Katia Koelle - Curriculum vitae - ScholarBlogs

1 Koelle CV 2/10/2019

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

2 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

3 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. doi: 10.1073/pnas.1113342109

WHO-VMI Dengue Vaccine Modeling Group (2012). Assessing the potential of a candidate dengue vaccine with mathematical modeling. PLoS Neglected Tropical Diseases. 6(3), e1450. doi: 10.1371/journal.pntd.0001450 (The group consists of 28 experts in dengue epidemiology, clinical practice, immunology, virology, vaccinology, entomology, and mathematical modeling.)

4 Koelle CV 2/10/2019

Koelle, K. and D.A. Rasmussen (2012). Rates of coalescence for common epidemiological models at equilibrium. Journal of the Royal Society, Interface. 9(70), pp.997-1007. doi: 10.1098/rsif.2011.0495

Meyers, L.A., Kerr, B., and K. Koelle (2011). Network Perspectives on Infectious Disease Dynamics. Interdisciplinary Perspectives on Infectious Diseases. Volume 2011 (2011), Article ID 146765. doi: 10.1155/2011/146765

Rasmussen, D.A., Ratmann, O., and K. Koelle (2011). Inference for nonlinear epidemiological models using genealogies and time series. PLoS Computational Biology. 7 (8), e1002136. doi: 10.1371/journal.pcbi.1002136

Koelle, K., Ratmann, O., Rasmussen, D.A., Pasour, V., and J. Mattingly (2011). A dimensionless number for understanding the evolutionary dynamics of antigenically variable RNA viruses. Proceedings of the Royal Society, Series B. 278, pp. 3723-3730. doi: 10.1098/rspb.2011.0435

Koelle, K., Khatri, P., Kamradt, M., and T. Kepler (2010). A two-tiered model for studying the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza. Journal of the Royal Society, Interface. 7, pp.1257-1274. doi: 10.1098/rsif.2010.0007

Koelle, K., Kamradt, M., and M. Pascual (2009). Understanding the dynamics of rapidly evolving pathogens through modeling the tempo of antigenic change: influenza as a case study. Epidemics. 1, pp. 129-137. doi: 10.1016/j.epidem.2009.05.003

Koelle, K (2009). The impact of climate on the disease dynamics of cholera. Clinical Microbiology and Infection. 15(s1), pp. 29-31. doi: 10.1111/j.1469-0691.2008.02686.x

Nagao, Y. and K. Koelle (2008). Decreases in dengue transmission may act to increase the incidence of Dengue Hemorrhagic Fever. PNAS. 105(6), pp. 2238-2243. doi: 10.1073/pnas.0709029105

Cobey, S. and K. Koelle (2008). Capturing escape in infectious disease dynamics. Trends in Ecology and Evolution. 23(10), pp.572-577. doi: 10.1016/j.tree.2008.06.008

Pascual, M., Cazelles, B., Bouma, M., Chaves, L., and K. Koelle (2008). Shifting patterns: malaria dynamics and rainfall variability in an African highland. Proceedings of the Royal Society, B. 275. pp.123-132.

Finkelman, B., Viboud, C., Koelle, K., Ferrari, M., Bharti, N., and B. Grenfell (2007). Global Patterns in Seasonal Activity of Influenza A/H3N2, A/H1N1, and B from 1997 to 2005: Viral Coexistence and Latitudinal Gradients. PLoS One. 2(12): e1296.

Koelle, K., Cobey, S., Grenfell, B. and M. Pascual (2006). Epochal evolution shapes the phylodynamics of interpandemic influenza A (H3N2) in humans. Science. 314. pp. 1898-1903.

Koelle, K., Pascual, M., and M. Yunus (2006). Serotype cycles in cholera dynamics. Proceedings of the Royal Society, B. 273. pp. 2879-2886.

Pascual, M., Koelle, K., and A. Dobson (2006). Hyperinfectivity in Cholera: A New Mechanism for an Old Epidemiological Model? PLoS Medicine. 3 (6). p. e280.

Koelle, K., Rodó, X., Pascual, M., Yunus, M., and G. Mostafa (2005). Refractory periods to climate forcing in cholera dynamics. Nature. 436. pp. 696-700.

Koelle, K., Pascual, M., and M. Yunus (2005). Pathogen adaptation to seasonal forcing and climate change. Proceedings of the Royal Society, B. 272. pp. 971-977.

