Validating and Leveraging Non-SARS-CoV-2 Respiratory Infection as a Negative Control Outcome in a Phase 3 COVID-19 Vaccine Trial with Extended Observational Follow-Up

Published in American Journal of Epidemiology, 2025

Irrelevant infection endpoints confirmed as a valid negative control for COVID-19 and are leveraged to detect bias in hazard-based, time-varying vaccine efficacy estimates.

Recommended citation: Ashby, Ethan, et al. (2025). "Validating and Leveraging Non-SARS-CoV-2 Respiratory Infection as a Negative Control Outcome in a Phase 3 COVID-19 Vaccine Trial with Extended Observational Follow-Up." American Journal of Epidemiology. https://academic-oup-com.offcampus.lib.washington.edu/aje/advance-article/doi/10.1093/aje/kwaf176/8239036?utm_source=advanceaccess&utm_campaign=aje&utm_medium=email

Negative Control Outcome Adjustment in Early-Phase Randomized Trials: Estimating Vaccine Effects on Immune Responses in HIV Exposed Uninfected Infants

Published in Statistics in Medicine, 2025

Adjustment for off-target endpoints can improve the efficiency of early-phase randomized trials.

Recommended citation: Ashby, Ethan, et al. (2025). "Negative Control Outcome Adjustment in Early-Phase Randomized Trials: Estimating Vaccine Effects on Immune Responses in HIV Exposed Uninfected Infants." Statistics in Medicine. https://onlinelibrary.wiley.com/doi/10.1002/sim.70142

Chemical Inhibition of Bromodomain Proteins in Insect-Stage African Trypanosomes Perturbs Silencing of the Variant Surface Glycoprotein Repertoire and Results in Widespread Changes in the Transcriptome

Published in Microbiology Spectrum, 2023

Investigating time-course transcriptional response to Bdf3 inhibition in the parasite that causes sleeping sickness.

Recommended citation: Ashby, Ethan C. (2023). "Chemical Inhibition of Bromodomain Proteins in Insect-Stage African Trypanosomes Perturbs Silencing of the Variant Surface Glycoprotein Repertoire and Results in Widespread Changes in the Transcriptome." Microbiology Spectrum. 1(1). https://journals.asm.org/doi/full/10.1128/spectrum.00147-23

The timing of transcription of RpoS-dependent genes varies across multiple stresses in Escherichia coli K-12

Published in mSystems, 2023

This paper examines the timing of E. coli transcriptional response to different stresses.

Recommended citation: Adams, Josephine, et al. (2023). "The timing of transcription of RpoS-dependent genes varies across multiple stresses in Escherichia coli K-12." mSystems. https://www.biorxiv.org/content/biorxiv/early/2023/06/26/2023.02.17.528066.full.pdf

Genomic Occupancy of the Bromodomain Protein Bdf3 Is Dynamic during Differentiation of African Trypanosomes from Bloodstream to Procyclic Forms

Published in MSphere, 2022

Cut&Run data analysis demonstrates Bdf3 protein occupancy changes at different sites on the T. brucei genome.

Recommended citation: Ashby, Ethan, et al. (2022). "Genomic Occupancy of the Bromodomain Protein Bdf3 Is Dynamic during Differentiation of African Trypanosomes from Bloodstream to Procyclic Forms." MSphere . 7(3). https://journals.asm.org/doi/full/10.1128/msphere.00023-22

Reproducing: Sharp Instruments for Classifying Compliers and Generalizing Causal Effects

Published: May 20, 2023

Reproducing a paper on instrumental variables by Ed Kennedy and Colleagues.

HERCULES: a three-arm noninferiority trial of a anti-HER2 cancer vaccine

Published: May 20, 2022

Mock clinical trial protocol developed for Design of Medical studies course.