This page provides a full catalog of CIDMATH’s publications and other works like tools, code packages, dashboards, and more.

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Protocol: RSV-A and RSV-B Amplicon Sequencing from Solid-Phase Wastewater Using the NEBNext® RSV Primer Module

Rachida et al., protocols.io 2026

 
Publication: Common misspecification of the generation interval leads to reproduction number underestimation in phylodynamic inference

Park et al. Epidemics 2026

Code: Generation of mock sequence data 

Park GitHub

 

Pre-print: Subtype dynamics reveal horizon-dependent structure in influenza predictability

Mao et al. medRxiv 2026

 
Publication: Respiratory Syncytial Virus Seasonality and Disease Severity among Children Under 5 in Atlanta, Georgia, United States, 2018–2023

Valice et al. Open Forum Infectious Diseases 2026

 
Tool: VaxImpactMap

 

Tool: Shedding Hub

 

Pre-print: A bootstrap particle filter for viral Rt inference and forecasting using wastewater data

Xiao et al. medRxiv 2026

Code: Rt wastewater inference particle filter

koellelab GitHub

 
Pre-Print: Study protocol for estimating modern US social contact patterns: The ENGAGED study

Shiiba et al. medRxiv 2026

 

Pre-Print: Where do We Poop? City-Wide Simulation of Defecation Behavior for Wastewater-Based Epidemiology

Amiri et al. arxiv 2026

 

Tool: ENGAGED Dashboard

 

Pre-print: Vaccine efficacy against naturally asymptomatic infections: A novel estimand for quantifying vaccine effects

Rogawski McQuade et al. medRxiv 2025

 

Pre-print: Target trial emulation without matching: a more efficient approach for evaluating vaccine effectiveness using observational data

Wu et al. arxiv 2025

Tool: nomatch R package
 
Publication: Deep-learning neural networks for endemic measles dynamics: comparative analysis and integration with mechanistic models

Madden and Lau GitHub