About me

I am broadly interested in the ecology, evolution and population genetics of microorganisms. The high mutation rates, short generation times, and rapid evolution of RNA viruses makes studying the population dynamics of many pathogens interesting and important from theroetical and public health perspectives. My thesis work in the Lauring Lab at the University of Michigan provided an oportunity to unite these perspectives and develop a passion for computational biology. In short, I sequenced patient isolates and used mathematical models to help untangle the complex ecological and evolutionary processes that drive influenza evolution within individuals during an infection and between individuals during transmission. As a postdoctoral research associate am I applying this expertise to help monitor and track viral outbreaks in real-time.

Curriculum Vitae


One of the most rewarding aspects of my research has been interacting with and learning from a great community of computationally minded bioglogists. While most of the code I've developed is tailored to my specific research aims. Some questions have lead to a few broadly applicable programs, which I hope are useful to others.

Learn more Interactive variant calling validation

Recent Publications

1.Fitzsimmons WJ, Woods RJ, McCrone JT, Woodman A, Arnold JJ, Yennawar M, Evans R, Cameron CE, Lauring AS. 2018. A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus. PLoS Biol 16:e2006459.
2. McCrone JT , Woods RJ, Martin ET, Malosh RE, Monto AS, Lauring AS. 2018. Stochastic processes constrain the within and between host evolution of influenza virus. eLife 7:24.
McCrone JT, Lauring AS. 2017. Genetic bottlenecks in intraspecies virus transmission . Submitted.
4. Debbink K*, McCrone JT* , Petrie JG, Truscon R, Johnson E, Mantlo EK, Monto AS, Lauring AS. 2017. Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses . PLoS Pathog 13:e1006194.
5. Visher E, Whitefield SE, McCrone JT, Fitzsimmons W, Lauring AS. 2016. The Mutational Robustness of Influenza A Virus . PLoS Pathog 12:e1005856.
6. McCrone JT, Lauring AS. 2016. Measurements of intrahost viral diversity are extremely sensitive to systematic errors in variant calling . J Virol 90:JVI.00667–16–6895.
7. Marino S, Gideon HP, Gong C, Mankad S, McCrone JT , Lin PL, Linderman JJ, Flynn JL, Kirschner DE. 2016. Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome . PLoS Comput Biol 12:e1004804.
8. Butchbach MER, Rose FF, Rhoades S, Marston J, McCrone JT , Sinnott R, Lorson CL. 2010. Effect of diet on the survival and phenotype of a mouse model for spinal muscular atrophy . Biochemical and Biophysical Research Communications 391:835–840.
* Equal contribution

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