Koelle, K. and J. Vandermeer (2005). Dispersal-induced desynchronization: from metapopulations to metacommunities. Ecology Letters. 8(2). pp. 167-175.

Buckee, C., Koelle, K., Mustard, M., and S. Gupta (2004). The effects of host contact network structure on pathogen diversity and strain structure. PNAS. 101(29). pp.10839-10844.

5 Koelle CV 2/10/2019

Koelle, K. and M. Pascual (2004). Disentangling extrinsic from intrinsic factors in disease dynamics: a nonlinear time series approach with an application to cholera. The American Naturalist 163(6), pp.901-913.

Savit, R., Koelle, K., Treynor, W., and R. Gonzalez (2004). Man and Superman: Human Limitations, Innovation, and Emergence in Resource Competition in Collectives and the Design of Complex Systems, eds. Tumer, K. & Wolpert, D. (Springer-Verlag, New York, NY).

Blower, S.M., Koelle, K., and J. Mills (2002). Health policy modeling: epidemic control, HIV vaccines and risky behavior in Quantitative Evaluation of HIV Prevention Programs, eds. Kaplan, E. H. & Brookmeyer, R. (Yale University Press, New Haven, CT).

Blower, S.M., Koelle, K., Kirschner, D.E., and J. Mills (2001). Live attenuated HIV vaccines: Predicting the tradeoff between efficacy and safety. PNAS. 98(6), pp. 3618-3623.

Blower, S.M., Koelle, K., and T. Lietman (1999). Antibiotic resistance- to treat… Nature Medicine 5(4), p. 358.

Pending, active, and completed research grants:

MIDAS R01 active 2018-2023 Integrating data streams to guide model design for norovirus vaccine decision-making PI: Benjamin Lopman (Emory University) co-Is: Katia Koelle, Juan Leon (Emory University), Andreas Handel (University of Georgia)

NIH R21 active 2018-2020 Antibody and viral determinants of protection against CMV infection PI: Sallie Permar (Duke University) co-PI: Katia Koelle

DARPA INTERfering and Co-Evolving Prevention and Therapy (InterCEPT) active 2017-2020 Viral Interdiction through Population Engineering and Restructuring ($5.17 million total) PI: Ruian Ke (North Carolina State University) Co-PIs: Katia Koelle, Chris Brooke (University of Illinois at Urbana-Champaign), Connie Chang (Montana State University), Laura Fabris (Rutgers University)

NIGMS-supported MIDAS Center of Excellence (U54GM111274) active 2014-2019 $2.5 million annually Center for Inference and Dynamics of Infectious Diseases (CIDID) PI: Elizabeth Halloran, Fred Hutchinson Cancer Research Center (FHCRC). Participating institutions: Univ. of Florida, Univ. of Michigan, Emory Univ., Northeastern Univ., Univ. of Georgia, Duke Univ., Univ. of Washington.

Collaborative Quantitative Approaches to Problems in the Basic and Clinical Sciences 2016-2017 ($50,000 Duke seed grant). Using tumor cell genealogies to understand tumor dynamics and predict clinical outcomes. Collaborators: Richard Durrett (Mathematics), Katia Koelle (Biology), Edward Patz (Pharmacology and Cancer Biology)

James S. McDonnell Foundation Complex Systems Research Award ($448,937) 2009-2015 Derivation and application of a dimensionless quantity for understanding viral evolution. PI: Koelle

6 Koelle CV 2/10/2019

Australian Research Council/Discovery Project ($378,000 AUD) 2011-2014 Understanding mutation and genetic reassortment in viruses: New mathematical models of viral dynamics and evolution. PIs: Mark Tanaka and Peter White (UNSW), co-PIs: Roland Regoes (ETH Zurich), Koelle.

NIH ($2.1 million) 2010-2014 Implementation science to optimize malaria vector control and disease management. PI: Randall Kramer, involved researchers: Miranda, Paul, Koelle, Fowler, Moser, Osgood, Lesser, O’Meara, Platt, Dai, Turner, Vernia.

NSF, Advancing Theory in Biology Program ($610,071) 2008-2013 Combining ecological and molecular models to understand the evolutionary dynamics of influenza. PI: Koelle

Duke Global Health Institute Global Environmental Health Pilot project ($41,450) 2010-2011 Modeling the effect of climate change and land cover change on malaria risk in the Brazilian Amazon PI: James Clark, involved researchers: Denis Valle, Marcelo Urbano Ferreira, Monica da Silva Nunes, Alan Gelfand, Koelle, Alex Pfaff.

