Steve Krone: Research by Subject

Most of this work was supported by the National Institutes of Health and the National Science Foundation.

Spatial Structure

  • Phage-Bacterial Dynamics with Spatial Structure: self organization around phage sinks can promote high cell densities
    Bull JJ, Christensen K, Scott C, Jack BR, Crandall C, and Krone SM. Antibiotics (Special Issue on "Bacteriophages: Alternatives to Antibiotics and Beyond") (2018), doi:10.3390/antibiotics7010008.
    abstract | pdf

  • Models for the directed evolution of bacterial allelopathy: bacteriophage lysins
    Bull JJ, Crandall C, Rodriguez A, and Krone SM. PeerJ (2015) 3:e879; DOI 10.7717/peerj.879.
    abstract | pdf

  • The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress
    Ally D, Wiss VR, Deckert G, Green D, Roychoudhury P, Wichman HA, Brown CJ, and Krone SM. PLoS ONE (2014) 9, e88702.
    abstract | pdf

  • Fitness benefits of low infectivity in a spatially structured population of bacteriophages
    Roychoudhury P, Shrestha N, Wiss VR, Krone SM. Proceedings of the Royal Society B (2014) 281, 20132563.
    abstract | pdf

  • Adaptive regulatory substitutions affect multiple stages in the life cycle of the bacteriophage phiX174
    (with C.J. Brown, A.D. Stancik, P. Roychoudhury) BMC Evolutionary Biology (2013) 13, 66.
    abstract | pdf

  • Invasion of E. coli biofilms by antibiotic resistance plasmids
    (with J. Król, A. Wojtowicz, L.M. Rogers, H. Heuer, K. Smalla, E.M. Top) Plasmid (2013) 70(1): 110-119. abstract | pdf

  • Influence of humans on evolution and mobilization of the environmental antibiotic resistome
    Gaze WH, Krone SM, Larsson J, Li X-Z, Robinson JA, Simonet P, Smalla K, Timinouni M, Topp E, Wellington EM, Wright GD, Zhu Y-G. Emerging Infectious Diseases (2013) 19. abstract | online article

  • On the Meaning and Estimation of Plasmid Transfer Rates for Surface-Associated and Well-Mixed Bacterial Populations
    (with X. Zhong, J. Droesch, and E.M. Top). Journal of Theoretical Biology (2012) 294, 144-152.
    abstract | pdf

  • Stochastic Spatial Models. (2012) pp 666-670, in Hastings, A. and Gross, L. (eds.) Encyclopedia of Theoretical Ecology, University of California Press, Berkeley, CA.

  • Increased transfer of a multi-drug resistance plasmid in Esherichia coli biofilms at the air-liquid interface
    (with J.E. Krol, H.D. Nguyen, L.M. Rogers, H. Beyenal, and E.M. Top). Applied and Environmental Microbiology (2011) 77: 5079-5088.
    abstract | pdf

  • Dual Reporter System for in situ Detection of Plasmid Transfer in Aerobic and Anaerobic Conditions
    (with J.E. Krol, L.M. Rogers, and E.M. Top). Applied and Environmental Microbiology (2010) 76: 4553 - 4556.
    abstract | pdf

  • Accounting for Mating Pair Formation in Plasmid Population Dynamics
    (with X. Zhong, J.E. Krol, and E.M. Top). Journal of Theoretical Biology (2010) 262, 711-719.
    abstract | pdf

  • Space, Time and Host Evolution Facilitate Coexistence of Competing Bacteriophages: Theory and Experiment
    (with L.C. Coberly, W. Wei, K.Y. Sampson, J. Millstein, and H.A. Wichman). American Naturalist (2009) 173, E121-E138.
    abstract | pdf

  • Spatial Structure and Nutrients Promote Invasion of IncP-1 Plasmids in Bacterial Populations
    (with R. Fox, X. Zhong, and E.M. Top). The ISME Journal: Multidisciplinary Journal of Microbial Ecology (2008) 2, 1024-1039.
    abstract | pdf

  • Modeling Phage Plaque Growth
    (with S.T. Abedon). (2008) In Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial Viruses, Cambridge University Press, Abedon, S.T. (ed).

