lab’s work involves metagenomic and comparative genomic analysis of clinical samples, and the development of software tools to interpret complex genomic data. These efforts are critical for identifying emerging infectious threats, understanding the genetic basis of virulence, and informing public health responses. As sequencing technologies have advanced, so too has the lab’s need for scalable, high-performance computing infrastructure.

That’s where AWS at Emory has become a transformative partner.

“AWS at Emory has become a necessary part of our daily research operations,” says Charlotte Royer, a bioinformatician in the Read Lab who has worked extensively with AWS tools. “In our lab, where we focus on pathogen detection and comparative genomics, the ability to scale up analysis of massive genomic datasets efficiently is critical. We use EC2 instances to run our high-throughput genomic analysis pipelines.”

“Recently, we collaborated with the AWS team at Emory to deploy a large language model (LLM) using SageMaker, aimed at accelerating gene function analysis and interpretation. Their support was exceptional, they helped us assess the computational resources needed, guided us through model deployment, and provided hands-on assistance with debugging. Whether the issue was minor or complex, the team was always responsive and knowledgeable.”

“The flexibility and scalability of AWS services have allowed us to push the boundaries of what’s possible in microbial genomics, from metagenomic diagnostics to exploring the genomic mechanisms behind pathogen virulence. Our experience with AWS at Emory has been outstanding, and we’re excited to continue expanding our use of these tools as we pursue new questions in infectious disease research.”

The Read Lab’s experience exemplifies how cloud-based infrastructure can empower academic research teams to scale their work, adopt new technologies like machine learning, and stay at the forefront of scientific discovery. AWS at Emory has not only provided the technical backbone for these efforts but has also served as a collaborative partner in innovation.