Duke University Center for Comparative Biology of Vulnerable Populations ($33,000) 2008-2009 A bioeconomic approach to managing insecticide resistance in malaria control. PI: Randall Kramer, involved researchers: Koelle, Zachary Brown.

Invited seminar talks (*upcoming):

Global Infectious Disease seminar series, UW Madison, WI* 2019

Institute for Molecular Virology, UW Madison, WI* 2019

Center for Communicable Diseases, Harvard School of Public Health, Boston, MA* 2019

Department of Ecology and Evolutionary Biology, UC Santa Cruz, CA 2018

IBM Research, Distinguished Speaker Series, San Jose, CA 2018

Program in Microbiology and Molecular Genetics, Emory University, Atlanta, GA 2018

University of Illinois, Urbana Champaign 2018

Center for Infectious Disease Dynamics, Pennsylvania State University, State College, PA 2017

Department of Biology, University of Kentucky, Lexington, KY 2017

Program in Population, Behavior, Ecology, and Evolution, Emory University, Atlanta, GA 2017

North Carolina Central University, TriCEM at NCCU, Durham, NC 2017

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 2016

Computational Ecology and Epidemiology Seminar, University of Georgia, Athens, GA 2016

Evolutionary Microbiology Seminar, Georgia Tech, Atlanta, GA 2016

Centers for Disease Control and Prevention, Atlanta, GA 2016


Department of Biology, Emory University, Atlanta, GA 2016

7 Koelle CV 2/10/2019

Program in Ecology and Evolution, NC State, Raleigh, NC 2015

Infectious Disease Epidemiology seminar, Harvard School of Public Health, Boston, MA 2015

Dept. of Ecology and Evolutionary Biology seminar, Princeton University, Princeton, NJ 2014

Virology in Progress Mini-symposium on Ebola, UNC, Chapel Hill, NC 2014

Program in Ecology seminar, UNC, Chapel Hill, NC 2014

Department of Biology seminar, University of Pennsylvania, Philadelphia, PA 2014

Program in Population, Behavior, Ecology, and Evolution seminar, Emory Univ., Atlanta, GA 2013

Graduate Program in Organismic and Evolutionary Biology seminar series, 2012

University of Massachusetts, Amherst, MA

Infectious Diseases Seminar, Harvard School of Public Health, Boston, MA 2012

Fred Hutchinson Cancer Research Center, Seattle, WA 2012

Ecology and Evolution seminar series, University of California at Davis, 2011

Davis, CA

Odum School of Ecology seminar series, University of Georgia, Athens, GA 2011

Mathematical Biosciences Institute (MBI), The Ohio State University, 2011

Columbus, OH

Center for the Study of Complex Systems, University of Michigan at Ann Arbor 2011

Ann Arbor, MI

Department of Integrative Biology, University of Texas at Austin, Austin, TX 2009

Los Alamos National Laboratory, Los Alamos, NM 2009

Zentrum für Infektionsbiologie und Immunität (Humboldt-Universität) /IMPBS, 2009

Berlin, Germany

Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 2008

Biomathematics seminar series, NC State, Raleigh, NC 2008


School of Public Health, Yale University, New Haven, CT 2007

Ecology Seminar, University of North Carolina at Chapel Hill, Chapel Hill, NC 2007

Ecology and Evolutionary Biology Seminar, University of Michigan, Ann Arbor, MI 2007

Center for Infectious Disease Dynamics, Pennsylvania State University, State College, PA 2006

Department of Biology, Duke University, Durham, NC (job talks) 2006

Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway 2005

Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI (thesis defense) 2005

Emerging Infectious Diseases Seminar, Harvard University, Boston, MA 2005

Invited presentations at meetings (*upcoming):

Jacques Monod Conference, Virus evolution of the mutualist-parasite continuum,

Roscoff, France* 2019

8 Koelle CV 2/10/2019

American Society for Microbiology Microbe meeting, The Social Lives of Viruses

San Francisco, CA* 2019

SIAM Conference on Applications of Dynamical Systems, Snowbird, UT* 2019

Santa Fe Institute, Integrating Critical Phenomena and Multi-scale Selection in

Viral Evolution Working Group, Santa Fe, NM 2018

Society for Molecular Biology and Evolution Satellite Meeting, Genome Evolution

in Pathogen Transmission and Disease, Kyoto, Japan 2018

DARPA PI meeting, New York, NY 2018

Santa Fe Institute, Aging and Infectious Disease Working Group, Santa Fe, NM 2018

