Curriculum Vitae.

Education

Ph.D. (Applied Mathematics). University of Arizona, 1999.
Dissertation Title: Hamiltonian Limits and Subharmonic Resonance in Models of Population Fluctuations.
Advisor: Prof. W. M. Schaffer

M.A. (Mathematics). University of Hawai'i, 1992.

B.A. summa cum laude (Mathematics). Rice University, 1989.

Appointments

2008-

Senior Research Fellow, Fogarty International Center for Advanced Study in the Health Sciences, National Institutes of Health.

2005-

Assistant Professor of Ecology & Evolutionary Biology and Mathematics, University of Michigan, Ann Arbor.

2005-

Primary Faculty Member of the Center for the Study of Complex Systems, University of Michigan, Ann Arbor.

2004-2005

Research Assistant Professor of Mathematics, University of Tennessee, Knoxville.

2002-2005

Assistant Professor of Ecology & Evolutionary Biology, University of Tennessee, Knoxville.

2001-2002

Visiting Research Assistant Professor of Mathematics. University of California, Davis.

2000-2002

National Science Foundation Postdoctoral Research Fellow. Department of Environmental Science & Policy, University of California, Davis. Mentor: Alan Hastings.

1999-2000

Postdoctoral Research Associate. Program in Applied Mathematics, University of Arizona. Mentor: J. M. Cushing.

1998

Graduate Research Associate. Department of Ecology & Evolutionary Biology, University of Arizona.

1997-1998

Flinn Foundation Fellow. Program in Applied Mathematics, University of Arizona.

1994-1997

National Science Foundation Graduate Research Fellow. Program in Applied Mathematics, University of Arizona.

1993-1994

Adjunct Instructor of Mathematics, University of Arizona.

1993

Adjunct Instructor of Mathematics, Pima County Community College, Tucson, Arizona.

1991-1992

Graduate Teaching Assistant, Department of Mathematics, University of Hawai'i, Manoa.

Honors and Awards

Biological Sciences Scholar, University of Michigan, 2005-.

National Science Foundation Mathematical Sciences Postdoctoral Fellowship, 2000-2003.

National Science Foundation Biological Informatics Postdoctoral Fellowship, 2000 (refused).

Flinn Foundation Postdoctoral Fellowship, 1999-2000.

Flinn Foundation Graduate Fellowship, 1997-1998.

National Science Foundation Graduate Research Fellowship, 1994-1997.

Flinn Foundation Scholarship, 1995-1997.

National Merit Scholarship, 1985-1989.

Full Scholarship to Rice University, 1986-1989.

Valedictorian, Andress High School Class of 1985.

Working Groups

• Organizer of Research and Policy in Infectious Disease Dynamics (RAPIDD) Working Group on ``Statistical Inference for Disease Dynamics'' (2009-).
• Co-organizer of Research and Policy in Infectious Disease Dynamics (RAPIDD) Working Group on ``Scaling from Within- to Between-Host Dynamics and Evolution'' (2009-).
• Co-organizer of National Center for Ecological Analysis and Synthesis (NCEAS) Working Group on ``Unifying approaches to statistical inference in ecology'' (2007-2009).
• Invited participation in National Evolutionary Synthesis Center (NESCent) ``Hackathon on Comparative Methods in R'' (2007-2008).
• Invited participation in NCEAS Working Group on ``Seasonality and the population dynamics of infectious diseases'' (2003-2005).

