Ryan Doughty | Treangen lab at Rice University

Ryan (2nd year PhD student, Computer Science), obtained his BS in Computer Science from Case Western Reserve University. During his undergraduate studies, he worked with Dr. Treangen on large-scale wastewater analyses and targeted metagenomic sequencing methods. He also spent six months in Vigo, Spain, working in Dr. David Posada’s lab, focusing on gut-virome biomarkers in colorectal cancer. Additionally, he interned at Intellia Therapeutics for a summer, where he contributed to developing machine learning methods for CRISPR Cas-9 guide design. Ryan’s current research interests center around string algorithms for high-performance genomics and comprehending the global virosphere through viral genomic analyses. Ryan is supported by a training fellowship from the Gulf Coast Consortia, on the NLM Training Program in Biomedical Informatics & Data Science (T15LM007093)

A few of Ryan’s recent publications: (Doughty et al., 2025) (Gold et al., 2025) (Laird et al., 2025) (McCall et al., 2023).

References

2025

bronko: ultrafast, alignment-free detection of viral genome variation

Ryan D Doughty, Michael J Tisza, and Todd J Treangen

bioRxiv, 2025
Impact of ventilation on respiratory virus transmission in college residence hall cohorts: potential for causal inference about mode of transmission

T Louis Gold, Kathleen M McPhaul, Huang Lin, and 7 more authors

Influenza and Other Respiratory Viruses, 2025
Inter-tool analysis of a NIST dataset for assessing baseline nucleic acid sequence screening

Tyler S Laird, Kevin Flyangolts, Craig Bartling, and 8 more authors

Applied Biosafety, 2025

2023

Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance

Camille McCall, Ryan A Leo Elworth, Kristine M Wylie, and 7 more authors

ACS ES&T Water, 2023

Bib

@article{mccall2023targeted,
  title = {Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance},
  author = {McCall, Camille and Leo Elworth, Ryan A and Wylie, Kristine M and Wylie, Todd N and Dyson, Katherine and Doughty, Ryan and Treangen, Todd J and Hopkins, Loren and Ensor, Katherine and Stadler, Lauren B},
  year = {2023},
  journal = {ACS ES\&T Water},
  publisher = {American Chemical Society},
  volume = {3},
  number = {9},
  pages = {2955--2965}
}