Computational and Evolutionary Genomics Research in the Pfeifer Lab focuses on:

Primate population genomics
Interactions between mutation, recombination, natural selection, and population history shape the genetic differences among individuals, populations, and species. Perhaps for anthropocentric reasons, a focal point of many studies has been the characterization of these processes in humans and their closest extant evolutionary relative, chimpanzees (Auton*, Fledel-Alon*, Pfeifer*, Venn* et al., Science 2012; Leffler*, Gao*, Pfeifer*, Ségurel* et al., Science 2013; Pfeifer & Jensen, GBE 2016). However, less effort has been put toward comparative genomic analyses by studying non-ape primates. Extending our previous research on the topic, we are working towards gaining a better understanding of fine-scale changes in rates and patterns of mutation and recombination through deeper evolutionary time within the primate clade (Pfeifer, MBE 2017; Pfeifer, Evolution 2017; Tran & Pfeifer, eLS 2018; Pfeifer, Springer Nature 2020; Pfeifer, MBE 2020; Pfeifer, GigaScience 2021; Bergeron et al., eLife 2022; Ghafoor*, Santos*, Versoza* et al., GBE 2023; Versoza*, Weiss* et al., GBE 2023).

Picture credits: Sergey Yeliseev, Riyaad Minty, and Susanne Pfeifer.

Viral genomics
Human cytomegalovirus (HCMV) is a large herpesvirus critically important to human health due to its ubiquitous occurrence – with adult infection rates ranging from 30–90% in industrialized countries to almost 100% in emerging countries. Although primary infections are generally asymptomatic in healthy hosts, HCMV infections can lead to severe effects in immuno-suppressed or immuno-naïve hosts, including fetuses and newborns. HCMV infections affect ~0.5% of all live births in the United States – making it the most common source of infection-related congenital (i.e., before birth) infections. HCMV utilizes effective immune evasion techniques and, as a result, it is currently neither possible to prevent transmission from mother to fetus (due to an absence of an effective vaccine), nor to reduce severity of disease in the infant. As a consequence, a better understanding of the underlying biological and evolutionary processes at play during infection is indispensable to the future development of novel disease prevention and treatment strategies. In collaboration with the Jensen, Kowalik, and Trumble Labs, we work to characterize the evolutionary processes driving infection (e.g., Renzette et al., J. Virol. 2017; Pokalyuk et al., Mol. Ecol. 2017; Sackman et al., Pathogens 2018; Wang et al., Viruses 2021; Howell et al., GBE 2023; Moström et al., PLoS Pathogens 2023). This characterization will better illuminate the causes and consequences underlying this major threat to global health.

Due to the difficulties inherent to working with primate samples, my course-based undergraduate research experience (CURE) in “Computational Genomics” also focuses on viruses – specifically bacteriophages, which are routinely used as anti-microbial agents in agriculture, biotechnology, and medicine. So far, this course has been highly successful, leading to several student-led publications from the past five semesters (Crane et al., G3 2020; Milhaven et al., MRA 2021; Crane et al., G3 2021; Howell et al., G3 2022; Howell et al., MRA 2022; Versoza & Pfeifer, Microorganisms 2022; Versoza et al., MRA 2022; Versoza et al., Viruses 2022; Milhaven et al., MRA 2023; Milhaven et al., Microorganisms 2023; Howell*, Versoza* et al., Virus Evol. 2024).

The Pfeifer Lab is in the School of Life Sciences at Arizona State University, and we are part of a large and collaborative group in evolutionary genomics at ASU – see We are also members of the Center for Evolution & Medicine, and the Center for Mechanisms of Evolution.

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