Peer-reviewed Publications

1. D. He, E. L. Ionides, and A. A. King (2009), ``Plug-and-play inference for disease dynamics: Measles in large and small towns as a case study'' Journal of the Royal Society Interface, in press, doi:10.1098/rsif.2009.0151.
2. E. C. Farrer, D. E. Goldberg, and A. A. King (2009), ``Time lags and the balance of positive and negative interactions in driving grassland community dynamics'' American Naturalist, in press.
3. A. A. King, S. Shrestha, E. T. Harvill, and O. N. Bjørnstad (2009), ``Evolution of acute infections and the invasion-persistence trade-off'' American Naturalist, 173:446-455.
4. J. A. Scales, A. A. King, and M. A. Butler (2009), ``Running for your life or running for your dinner: What drives fiber-type evolution in lizard locomotor muscles?'' American Naturalist, 173:543-553.
5. C. Bretó, D. He, E. L. Ionides, and A. A. King (2009), ``Time series analysis via mechanistic models'' Annals of Applied Statistics, 3:319-348.
6. A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma (2008), ``Inapparent infections and cholera dynamics'', Nature 454:877-880.
7. D. Dimitrov, A. A. King, and T. G. Hallam (2008), ``Modeling evolution and persistence of neurological viral diseases in wild populations''. Mathematical Biosciences and Engineering 5:729-741.
8. E. L. Ionides, C. Bretó, and A. A. King (2008), ``Modeling disease dynamics: Cholera as a case study'', Chapter 8 in A. Biswas, S. Datta, J. Fine, M. Segal (eds.) Statistical Advances in the Biomedical Sciences.
9. E. L. Ionides, C. Bretó, and A. A. King (2006), ``Inference for nonlinear dynamical systems'' Proceedings of the National Academy of Sciences of the U.S.A. 103:18438-18443.
10. Robert A. Desharnais, R. F. Costantino, J. M. Cushing, Shandelle M. Henson, Brian Dennis, and Aaron A. King (2006), ``Experimental support of the scaling rule for demographic stochasticity'' Ecology Letters 9:537-547.
11. R. F. Costantino, Robert A. Desharnais, J. M. Cushing, Brian Dennis, Shandelle M. Henson, and Aaron A. King (2005), ``Nonlinear population dynamics: The flour beetle Tribolium as an effective tool of discovery'' Advances in Ecological Research 37:101-141.
12. Aaron A. King (2005), ``Phase plane'', in Alwyn Scott (ed.), Encyclopedia of Nonlinear Science, pp. 712-714. Routledge, New York.
13. Marguerite Butler and Aaron A. King (2004), ``Phylogenetic comparative analysis: a modeling approach for adaptive evolution'', The American Naturalist 164:683-695.
14. A. A. King, R. F. Costantino, J. M. Cushing, S. M. Henson, R. A. Desharnais, and B. Dennis (2004), ``Anatomy of a chaotic attractor: subtle model-predicted patterns revealed in population data'' Proceedings of the National Academy of Sciences, U.S.A. 101:408-413.
15. Aaron A. King and Alan Hastings (2003), ``Spatial mechanisms for coexistence of species with a shared natural enemy'', Theoretical Population Biology 64: 431-438.
16. Shandelle M. Henson, Aaron A. King, R. F. Costantino, J. M. Cushing, Brian Dennis, and Robert A. Desharnais (2003), ``Explaining and predicting patterns in stochastic population systems'', Proc. R. Soc. Lond. B 270: 1549-1553.
17. A. A. King, R. A. Desharnais, S. M. Henson, R. F. Costantino, and J. M. Cushing (2002), `` Random Perturbations and Lattice Effects in Chaotic Population Dynamics'', Science 297:2163.
18. S. M. Henson, R. F. Costantino, J. M. Cushing, Robert A. Desharnais, Brian Dennis, and Aaron A. King (2001), ``Lattice Effects Observed in Chaotic Dynamics of Experimental Populations'', Science 294:602-605.
19. Aaron A. King and William M. Schaffer (2001), ``The Geometry of a Population Cycle: A Mechanistic Model of Snowshoe Hare Demography'', Ecology 82:814-830.
20. W. M. Schaffer, B. S. Pederson, K. Moore, O. Skarpaas, A. A. King, and T. V. Bronnikova (2001), ``Subharmonic resonance and multi-annual oscillations in northern mammals: a nonlinear dynamical systems perspective'', Chaos, Solitons, and Fractals 12:251-264.
21. J. M. Cushing, Shandelle M. Henson, Robert A. Desharnais, Brian Dennis, R. F. Costantino, and Aaron King (2001), ``A Chaotic Attractor in Ecology: Theory and Experimental Data'', Chaos, Solitons, and Fractals 12:219-234.
22. Aaron A. King and William M. Schaffer (1999), ``The Rainbow Bridge: Hamiltonian Limits and Resonance in Predator Prey Dynamics'', Journal of Mathematical Biology 39:439-469.
23. Aaron King and Alwyn Scott (1998), ``The Dimensions of Creativity'', in S. R. Hameroff, A. W. Kaszniak, & A. C. Scott (eds.) Toward a Science of Consciousness 2, MIT Press, Cambridge, Mass.
24. A. A. King, W. M. Schaffer, J. Treat, C. Gordon, and M. Kot (1996), ``Weakly Dissipative Predator-Prey Systems'', Bulletin of Mathematical Biology 58:835-860.

