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Katia Koelle - Curriculum Vitae

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Katia Koelle - Curriculum Vitae Katia Koelle - Curriculum vitae RESEARCH Education: University of Michigan at Ann Arbor: Ph.D., 2001-2005 Ecology and Evolutionary Biology, 2005, Host immunity and climate forcing in cholera dynamics and evolution Dr. Mercedes Pascual, advisor University of Michigan at Ann Arbor: Certificate in Complex Systems, 2003 2001-2003 Stanford University: B.S., Biological Sciences, 1997 1993-1997 Professional experience: Faculty member, Program in Microbiology and Molecular Genetics (MMG) 2018-present Emory University, Atlanta, GA Faculty member, Program in Population Biology, Ecology, and Evolution 2017-present Emory University, Atlanta, GA Associate Professor, Biology Department, Emory University, Atlanta, GA 2017-present Co-director, Theory and Modeling of Living System Initiative, Emory University 2018-present Associate Professor, Biology Department, Duke University, Durham, NC 2014-2017 Duke Global Health Institute Affiliate, Duke University, Durham, NC 2009-2017 Assistant Professor, Biology Department, Duke University, Durham, NC 2007-2014 Post-doctoral Fellow, Center for Infectious Disease Dynamics, 2006-2007 The Pennsylvania State University, Dr. Bryan Grenfell, advisor Research Scientist, Widevine Technologies, Seattle, WA and Ann Arbor, MI 1999-2001 Research Assistant, Department of Microbiology and Immunology, UCSF, CA 1998-1999 Awards, honors, and fellowships: Recipient of Duke Univ.’s Thomas Langford Lectureship Award 2015 Recipient of Popular Science’s Brilliant 10 award 2014 Elected to Faculty of 1000: Theoretical Ecology section 2009 Recipient of the PNAS Cozzarelli Prize 2008 Recipient of the Volterra Award for best oral presentation 2004 Awarded by the Theory Section of the Ecological Society of America (ESA) Recipient of the Rackham Outstanding Graduate Student Instructor Award 2004 University of Michigan at Ann Arbor, Ann Arbor, MI Recipient of the E.C. Pielou Award for best oral presentation 2003 Awarded by the Statistical Ecology Section of the ESA 1 Koelle CV 2/10/2019 Publications: Farrell, A., Brooke, C., Koelle, K., and R. Ke (in review). Coinfection of semi-infectious particles can contribute substantially to influenza infection dynamics. Craig, R., Kunkel, E., Crowcroft, N., Fitzpatrick, M., de Melker, H., Althouse, B., Merkel, T., Scarpino, S.V., Koelle, K., Carlsson, R., and S. Bolotin (in review). Asymptomatic infection and transmission of pertussis in households: A systematic review. Koelle, K., Farrell, A., Brooke, C., and R. Ke (in review). Within-host infectious disease models accommodating cellular coinfection, with an application to influenza. bioRxiv. doi: 10.1101/359067 Li, Z., Zarnitsyna, V., Lowen, A., Weissman, D., Koelle, K., Kohlmeier, J. and R. Antia (2019). Why Are CD8 T Cell Epitopes of Human Influenza A Virus Conserved? Journal of Virology. doi: 10.1128/JVI.01534-18 Nelson, C., Vera Cruz, D. Su, M., Xie, G., Vandergrift, N., Pass, R., Forman, M., Diener-West, M., Koelle, K., Arav-Boger, R. and S. Permar (2018). Intrahost dynamics of human cytomegalovirus variants acquired by seronegative glycoprotein B vaccinees. Journal of Virology. doi: 10.1128/JVI.01695- 18 Gallagher, M. E., Brooke, C.B., Ke, R., and K. Koelle (2018). Causes and consequences of spatial within- host viral spread. Viruses. doi: 10.3390/v10110627. In special issue: ‘What’s new with the flu?’ Ben-Shachar, R. and K. Koelle (2018). Transmission-clearance trade-offs indicate that dengue virulence evolution depends on epidemiological context. Nature Communications. doi: 10.1038/s41467- 018-04595-w. McKenney, E., Koelle, K., Dunn, R., and A. Yoder (2018). The ecosystem services of animal microbiomes. Molecular Ecology. doi: 10.1111/mec.14532 Raghwani, J., Thompson, R., and K.Koelle (2017). Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution. Virus Evolution. doi: 10.1093/ve/vex034 Sobel Leonard, A., Weissman, D., Greenbaum, B., Ghedin, E., and K. Koelle (2017). Transmission bottleneck size estimation from pathogen deep-sequencing data, with an application to human influenza A virus. Journal of Virology. doi: 10.1128/JVI.00171-17 Nelson, C.S., Vera Cruz, D., Tran, D., Bialas, K.M., Stamper, L., Wu, H., Gilbert, M., Blair, R., Alvarez, X., Itell, H., Chen, M., Deshpande, A., Chiuppesi, F., Wussow, F., Diamond, D.J. Vandergrift, N., Walter, M., Barry, P.A., Cohen-Wolkowiez, M., Koelle, K., Kaur, A., and S.R. Permar (2017). Preexisting antibodies can protect against congenital cytomegalovirus infection in monkeys. JCI Insight. doi: 10.1172/jci.insight.94002 Sobel Leonard, A., McClain, M., Smith, G. Wentworth, D. Halpin, R., Lin, X., Ransier, A., Stockwell, T., Das, S., Gilbert, A., Lambkin-Williams, R., Ginsburg, G., Woods, C., Koelle, K., and C. Illingworth (2017). Limited effective reassortment shapes influenza evolution in a human host. PLoS Pathogens. doi: 10.1371/journal.ppat.1006203 Flasche, S.