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

 

PUBLICATIONS    |   TOOLS    |   PROTOCOLS

PUBLICATIONS & PRE-PRINTS

Fig. 1

Common Misspecification of the Generation Interval Leads to Reproduction Number Underestimation in Phylodynamic Inference
Epidemics (2026)
Yeongseon Park, Katia Koelle

github link

Subtype Dynamics Reveal Horizon-Dependent Structure in Influenza Predictability
medRxiv (2026)
Yicheng Mao, Benjamin Lopman, Katia Koelle, Max SY Lau

Respiratory Syncytial Virus Seasonality and Disease Severity Among Children Under 5 in Atlanta, Georgia, United States, 2018-2023
Open Forum Infectious Diseases (2026)
Emily Valice, Kyle P Openo Christina A Rostad, Chandler Surell, Emily Bacon, Sabrina Hendrick, Allison T Chamberlain 

Parameterization of infectivity, case detection, and shedding load profiles for the mock dataset. (A) The infectivity profile fi, given by a modified negative binomial distribution with parameters r = 3.90 and p = 0.45. (B) The case detection profile ci, given by a modified negative binomial distribution with parameters r = 11.53 and p = 0.80. (C) The shedding load profile ωi, given by a modified negative binomial distribution with parameters r = 3.15 and p = 0.24. We model a total of n = 40 compartments, indexed from i = 0 to i = n − 1. The negative binomial distributions in panels (A)-(C) are modified by setting f0, c0, and ω0 to 0, respectively, and renormalizing the probability masses to sum to 1. (D) Infectivity profile shown as a function of time since infection. (E) Case detection profile shown as a function of time since infection. (F) Shedding load profile shown as a function of time since infection. Gray distributions in panels (D)-(F) show 10000 samples from the time-since-infection distributions assumed in Huisman et al. (2022).

A Bootstrap Particle Filter for Viral Rt Inference and Forecasting Using Wastewater Data
medRxiv (2026)
Wenfei Fiona Xiao, Yuke Wang, Nikunj Goel, Marlene Wolfe, Katia Koelle

github link

Estimating Modern US Social Contact Patterns, the ENGAGED Study: A Study Protocol for a Staggered Longitudinal Cohort Study
BMJ Open (2026)
Machi Shiiba, Marina Bruck, Musu Sesay, Alexander Hudgins, Marni Segall, Pragati Prasad, Charlotte Doran, Aaron Siegler, Felipe Lobelo, A Blythe Ryerson, Ben Lopman, Kristin Nelson, Sharia Ahmed

Refer to caption

Where do We Poop? City-Wide Simulation of Defecation Behavior for Wastewater-Based Epidemiology
arxiv.org (2026)
Hossein Amiri, Akshay Deverakonda, Yuke Wang, Andreas Züfle

Vaccine Efficacy Against Naturally Asymptomatic Infections: A Novel Estimand for Quantifying Vaccine Effects
medRxiv (2025)
Elizabeth Rogawski McQuade, Razieh Nabi, Allison Codi, Natalie Dean, Marc Lipsitch, David Benkeser

Refer to caption

Target Trial Emulation Without Matching: A More Efficient Approach for Evaluating Vaccine Effectiveness Using Observational Data
arxiv (2025)
Emily Wu, Elizabeth Rogawski McQuade, Mats Stensrud, Razieh Nabi, David Benkeser

github link

Deep Neural Networks for Endemic Measles Dynamics: Comparative Analysis and Integration with Mechanistic Models
Computational Biology (2024)
Wyatt G Madden, Wei Jin, Benjamin Lopman, Andreas Züfle, Benjamin Dalziel, C Jessica E Metcalf, Bryan T Grenfell, Max SY Lau

github link

TOOLS

VaxImpact Map
Quantifying the health and economic costs of declining childhood vaccination
 
Explore the map

 

Shedding Hub
Curating data, statistical models, and interactive tools for researchers & public health professionals
 
EXPLORE THE hub

 

ENGAGED Study Dashboard
Estimating social contact patterns of individuals in the Atlanta Metro area
 
explore the daTA
 

PROTOCOLS

Heat&Run® gDNA Removal Kit

RSV-A and RSV-B Amplicon Sequencing from Solid-Phase Wastewater Using the NEBNext® RSV Primer Module
protocols.io (2026)
Saïd Rachida, Alaa Ahmed, Hannah Cordova Dakannay, Abby Paulos, Orlando Sablon, Marlene Wolfe, Anne Piantadosi

 

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