Centre International de Rencontres Mathématiques (CIRM),

Probability and Biological Evolution, Marseille, France 2018

DARPA PI meeting, Arlington, VA 2018

Institute for Disease Modeling (IDM), Evolutionary Epidemiology, Bellevue, WA 2018

American Physical Society March Meeting, Predicting Viral Evolution, Los Angeles, CA 2018

University of Georgia PuDong DC delegate visit 2017

DARPA PI meeting, San Francisco, CA 2017

Physical Concepts and Computational Models in Immunology, MIT, Cambridge, MA 2017

Next Generation Informatics for Global Health: Disease Dynamics and 2017

Digital Epidemiology, Hong Kong

Ecology and Evolution of Infectious Disease meeting, Santa Barbara, CA 2017

Immunology and Evolution of Influenza Symposium at Emory, Atlanta, GA 2017

MIDAS annual meeting, Atlanta, GA 2017

Keystone symposium on Modeling Viral Infections and Immunity, Estes Park, CO 2017

5th Annual Disease Modeling Symposium, Institute for Disease Modeling, Bellevue, WA 2017

Symposium on Influenza Antigenic Diversity, Athens, GA 2017

DARPA PI meeting, Arlington, VA 2017

Mathematical Approaches to Evolutionary Trees and Networks, Banff, Canada 2017

Banff International Research Station (BIRS)

American Mathematical Society Sectional meeting, “Mathematical Modeling of 2016

Infectious Disease and Immunity, Raleigh, NC

CMI-TriCEM meeting on modeling infectious disease dynamics, Raleigh, NC 2016

Exploring Predictive Models for Improving Influenza Vaccine Virus Selection, Princeton, NJ 2016

A workshop of WHO collaborating centers on influenza and academic research groups

EMBO/EMBL conference, Heidelberg, Germany 2016

New model systems for linking ecology and evolution

NIGMS MIDAS meeting, Washington, NC 2016

Duke Provost Forum on Conservation and Health, Durham, NC 2016

9 Koelle CV 2/10/2019

Populations, Evolution, and Physics, Aspen, Colorado 2016

European Society for Evolutionary Biology, Lausanne, Switzerland 2015

(presented by collaborator, given unforeseen circumstances that did not allow me to travel)

Society for Molecular Biology and Evolution, Vienna, Austria 2015

(presented by collaborator, given unforeseen circumstances that did not allow me to travel)

New Directions in Probabilistic Models of Evolution, Simons Institute, Berkeley, CA 2014

Epidemics4, Amsterdam, The Netherlands (Plenary speaker) 2013

Symposium: Combining genetic and epidemiological data to unravel infectious 2013

disease dynamics, Utrecht, The Netherlands (Plenary speaker) American Public Health Association (APHA) meeting, Boston, MA 2013

Invited session: Meeting the threat of infectious diseases with statistical models:

Influenza as a case study

Ecological Society of America, Minneapolis, MN 2013

Invited ignite session: Is the interaction of evolutionary and ecological dynamics

widespread or a special case?

Ecology and Evolution of Infectious Disease Conference, 2013

The Pennsylvania State University, State College, PA

International Conference Frontiers in Systems and Synthetic Biology '13 (FSSB'13), 2013

Georgia Institute of Technology, Atlanta, GA

Disease Dynamics 2013 Conference, Pacific Institute for the Mathematical Sciences 2013

UBC, Vancouver, Canada

National Institute for Mathematical and Biological Synthesis (NIMBioS), 2012

Knoxville, TN, Investigative workshop: Modeling dengue fever

Next-generation molecular and evolutionary epidemiology of infectious disease, 2012

Meeting of the Royal Society. London, England

MAC-EPID symposium, University of Michigan at Ann Arbor, MI 2011

ASN Vice Presidential Symposium, Evolution meeting, Norman, OK 2011

Invited session: A critical look at reciprocity in ecology and evolution

Centre for Infection Dynamics, Utrecht, The Netherlands 2011

Infection Dynamics: Bridging the Gap Between Theory and Application

Climate Change: Health and Ecology, Uppsala University, Uppsala, Sweden 2010

WHO/VMI dengue vaccine modeling group, Geneva, Switzerland 2010

16th Annual Symposium on German-American Frontiers of Science, Potsdam, Germany 2010

Conference on Computational and Mathematical Population Dynamics, Bordeaux, France 2010