Abstracts and preprints are available at http://www.umich.edu/~kingaa/.

Manuscripts submitted

1. J. Vandermeer and A. A. King (2009), ``Consequential classes of resources: Subtle global bifurcation with dramatic ecological consequences in a simple population model'' Journal of Theoretical Biology, in revision.
2. C. Cressler, A. A. King, and E. E. Werner (2009), ``The foraging-predation risk tradeoff and the evolution of multiple-defense plasticity'' American Naturalist, submitted.
3. E. L. Ionides, A. Bhadra, and A. A. King (2009), ``Iterated Filtering'' Electronic Journal of Statistics, submitted.
4. J. L. Zelner, A. A. King, C. L. Moe, and J. N. S. Eisenberg (2009) ``Inference for Household Transmission Systems: An Analysis of Secondary Transmission in a Norovirus Outbreak'' American Journal of Epidemiology, in review.

Technical Reports

1. E. L. Ionides, C. Bretó, and A. A. King (2006), ``Parameter estimation for nonlinear state space models'', Statistics Department Technical Report #438. University of Michigan, Department of Statistics.

Research Grants

2008-2011

National Oceanic and Atmospheric Administration Grant: ``Cholera prediction: the role of the oceans and nonlinear disease dynamics'' Oceans and Human Health Program. Award of $943,168.

2005-2008

National Science Foundation, Division of Environmental Biology Grant: ``A Direct Modeling Approach for Phylogenetic Comparative Analysis''. Systematics Program. Award of $361,461.

2004-2008

National Science Foundation, Division of Biological Sciences Grant: ``Collaborative Research: The interplay of extrinsic and intrinsic factors in epidemiological dynamics: cholera as a case study''. Ecology of Infectious Diseases Program. Award of $942,000.

2004-2006

National Science Foundation, Division of Biological Sciences Grant: ``Ecological Influences on Rabies Infections in Bats''. Ecology of Infectious Diseases Program. Award of $1,496,000.

2000-2003

National Science Foundation Mathematical Science Postdoctoral Research Fellowship. Award of $90,000.

2000-2002

National Science Foundation Biological Informatics Postdoctoral Research Fellowship (refused). Award of $100,000.

1994-1997

National Science Foundation Graduate Research Fellowship.

Teaching Grants

2007-2012

National Science Foundation, Division of Mathematical Sciences Grant: 'UBM-Institutional: SUBMERGE -- Supplying Undergraduate Biology and Mathematics Education and Research Group Experiences to Students at the University of Michigan' Interdisciplinary Training for Undergraduates in Biology & Mathematics Program. Award of $905,000.