*, Jit, M., Rodriguez-Barrauer*, I., Coudeville*, L.,Recker*, M., Koelle*, K., Milne*, G., Hladish*, T., Perkins*, A., Dorigatti, I., Cummings, D., Espana, G., Kelso, J., Longini, I., Lorenco, J., Pearson, C., Reiner, R.C., and N. Ferguson (2016) The long term safety, public health impact, and cost effectiveness of routine vaccination with Dengvaxia®: a model comparison study. PLoS Medicine. *authors contributed equally. doi: 10.1371/journal.pmed.1002181 Ben-Shachar, R., Schmidler, S.C., and K. Koelle (2016). Drivers of inter-individual variation in dengue viral load dynamics. PLoS Computational Biology. doi: 10.1371/journal.pcbi.1005194 Sobel Leonard, A., McClain, M., Smith, G. Wentworth, D. Halpin, R., Lin, X., Ransier, A., Stockwell, T., Das, S., Gilbert, A., Lambkin-Williams, R., Ginsburg, G., Woods, C., and K. Koelle (2016) Deep sequencing of influenza A virus from a human challenge study reveals a large founder population 2 Koelle CV 2/10/2019 size and rapid intrahost viral evolution. Journal of Virology. Selected as a Journal of Virology Spotlight Feature. doi: 10.1128/JVI.01657-16 Flasche, S.*, Jit, M., Rodriguez-Barrauer*, I., Coudeville*, L., Recker*, M., Koelle*, K., Milne*, G., Hladish*, T., Perkins*, A., Dorigatti, I., Cummings, D., Espana, G., Kelso, J., Longini, I., Lorenco, J., Pearson, C., Reiner, R.C., and N. Ferguson (2016) Comparative modelling of dengue vaccine public health impact. Report to the Strategic Advisory Groups of Experts (SAGE) on Immunization. (SAGE recommendations will be the basis for WHO global public health policy for appropriate use of Dengvaxia®, Sanofi Pasteur’s dengue vaccine.) *authors contributed equally. Koelle, K. and D.A. Rasmussen (2015). The effects of a deleterious mutation load on patterns of influenza A/H3N2’s antigenic evolution in humans. eLife. doi: 10.7554/eLife.07361 Ben-Shachar, R. and K. Koelle (2015). Minimal within-host dengue models highlight the specific roles of the immune response in primary and secondary dengue infections. Journal of the Royal Society, Interface. 12 (103), p. 20140886. doi: 10.1098/rsif.2014.0886 Koelle, K. and D.A. Rasmussen (2014). Influenza: prediction is worth a shot. Nature. 507 (7490), pp. 47- 48. doi:10.1038/nature13054 Rasmussen, D.A., Volz, E., and K. Koelle (2014). Phylodynamic inference for structured epidemiological models. PLoS Computational Biology. 10(4), p. e1003570. doi: 10.1371/journal.pcbi.1003570 Rasmussen, D.A., Boni, M., and K. Koelle (2014). Reconciling phylodynamics with epidemiology: The case of dengue virus in southern Vietnam. Molecular Biology and Evolution. 31(2): pp.258-271. doi: 10.1093/molbev/mst203 Scholle, S.O., Ypma, R., Lloyd, A.L., and K. Koelle (2013). Viral substitution rate variation can arise from the interplay between within-host and epidemiological dynamics. The American Naturalist. 182(4), pp.494-513. doi: 10.1086/672000. (Stacy received Honorable Mention for the 2013 Student Paper of the Year Award from the American Naturalist for this paper.) Yuan, H. and K. Koelle (2013). The evolutionary dynamics of receptor binding avidity in influenza A: a mathematical model for a new antigenic drift hypothesis. Philosophical Transactions of the Royal Society, B. 368 (1614): p. 20120204. doi: 10.1098/rstb.2012.0204 Luo, S. and K. Koelle (2013). Navigating the devious course of evolution: the importance of mechanistic models for identifying eco-evolutionary dynamics in nature. The American Naturalist.181, pp. S58-S75. doi: 10.1086/669952 Volz, E.M., Koelle, K., and T. Bedford (2013). Viral phylodynamics. PLoS Computational Biology. 9(3): e1002947. doi: 10.1371/journal.pcbi.1002947 Wu, S., Koelle, K., and A. Rodrigo (2013). Coalescent entanglement and the conditional dependence of the times to common ancestry of mutually exclusive pairs of individuals. Journal of Heredity. 104 (1): 86-91. doi: 10.1093/jhered/ess074 Ratmann, O., Donker, G., Meijer, A., Fraser, C., and K. Koelle (2012). Phylodynamic inference and model assessment with Approximate Bayesian Computation: influenza as a case study. PLoS Computational Biology. 8(12):e1002835. doi: 10.1371/journal.pcbi.1002835 Luo, S., Reed, M., Mattingly, J., and K. Koelle (2012). The impact of host immune status on the within- host and population dynamics of antigenic immune escape. Journal of the Royal Society, Interface. 9 (75), pp. 2603-2613. doi: 10.1098/rsif.2012.0180 Arinaminpathy, N., Ratmann, O., Koelle, K., Epstein, S.L., Price, G.E., Viboud, C., Miller, M., and B. Grenfell (2012). Impact of cross-protective vaccines on the epidemiological and evolutionary dynamics of influenza. PNAS. 109(8), pp. 3173-3177.
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