Ecological Society of America, Albuquerque, NM 2009

Invited theory section symposium: The interplay of ecology and evolution at

‘micro’ and ‘macro’ scales: empirically-motivated theory

10 Koelle CV 2/10/2019

Gordon Research Conference, Microbial Population Biology, Proctor Academy, NH 2009

Bath Institute for Complex Systems, University of Bath, Bath, UK 2009

Mathematical Biology: Multiply Structured Populations

American Mathematical Society, North Carolina State University 2009

Workshop on Evolution in Health and Disease, Lisbon, Portugal 2008

Instituto Gulbenkian de Ciência

Ecological Society of America, Milwaukee, WI 2008

Invited theory section symposium: Transient dynamics in ecological theory

Viral Paradigms: Molecules, Populations, Ecosystems and Infectious Disease, 2008

Georgia Institute of Technology, Atlanta, GA

10th Annual Symposium on Japanese-American Kavli Frontiers in Science, 2007

Shonan Village Center, Kanagawa, Japan

Environmental Changes, Microbial Systems and Infections, Madrid, Spain 2007

12th Scientific Symposium of the Lilly Foundation

Workshop on evolution of cancer and viruses, Lisbon, Portugal 2007


Co-Evolution of Hosts and Pathogens, DIMACS workshop, Rutgers, NJ 2006

Workshop on pathogen diversity and disease epidemiology, Lisbon, Portugal 2006


Ecology and Evolution of Infectious Diseases Conference, Fort Collins, CO 2005

PI meeting: Program on Climate Variability and Human Health, Atlanta, GA 2004

Contributed presentations at meetings (*upcoming):

Epidemics6 Conference, Barcelona, Spain 2017

6th International Calicivirus Conference, Savannah, GA 2016

International Society for Evolution, Medicine, and Public Health meeting, Durham, NC 2016

Kavli Institute for Theoretical Physics (KITP), UC Santa Barbara, Santa Barbara, CA 2014

Evolution meeting, Raleigh, NC 2014

Ecology and Evolution of Infectious Disease (poster), Fort Collins, CO 2014

21st-Century Naturalists: ASN Conference, Asilomar, CA 2014

Ecological Society of America meeting, Portland, OR 2012

RAPIDD phylodynamics workshop, NESCent, Durham, NC 2011

Ecological Society of America meeting, Austin, TX 2011

Jacques-Monod Conference on Host-Parasite Interactions, Roscoff, France 2007

Ecological Society of America, Memphis, TN 2006

Ecological Society of America, Montreal, Canada 2005

European Conference on Mathematical and Theoretical Biology, Dresden, Germany 2005

11 Koelle CV 2/10/2019

Northeast Ecology and Evolution Conference, State College, PA 2005

Ecological Society of America, Portland, OR 2004

Computational and Mathematical Population Dynamics, Trento, Italy 2004

Ecological Society of America, Savannah, GA 2003

TEACHING/TRAINING

Biology 241: Evolution Fall 2018 Class size: 62

Biology/Math 490: Mathematics and Disease (part of the Math + X initiative) Spring 2017 Class size: 15

Biology 209D: Ecology of Human Health Fall 2016 Class size: 40

UPGEN 778: Genetic and Genomic Solutions to Biological Problems Fall 2015 Module: Molecular phylogenetics. Class size: 12

UPE 702: Ecological Perspectives: ecophysiology to ecosystems Fall 2015 Topic: Population ecology. Class size: 9

Biology 365: Physiology, Ecology, and Evolution of Infectious Disease Fall 2015 Class size: 40

Biology 726: Dynamic Modeling of Biological Systems Fall 2014 Cross-listed with CBB 726/Math 573S, Co-taught with John Harer (Duke Math) Class size: 14 graduate/upper-level undergraduate students

Biology 365: Physiology, Ecology, and Evolution of Infectious Disease Spring 2014 Class size: 40

Biology 726: Dynamic Modeling of Biological Systems Fall 2013 Class size: 12 graduate students


Sociology 180: Perception of the Self, Society, and the Natural World Spring 2013 Class size: 18, first year Baldwin Scholars class

Biology 790: Topics in Biology: Dynamic Modeling of Biological Systems Fall 2012 Class size: 7 graduate students (enrolled), 7 post-docs (auditing)

Biology 146: Physiology, Ecology, and Evolution of Infectious Disease Fall 2011 Class size: 37



Biology 116: Ecology and Evolution Fall 2009 Class size: 78

Biology 295S: Senior seminar: Ecology and Evolution of Infectious Disease Spring 2009 Class size: 12