Invited Lectures

1. Seminar, Department of Physics, Oakland University (September 17, 2009).
2. ``Plug-and-play inference for stochastic dynamical systems'', Workshop on Statistical Methods for Dynamic System Models, Vancouver, British Columbia (June 6, 2009).
3. ``Cholera in Bengal: multiple transmission modes, multiple infection outcomes'', Ecology & Evolution of Infectious Disease Conference, University of Georgia (May 22, 2009).
4. Seminar, Department of Ecology & Evolution, University of Chicago (February 9, 2009).
5. Mathematical and Computational Biology Seminar, Department of Mathematics, University of California, Berkeley (September 17, 2008).
6. ``New insights into cholera dynamics: asymptomatic infections, rapid loss of immunity, and mode of transmission'', Seminar, National Center for Ecological Analysis and Synthesis, Santa Barbara, California (December 6, 2007).
7. Seminar, Department of Biology, Case Western Reserve University, Cleveland, Ohio (October 17, 2007).
8. ``Rigorous inference for partially-observed Markov processes'', Lecture, Mathematical Modeling and Analysis of Populations in Biological Systems Conference, Tucson, Arizona (October 5, 2007).
9. Seminar, Applied and Interdisciplinary Mathematics Program, University of Michigan, Ann Arbor, Michigan (February 23, 2007).
10. Seminar, Department of Epidemiology, University of Michigan, Ann Arbor, Michigan (January 24, 2007).
11. ``Between-host consequences of within-host dynamics: the case of the Bordetellae'', Lecture, Bridging the Scales of Disease Dynamics 2006, Pacific Institute of Mathematical Sciences, University of British Columbia, Vancouver (September 29, 2006).
12. ``Anatomy of a chaotic attractor: temporal patterns and lattice effects in population dynamics'', Seminar, W. K. Kellogg Biological Station (January 13, 2006).
13. ``Rhythm and noise: Detection of temporal patterns in ecological data and what it tells us'', Keynote Lecture, TIMBER 2005, A Conference on Quantitative Biology, Appalachian State University, Boone, North Carolina (November 4, 2005).
14. Seminar, Program in Applied and Interdisciplinary Mathematics, University of Michigan, Ann Arbor (October 28, 2005).
15. ``Linking mechanistic models with epidemiological data: parameter estimation in the face of incomplete information'', Symposium Lecture, Ecological Society of America Annual Meeting, Montréal, Québec, (August 12, 2005).
16. ``Linking mechanistic models with epidemiological data: parameter estimation in the face of incomplete information'', Symposium Lecture, SIAM Conference on Applications of Dynamical Systems, Snowbird, Utah (May 26, 2005).
17. ``Discrete-state biological dynamics: Stochastic models and deterministic skeletons'', Lecture, Joint Mathematics Meetings, Atlanta, Georgia (January 8, 2005).
18. ``Anatomy of a chaotic attractor: subtle model-predicted patterns revealed in population data'', Lecture, Joint Mathematics Meetings, Phoenix, Arizona (January 7, 2004).
19. ``Chaos in a Bottle: Experimental Studies of Nonlinear Population Dynamics'', Lecture, University of Tennessee Chapter of the Society for Industrial and Applied Mathematics, University of Tennessee, Knoxville (November 5, 2003).
20. ``Which deterministic skeleton? Multiple skeletons and lattice effects in stochastic population models'', Lecture, Ecological Society of America Annual Meeting, Savannah, Georgia, (August 7, 2003).
21. ``The Hunt for Chaos'' and ``Patterns in Chaos'', Lectures, Rocky Mountain Mathematics Consortium Summer Conference, University of Wyoming, Laramie, Wyoming, (July 7-18, 2003).
22. ``Some Hamiltonian problems in population dynamics'', Lecture, Differential Equations Seminar, University of Tennessee, Knoxville, Tennessee (October 28, 2002).
23. ``Order in Real Data: Model-Predicted Temporal Patterns in Chaotic Population Data'', Lecture, Ecological Society of America Annual Meeting, Tucson, Arizona (August 4, 2002).
24. ``From the Pendulum to the Lynx and the Hare'', Seminar, Department of Ecology & Evolutionary Biology, University of Arizona, (January 19, 1999).

