An Applied Genomic Epidemiology Handbook: A Practical Guide to Leveraging Pathogen Genomic Data in Public Health provides rationale, theory, and implementation guidance to help public health practitioners incorporate pathogen genomic data analysis into their investigations.

Allison Black is a genomic epidemiologist passionate about strengthening public health's ability to use pathogen genomic data for outbreak response, disease surveillance, and decision-making. While she trained as an academic genomic epidemiologist, she now leads molecular epidemiology activities at the Washington State Department of Health.

Gytis Dudas is an evolutionary biologist at Vilnius University's Life Sciences Center working on RNA virus evolution at both long- and short-term scales. Most of Gytis' PhD and postdoctoral work focused on the genomic epidemiology of Ebola virus in West Africa and MERS coronavirus in the Arabian Peninsula.

Chapter 1 ¿ The Value of Pathogen Genomics in Applied Epidemiology

Allison Black and Gytis Dudas

Chapter 2 ¿ Fundamental Theory in Genomic Epidemiology

Allison Black and Gytis Dudas

Chapter 3 ¿ Sample Selection

Allison Black

Chapter 4 ¿ Public Health Use Cases of Genomic Epidemiology

Allison Black

Chapter 5 ¿ Case Studies in Applying Genomic Epidemiology

Allison Black and Gytis Dudas

Chapter 6 ¿ Tools and Methods for Applied Genomic Epidemiological Analysis

Allison Black and Gytis Dudas

Chapter 7 ¿ A Deeper Dive into Viral Genomic Complexity

Gytis Dudas

Chapter 8 ¿ Genomic Epidemiology of Bacteria

Taj Azarian and Allison Black