Biology 116: Ecology and Evolution Fall 2008 Class size: 78

12 Koelle CV 2/10/2019

Training of post-doctoral researchers:

(1) Virginia Pasour (2008-2009, current position: Army Research Office (ARO) Biomathematics Program Officer, Research Triangle Park, NC); (2) Oliver Ratmann (2009-2012, current position: Sir Henry Wellcome Research Fellow, Imperial College London with Dr. Christophe Fraser, London, England (3) Jayna Raghwani (2012-2013, current position: post-doctoral fellow, Oxford University with Dr. Oliver Pybus, Oxford, England); (4) Molly Gallagher (2017-current); (5) Jeremy Harris (2017-current).

Graduate students advised:

(1) Shishi Luo (co-advised by Mike Reed, 2007 - 2013, Ph.D. in Mathematics); (2) Hsiang-Yu Yuan (2007 - 2013, Ph.D. in Computational Biology); (3) Mimi Lin (co-advised by Cliff Cunningham, 2008 - 2010, M.S. in Biology); (4) David Rasmussen (2008 - 2014, Ph.D. in Biology); (5) Chris Castorena (2009 -2013, M.S. in Computational Biology); (6) Stacy Scholle (2010 - 2016, Ph.D. in Biology); (7) Rotem Ben-Shachar (2011 - 2016, Ph.D. in Computational Biology); (8) Ashley Sobel (2012 - 2016, M.D. & Ph.D. in Biology); (9) Diana Vera Cruz (2015 – current; Ph.D. in Computational Biology); (10) Brent Allman (2016-current; PhD. in Population Biology, Ecology, and Evolution); (11) Ellie Mainou (2016-current; M.S. in Population Biology, Ecology, and Evolution); (12) Michael Martin (2018 – current; Ph.D. in Population Biology, Ecology, and Evolution).

On graduate committees of: 31 graduate students in total since 2007 (excluding my own students’ committees).

DUKE: (1) Michelle Hersh (Ph.D. in Ecology 2009, advisor: James Clark); (2) Bernadette O’Reilly (M.S. in Biology 2009, advisor: Rytas Vilgalys); (3) Supriya Munshaw (Ph.D. in Computational Biology 2010, advisor: Thomas Kepler); (4) Seiji Kumagai (M.S. in Biology 2010, advisor: William Wilson); (5) Meredith Barrett (Ph.D. in Ecology 2011, advisor: Anne Yoder); (6) Hannah Reynolds (Ph.D. in Biology, advisor: Rytas Vilgalys); (7) David McCandlish (Ph.D. in Biology 2012, advisors: Paul Magwene, Dan McShea); (8) Zachary Brown (Ph.D. in Ecology, advisor: Randall Kramer); (9) Denis Valle (Ph.D. in Ecology 2013, advisor: James Clark); (10) Kathleen Burchardt-Pitcher (Ph.D. in Plant Pathology 2013, advisor: Marc Cubeta – NC State); (11) Colin Maxwell (Ph.D. in Biology 2016; advisors: Paul Magwene, Ryan Baugh); (12) Mercy Akinyi (Ph.D. in Biology 2017; advisor: Susan Alberts); (13) Erin McKenney (Ph.D. in Biology 2017; advisors: Allen Rodrigo, Anne Yoder); (14) Mariana Gomez-Schiavon (Ph.D. in Computational Biology 2016; advisor: Nick Buchler); (15) Kendra Smyth (Ph.D. in Ecology 2017; advisor: Christine Drea); (16) Allison Lopatkin (Ph.D. in Biomedical Engineering 2017, advisor: Lingchong You); (17) Firas Midani (pursuing Ph.D. in Computational Biology, advisor: Lawrence David); (18) Will Cao (Ph.D. in Biomedical Engineering 2017, advisor: Lingchong You); (19) Yuantong Ding (pursuing Ph.D. in Biology, advisor: Allen Rodrigo); (20) Randi Griffin (2016, M.S. in Evolutionary Anthropology, advisor: Charlie Nunn); (21) Brandt Levitt (Ph.D. in Molecular Genetics and Genomics 2017, advisor: Steven Taylor); (22) Cody Nelson (pursuing MD/Ph.D. in Molecular Genetics and Immunology, advisor: Sallie Permar). (23) Qualifying exam committee of: Greg Murphy (pursuing Ph.D. in Mechanical Engineering & Materials Sciences); (24) Jaydeep Srimani (Ph.D. in Biomedical Engineering 2017, advisor: Lingchong You). EMORY: (25) Molly Steele (pursuing Ph.D. in Epidemiology, Rollins School of Public Health, advisor: Ben Lopman); (26) Megan Hockman (pursuing Ph.D. in MMG, advisor: Anice Lowen); (27) Trieste Musial (pursuing Ph.D. in PBEE, advisors: Berry Brosi & Jaap de Roode); (28) Mahan Ghafari (pursing M.S. in PBEE, advisor: Daniel Weissman); (29) Tyler Smith (pursuing Ph.D. in Physics, advisor: Daniel Weissman); (30) Daniel Desautels (pursuing Ph.D. in PBEE, advisor: Dave Civitello); (31) Connor Morozumi (pursuing Ph.D. in PBEE, advisor: Berry Brosi).