Contributed Lectures

1. ``Boosting of acquired immunity through re-exposure: Dynamical consequences'', Lecture, Ecology Society of America Annual Meeting, Albuquerque, New Mexico (August 6, 2009)
2. ``Statistical inference using mechanistic models in continuous time: Measles as a case study'', Lecture, Ecology Society of America Annual Meeting, Milwaukee, Wisconsin (August 7, 2008)
3. ``New insights into cholera dynamics: Rapid loss of immunity, transmission mode, and climate drivers'', Lecture, Ecology Society of America Annual Meeting, San Jose, California (August 9, 2007)
4. ``A new view of cholera endemicity: routes of transmission and rapid loss of immunity'', Lecture, Ecology of Infectious Diseases and American Society of Tropical Medicine & Hygiene, Atlanta, Georgia (November 21, 2006).
5. ``Multiple skeletons and lattice effects in stochastic population models'', Lecture, Alcalá Second International Conference on Mathematical Ecology, Alcalá de Henares, Spain (September 5-9, 2003).
6. ``Spatial Mechanisms for Coexistence of Species Sharing a Common Natural Enemy'', Lecture, Ecological Society of America Annual Meeting, Tucson, Arizona (August 4-9, 2002).
7. ``Subtle Temporal Patterns in Tribolium Population Dynamics'', Lecture, International Conference on Mathematical and Theoretical Biology, Hilo, Hawai'i (July 16-19, 2001).
8. ``Host-parasitoid dynamics, apparent competition, and spatio-temporal pattern'', Seminar, Institute for Theoretical Dynamics, University of California, Davis (May 9, 2001).
9. ``Hamiltonian Limits and Subharmonic Resonance in Ecological Models: From the Pendulum to the Lynx and the Hare'', Symposium Lecture, AMS Western Sectional Meeting, Tucson, Arizona (November 14, 1998).
10. ``Subharmonic Resonance and Population Cycles'', Seminar, Department of Mathematics, University of Arizona (April 1 & 8, 1998).
11. ``Elucidating the Microcircuitry Underlying Polyphasic Response to Olfactory Stimulation'', Lecture and Poster, Flinn Foundation Biomedical Initiative Symposium, Tucson, Arizona (May 9-10,1997).
12. ``Using Mathematics to Sniff Out the Brain's Olfactory Code'', Lecture, Quantitative Modeling in Biology Seminar Series, University of Arizona, (February 26, 1997).
13. ``Persistent Remnants of Hamiltonian Topology in Predator-Prey Dynamics'', Lecture, Dynamics Days Arizona Conference (January 8-11, 1997).
14. ``Mathematical Modeling as a Tool in Neurophysiology'', Lecture, Foundation Biomedical Initiative Symposium, Scottsdale, Arizona (May 3-4, 1996).
15. ``The Dimensions of Creativity'', Lecture, Toward A Science of Consciousness II Conference (April 8-13, 1996).

Teaching Experience

2009

General Ecology. Program in Biology, University of Michigan, Ann Arbor, Fall term.

2009

Ecology and Evolution of Infectious Diseases Workshop, University of Georgia, Athens, May 16-19.

2009

Mathematical Ecology. Departments of Ecology & Evolutionary Biology and Mathematics, University of Michigan, Ann Arbor, Winter term.

2008

Ecology and Evolution of Infectious Diseases Workshop, Colorado State University, Ft. Collins, June 1-4.

2008

Interrogating Data with Models, Graduate Course, Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Winter term.

2007

General Ecology. Program in Biology, University of Michigan, Ann Arbor, Fall term.

2007

General Ecology. Program in Biology, University of Michigan, Ann Arbor, Winter term.

2006

Mathematical Ecology. Departments of Ecology & Evolutionary Biology and Mathematics, University of Michigan, Ann Arbor, Fall term.

2005

General Ecology. Program in Biology, University of Michigan, Ann Arbor, Fall term.

2004-2005

Mathematical Ecology. Departments of Ecology & Evolutionary Biology and Mathematics, University of Tennessee, Knoxville.

2003-2004

Mathematical Ecology. Departments of Ecology & Evolutionary Biology and Mathematics, University of Tennessee, Knoxville.

2003

Introduction to Modeling in Ecology, Evolution, and Behavior. Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville.

2002

Integral Calculus. Department of Mathematics, University of California, Davis.

2002

Ordinary Differential Equations. Department of Mathematics, University of California, Davis.

2000-2001

Guest lectures in course on Mathematical Methods in Population Biology, University of California, Davis.

1996

Calculus. Department of Mathematics, University of Arizona.

1993-1994

Calculus (with Laboratory). Department of Mathematics, University of Arizona.

1993

Two lower level mathematics courses. Pima County Community College, Tucson, Arizona.

1993

General Biology. Tucson Unified School District, Tucson, Arizona.

1991-1992

Trigonometry courses. Department of Mathematics, University of Hawai'i, Manoa.

1991

Calculus. Department of Mathematics, University of Hawai'i, Manoa.

