Group members

katia_koelle

Katia Koelle, PI

Katia is interested in the population dynamics and evolutionary dynamics of infectious diseases. Her research focuses on using modeling approaches to shed light on the drivers of evolutionary change in endemically circulating viral populations, most notably influenza and dengue viruses. Her work includes both model development and interfacing models with data. She is interested in viral dynamics at multiple scales, including at the epidemiological level and at the within-host level.

CV, Google Scholar

Email: katia.koelle[at]emory[dot]edu
Office: O. Wayne Rollins Research Center, Rm 1015

 

brent_allman

Brent Allman (2016-present; Population Biology, Ecology, and Evolution Ph.D. student)

Brent is interested in the evolution of sex in RNA viruses. We know that sex is an important driver of diversity in eukaryotic populations, but how do sexual mechanisms in RNA viruses do the same? For his dissertation, Brent will be using modeling and phylogenetic approaches to better understand how genetic reassortment in influenza A virus increases or limits genetic diversity among viral populations. He is excited about the development of theoretical predictions that can be tested with experiments and publicly available sequence data.

Google Scholar

Email: brent.elliott.allman[at]emory[dot]edu
Office: O. Wayne Rollins Research Center, Rm 1161

 

Lisa Bono (2021-present; Postdoctoral Fellow

Lisa studies the ecology and evolution of viruses by combining field, bench, and computational approaches. Her research focuses on the evolutionary ecology of viruses, both to understand viruses themselves, and as model systems for general questions in biology. She collaborates with Anice Lowen’s lab to examine the consequences of spatial spread for selection in experimentally evolving populations of influenza. She also works with the Pseudomonas phage phi6 to understand how ecology drives viral diversity and the evolution of host jumping.

Google Scholar

Email: Lisa.bono[at]emory[dot]edu
Office: O. Wayne Rollins Research Center, Rm 1161

 

Amber Coates (2020-present; Microbiology and Molecular Genetics Ph.D. student)

Amber is interested in viral evolution, specifically when it occurs in response to recombination or reassortment. These two mechanisms allow for new viral strains (or viral species) to arise during co-infection with multiple viruses. She has just joined the lab and has recently been studying recombination in seasonal coronaviruses.

Email: amber.nicole.coats[at]emory[dot]edu
Office: O. Wayne Rollins Research Center, Rm 1161

 

Mike Martin (2018-present;  Population Biology, Ecology, and Evolution Ph.D. student)

Mike is interested in using sequence analysis to better understand how viral pathogens evolve within infected hosts as well as at the population level. He has just joined the Koelle lab and his research to date has focused on identifying patterns of genomic diversity circulating in influenza virus populations within experimentally challenged human subjects.

GitHub
Google Scholar
Twitter
Email: michael.martin2[at]emory[dot]edu
Office: O. Wayne Rollins Research Center, Rm 1161

 

Yeongseon Park (2019-present;  Population Biology, Ecology, and Evolution Ph.D. student)

Yeongseon is interested in using genome sequences to understand the population and evolutionary dynamics of infectious disease. She has joined the lab recently and currently working on the estimation of epidemiological parameters using genetic variations in a viral population.

Email: yeongseon.park[at]emory[dot]edu
Office: O. Wayne Rollins Research Center, Rm 1161

 

Julie Zhu (2020-present; Undergraduate Student)

Julie is an undergraduate double majoring in Applied Math and Stats & Biology. She is interested in computational modeling and is currently working with Brent on a project about viral coinfection in the context of SARS-CoV-2.

 

Lab Pets

Oliver Coats – Public Relations

 

Cuddler-In-Chief

 

Harper Gallagher – Agent of Chaos

 

Former group members

Post-doctoral researchers:

Molly Gallagher (2017-2021): Molly is currently a Computational Epidemiologist at the Johns Hopkins University Applied Physics Laboratory. 

Jeremy Harris (2017-2020): Jeremy is currently a post-doc in Joshua Weitz’s group at Georgia Tech.

Jayna Raghwani (2012-2013): Jayna is currently a post-doc in Oli Pybus’s group at Oxford University.

Oliver Ratmann (2009-2012): Olli is currently a Lecturer in Statistics at Imperial College London

Virginia Pasour (2008-2009): Virginia is currently a Program Officer at the Army Research Office (ARO), in the area of biomathematics.

Graduate students:

Diana Vera Cruz (2015-2020): Ph.D. in Computational Biology and Bioinformatics. Diana studied viral evolution across scales and how it is impacted by immune selection. In 2020, she joined Sarah Cobey’s group at the University of Chicago as a Research Scientist.