Undergraduate research students: DUKE: Meredith Kamradt (independent study and work study student, 2008-2009); Priya Khatri (independent study student; completed honors thesis with Koelle, 2008-2010); Brian Adams (independent study student, 2008-2009); Rachel Northeim (completed undergraduate honors thesis with Koelle, 2008-2009); Kiron LeBeck (summer undergraduate research student, 2010); Rachel Willcutts (independent study student, 2010); Olivia Yvellez (summer undergraduate research student from

13 Koelle CV 2/10/2019

U. Chicago 2015); Eddie Zhao (independent study student, 2016); Alex Dai (independent study student, 2016); Vivek Sriram (work study student, 2017). EMORY: Young Hye Lee (sophomore, Emory University); Lily Zhong (sophomore, Emory University).

Associates in research: Nicole Nova (2015-2016, currently Ph.D. student at Stanford); Olivia Yvellez (2016-2017); Baptiste Elie (internship 2018-current).

Publications with contributions from undergraduates:

Koelle, K., Khatri, P., Kamradt, M., and T. Kepler (2010). A two-tiered model for studying the ecological and evolutionary dynamics of rapidly evolving viruses, with an application to influenza. Journal of the Royal Society, Interface. 7, pp.1257-1274. doi: 10.1098/rsif.2010.0007

Koelle, K., Kamradt, M., and M. Pascual (2009). Understanding the dynamics of rapidly evolving pathogens through modeling the tempo of antigenic change: influenza as a case study. Epidemics. 1, pp. 129-137. doi: 10.1016/j.epidem.2009.05.003

Education and outreach:

Interview with Quanta magazine 2018

Interviews with popular media: The Atlantic, WIRED, Science News 2017

Keystone Podcast: Modelling viral infection and immunity 2017

Interview with Michigan State University’s Scientific Virtues Project 2016

Department of Biology host to Voyager Academy AP Biology class 2016

Interview with Emily Monosson, author of Unnatural Selection: how we are changing 2014

life gene by gene.

Interview with Science News for Students, an educational online resource for 2014

students 12 years old and up

Regional Mathematics and Statistics Conference, UNC at Greensboro, Greensboro, NC, 2012

Plenary speaker; undergraduate/graduate conference promoting student research

Interview with NBC Learn, an educational online resource for K-12 classrooms 2012

One Health Intellectual Exchange Series, Research Triangle Park, NC 2011

Howard Hughes Undergraduate Research Program, Duke University, Durham, NC 2011

Periodic Tables- Science Café at the Broad Street Café, Durham, NC 2011

Rx for Science Literacy, Evolution and Medicine teacher workshop, Duke University 2011

Workshop organized by the North Carolina Association for Biomedical Research

Graduate workshop on Quantitative Immunology, San Antonio, TX 2010


Graduate workshop on Quantitative Immunology, Santa Fe Institute, Santa Fe, NM 2009

Darwin Day, NESCent, Research Triangle Park, NC 2009


The Institute for Mathematical Biology Education and Resources (TIMBER), 2008

Appalachian State University, Boone, NC. Plenary speaker;

14 Koelle CV 2/10/2019

undergraduate/graduate conference promoting student research

The North Carolina School of Science and Mathematics, Durham, NC 2008


SERVICE

Journal editor for:

eLife (Reviewing Editor, 2019); PLoS Biology (Academic Editor, 2016-present); Evolution (Associate Editor; 2018-present). Epidemics (Associate Editor; 2014-present); PLoS Computational Biology (Associate Editor, 2014 – 2017; Deputy Editor, 2017-2018); Theoretical Ecology (Editor, 2015- 2018); Axios Review (Editor; 2015-2017); Proceedings of the Royal Society, Series B (Associate Editor, 2013-2018);