1991-1992

English and Art History. Varsity International School, Honolulu, Hawai'i.

Graduate Students and Postdocs Supervised

Supervised the following students.

1. Sourya Shrestha (Ph.D., Applied Interdisciplinary Mathematics, University of Michigan, 2009)
2. Yancy Lo (M.S., Ecology & Evolutionary Biology, University of Michigan, 2009)
3. Frank Wright, (M.A. in Mathematics, University of Tennessee, 2005)
4. Clay Cressler (Ecology & Evolutionary Biology, University of Tennessee, University of Michigan)

Served on advisory committees for the following students.

1. Joseph Brown (EEB, University of Michigan)
2. Anindya Bhadra, (Statistics, University of Michigan)
3. David Allen (EEB, University of Michigan)
4. Mimi Lin (EEB, Duke University)
5. Sarah Cobey (Ph.D. in EEB, University of Michigan, 2009)
6. Diego Ruiz-Moreno (Ph.D. in EEB, University of Michigan, 2009)
7. Carles Bretó, (Ph.D. in Statistics, University of Michigan, 2007)
8. Sean McMahon (Ph.D. in EEB, University of Tennessee, 2006)
9. Tadashi Fukami (Ph.D. in EEB, University of Tennessee, 2003)
10. Paula Federico (Ph.D. in EEB, University of Tennessee)
11. Marc Cadotte (Ph.D. in EEB, University of Tennessee, 2006)
12. Wandi Ding (Ph.D. in Mathematics, University of Tennessee, 2006)

Professional Societies

• Ecological Society of America.
• Society for Mathematical Biology.
• Society for Industrial and Applied Mathematics.
• American Association for the Advancement of Science.

Software Development

Developer and maintainer of the following software packages.

• pomp, an R package for statistical inference using mechanistic models (partially-observed Markov processes)
• ouch, an R package for model-based phylogenetic comparative analysis of quantitative traits
• xloc, a public-domain package for numerical continuation and bifurcation analysis
• BifCurve, a Mathematica package for numerical continuation and bifurcation analysis
• NormalForm, a Mathematica package for symbolic normal-form analysis of vectorfields
• llama, a C++ library of efficient applied mathematics algorithms
• dlivr, a package for numerical analysis of dynamical systems with a Matlab/Octave/Mathematica interface
• arborize, a TCL/Tk program for semiautomatic extraction of dimensions and connectivity of neurons from confocal laser microscopic data

Academic Service

Associate Editor for Journal of Theoretical Biology

Associate Editor for Theoretical Population Biology

Reviewer for: Advances in Ecological Research, American Naturalist, Ecological Monographs, Ecology, Ecology Letters, Journal of Health, Population and Nutrition, Journal of Mathematical Biology, Journal of Theoretical Biology, Mathematical Biosciences, Oikos, Physical Review Letters, Physics Letters A, Proceedings of the National Academy of Sciences, U.S.A, Proceedings of the Royal Society, Series A & B, Public Library of Science Biology, Public Library of Science Medicine, Public Library of Science One, Science, SIAM Journal on Applied Mathematics, Theoretical Population Biology, Trends in Ecology & Evolution.

Departmental service:

• Department Seminar committee, Ecology & Evolutionary Biology, University of Michigan, 2008-.
• Graduate admissions committee, Ecology & Evolutionary Biology, University of Michigan, 2006-2008.
• Undergraduate affairs committee, Ecology & Evolutionary Biology, University of Tennessee, 2003-2004.
• Graduate Admissions Committee, Ecology & Evolutionary Biology, University of Tennessee, 2002-2005.
• Departmental Library Representative, Ecology & Evolutionary Biology, University of Tennessee, 2002-2005.
• Departmental Website Committee, Ecology & Evolutionary Biology, University of Tennessee, 2004-2005.

Served on the ``Nonlinear Dynamics in Biology'' Research and Training Group Admissions Committee, 2001.

Panelist on ``Nonlinear Dynamics in Biology'' Research and Training Group panels: ``Choosing a graduate school'', ``Finding a postdoc'', ``Balancing career and family concerns'', 2000-2001.

Served on the Board of Directors of the Tucson Waldorf School, 1999-2000.