Ellie Mainou (2018-2019): M.S. in Population Biology, Ecology and Evolution. Ellie’s research focused on the effect of disease control measures in the spread of viral infectious diseases and how such measures may inadvertently impose selection pressure on the pathogens. Her masters thesis involved mathematical modeling to assess how imperfect vaccination may impact dengue virulence evolution. In 2019, she is currently a PhD student in Biology at Penn State working with Jessica M. Conway.

Ashley Sobel Leonard (2012-2016): Ph.D. in Biology (along with an MD from Duke Medical School). Ashley’s research interests focused on the within- and between-host dynamics of influenza. Her thesis included the development and application of a statistical method to infer transmission bottleneck sizes between donor and recipient hosts and statistical analyses of influenza virus sequence data from a human challenge study to examine the speed of viral evolution within challenged hosts and to ascertain the degree of genetic linkage across the flu genome. In 2018, she moved to Seattle, where she is doing her residency while also doing research in Jesse Bloom’s group at the FHCRC.

Rotem Ben-Shachar (2011-2016): Ph.D. in Computational Biology and Bioinformatics. Rotem’s research interests focused on the within-host dynamics of dengue virus. Her thesis included the development of minimal within-host dengue models that were able to reproduce key features of the infection and testing different immunological hypotheses of dengue virus infections by confronting these models with viral load data. She further worked on examining transmission-clearance trade-offs in dengue virus and the effects these trade-offs have on dengue virulence evolution in different epidemiological contexts. After completing a post-doc with Eva Harris and Mike Boots at Berkeley, Rotem joined the Bay Area company Counsyl as a Computational Scientist.

Stacy Scholle (2010 – 2016): PhD student in Biology. Stacy’s research interests focused on the evolutionary dynamics of hepatitis C virus within chronically infected individuals.

Chris Castorena (2009 -2013): M.S. in Computational Biology and Bioinformatics. Chris’s research interested focused on the effect of vaccination on the age distribution of disease cases, with a focus on dengue virus. He finished with a Masters and has gone on to work in the private sector.

David Rasmussen (2008 – 2014): Ph.D. in Biology. After doing a post-doc with Tanja Stadler in Basel/ETH Zurich, David joined NC State University as an Assistant Professor in the Department of Entomology and Plant Pathology.

Mimi Lin (2007 – 2010): M.S. in Biology. Mimi now works for the Environmental Protection Agency in Research Triangle Park, NC

Hsiang-Yu (Sean) Yuan (2007 – 2013): Ph.D. in Computational Biology and Bioinformatics. After completing a post-doc with Steven Riley at Imperial College London, Sean joined the City University of Hong Kong as as Assistant Professor in Department of Biomedical Sciences.

Shishi Luo (2007-2013): Ph.D. in Mathematics, with honorary membership in the Koelle research group. After completing a post-doc with Alan Perelson at LANL and a second post-doc with Yun Song at Berkeley, Shishi joined the Bay Area company Helix as a Senior Bioinformatics Scientist.

Associates in research:

Olivia Yvellez, Associate in Research, 2016-2017. Olivia’s research focused on the effect of spatial expansions on rapidly evolving viruses, most notably rabies
virus and influenza virus. She started medical school in Fall 2018.

Nicole Nova, Associate in Research, 2015-2016. Nicole’s research focused on the evolutionary dynamics of antibodies within virus infected hosts. She is currently a PhD student in Biology at Stanford, working with Erin Mordecai.

Interns:

Baptiste Elie, Intern, 2018-2019.  Baptiste’s interniship was part of his masters studies at ENS Paris-Saclay. His research focused on influenza spatial dynamics and its impact in fitness variation at within-host and population level using a combination of phylogenetics, simulations and experimentation (in collaboration with Anice Lowen’s lab). He is currently doing his masters

Undergraduates:

Several undergrads have done independent studies and/or have written undergraduate theses in the group. These
include Brian Adams, Meredith Kamradt, Rachel Northeim, Priya Khatri, Rachel Willcutts, Alex Dai and Eddie Zhao.

Visitors:

Celeste Donato visited in October 2016 from Duke-NUS to work on age distribution patterns of influenza B virus. She is a research fellow in Vijay Dhanasekaran’s group.

Mark Tanaka visited for two weeks in Fall 2014 from the University of New South Wales to work on the dynamics of seasonal influenza viruses over the period of new flu pandemics.

Rolf Ypma visited May 2011 from RIVM, the Netherlands where he was a graduate student with Marijn van Ballegooijen and Jacco Wallinga. He now works at the Netherlands Forensic Institute, The Hague.

Andrea Richter visited Fall semester 2009 from Barcelona, where she was a graduate student in Xavier Rodo’s IC3 group.