Reviewer for:

Journals: Science, Nature, PLoS Biology, eLife, PNAS, The American Naturalist, Evolution, Ecology Letters, Journal of Theoretical Biology, PLoS Computational Biology, Journal of Molecular Evolution, Trends in Ecology and Evolution, PLoS Pathogens, Proceedings of the Royal Society B, Journal of the Royal Society: Interface, mSphere, Philosophical Transactions of the Royal Society B, Molecular Biology and Evolution, American Journal of Epidemiology, EcoHealth, Mathematical Biosciences, BMC Infectious Diseases, Sexually Transmitted Infections. I review approximately a dozen manuscripts a year.

Funding bodies: NSF BIOLOGY full proposal panel (2015) NSF BIOLOGY pre-proposal panel (2014) Marsden Fund reviewer (2013) Sir Henry Dale Fellowship reviewer (2013) NSF external reviewer (2011-2013) DAAD German Academic Exchange Service (2009, 2012, 2013, 2014) NSF BIO panel (2011) UK Wellcome Trust (2011) NSF Committee of Visitors for the Emerging Frontiers Division (2009)

Conference abstracts/session proposals: Epidemics6 (2017)

Epidemics5 (2015) Banff International Research Station Proposals (2012) Ecological Society of America Organized Oral Session proposals (2012)

Societies:

Ecological Society of America 2003-present

Society for Mathematical Biology 2007-present

Society for the Study of Evolution 2011-present

Society for Molecular Biology and Evolution 2017-present

American Society for Microbiology 2017-present

Atlanta Society of Mentors – Emory Chapter 2017-present

15 Koelle CV 2/10/2019

American Society for Virology 2018-present

Member:

Quantitative Theory and Methods (QTM) Planning Committee, Emory University 2018-present

Emory PBEE graduate program Executive Committee 2018-present

Emory Department of Biology, Biology Seminar Task Force Committee 2017

Duke Ecology Faculty Search Committee, Chair 2016-2017

Computational Biology and Bioinformatics Executive Committee 2015-2017

Duke Academic Council 2015-2017

Biology Computing Committee 2015-2017

Biology Graduate Admissions Committee 2010-2014 2016-2017

Biology Seminar Series Committee 2012-2013 2009-2010

Duke Academic Council 2009-2013

Biology Performance Review Committee 2009-2011

Computational Biology and Bioinformatics Graduate Admissions Committee 2009-2010 2012-2014

Microbial Ecology Search Committee, Nicholas School of the Environment 2008-2009

Other service:

External Peer Reviewer of CDC Influenza Division 2018

SciLine member 2017-present

Omenn Prize Committee 2018

Emory STEM Research and Career Symposium Judge 2017

External letter writer for promotion to tenure case 2017

Member of Scientific Committee, Epidemics6 2017

Co-organizer of TriCEM symposium on ‘The Use of Pathogen Genetic Data for 2015

Informing the Spread of Infectious Diseases Within and Between Hosts’

External letter writer for promotion to tenure case 2015

External reviewer for ETH Zurich’s medal for Ph.D. thesis 2015

Member of Scientific Committee, Epidemics5 2015

External search committee member for ETH Zurich’s Ecology and Evolution 2014

of Infectious Disease position

Co-organizer of Woman and Science Seminar Series, Duke University 2014-2016

Co-organizer of ESA Theory vs. Empiricism Ignite Session 2014

Organizer for workshop: Rapid Evolution and Sustainability 2012-2013

Mathematical Biosciences Institute, Columbus, OH

16 Koelle CV 2/10/2019

Co-organized with Jim Cushing, Steven Munch, and Patrick de Leenheer

External search committee member for ETH Zurich’s Ecology and Evolution 2013

of Infectious Disease position

Chair of the Ecological Society of America’s theoretical ecology section 2012-2013

Vice-chair of the Ecological Society of America’s theoretical ecology section 2011-2012

Organizer of the RAPIDD phylodynamics workshop, NESCent, Durham, NC 2011

Session Organizer, German-American Frontiers in Science, Irvine, CA 2011

Co-editor for a special issue in Interdisciplinary Perspectives on Infectious Disease 2010

Faculty of 1000 member and contributor 2009

Katia Koelle - Curriculum vitae - ScholarBlogs

Documents