  • Modeling the Spatial Dynamics of Plasmid Transfer and Persistence
    (with R. Lu, R. Fox, H. Suzuki, and E.M. Top). Microbiology (2007) 153, 2803-2816.
    abstract | pdf

  • Analyzing Animal Movements Using Brownian Bridges
    (with J. Horne, E.O. Garton, and J.S. Lewis). Ecology (2007) 88, 2354-2363.
    abstract | pdf | Appendix

  • Spatial Self-Organization in a Cyclic Resource-Species Model
    (with Y. Guan). Journal of Theoretical Biology (2006) 241, 14-25.
    abstract | pdf

  • Spatial Invasion by a Mutant Pathogen
    (with W. Wei). Journal of Theoretical Biology (2005) 236, 335-348.
    abstract | pdf

  • WinSSS: Stochastic Spatial Simulator
    (with Y. Guan) Bulletin of Ecological Society of America (2004) 85, Number 3, 102-104.

  • Spatial Models: Stochastic and Deterministic
    Mathematical and Computer Modelling (2004) 40, 393-409.
    abstract | pdf

  • A Spatial Model of Range-Dependent Succession
    (with C. Neuhauser). Journal of Applied Probability (2000) 37, 1044-1060.

  • The Two-Stage Contact Process
    Annals of Applied Probability (1999) 9, 331-351.

  • Stepping Stone Models with Extinction and Recolonization
    (with H. Kang and C. Neuhauser). Annals of Applied Probability (1995) 5, 1025-1060.

  • A Note on the Stepping Stone Model with Extinction and Recolonization
    (with H. Kang and C. Neuhauser). (1994) In Progress in Population Genetics and Human Evolution. P. Donnelly and S. Tavare, eds. Springer, New York.

Nonspatial Evolution

  • Adaptive regulatory substitutions affect multiple stages in the life cycle of the bacteriophage phiX174
    (with C.J. Brown, A.D. Stancik, P. Roychoudhury) BMC Evolutionary Biology (2013) 13, 66. abstract | pdf

Theoretical Population Genetics

1. Coalescent Theory

  • On the Meaning and Existence of an Effective Population Size
    (with P. Sjödin, I. Kaj, M. Lascoux, M. Nordborg). Genetics (2005) 169, 1061-1070.
    abstract | pdf

  • The Coalescent Process in a Population with Stochastically Varying Size
    (with I. Kaj). Journal of Applied Probability (2003) 40, 33-48.
    abstract | pdf

  • Separation of Time Scales and Convergence to the Coalescent in Structured Populations
    (with M. Nordborg). (2002) In Modern Developments in Theoretical Population Genetics, pp. 194-232, M. Slatkin and M. Veuille, editors. Oxford University Press.
    abstract | pdf | ps

  • Coalescent Theory for Seed Bank Models
    (with I. Kaj and M. Lascoux). Journal of Applied Probability (2001) 38, 285-300.
    abstract | pdf | figure 1

  • Ancestral Processes with Selection
    (with C. Neuhauser). Theoretical Population Biology (1997) 51, 210-237.
    abstract | pdf

  • The Genealogy of Samples in Models with Selection
    (with C. Neuhauser). Genetics (1997) 145, 519-534.

2. Diffusion Processes

  • Evolution and the duration of a doomed population
    Gomulkiewicz R, Krone SM, Remien CH. Evolutionary Applications (2017) 1-14. DOI: 10.1111/eva.12467.
    abstract | pdf

  • When Can One Detect Overdominant Selection in the Infinite Alleles Model?
    (with P. Joyce and T.G. Kurtz). Annals of Applied Probability (2003) 13, 181-212.
    abstract | pdf | dvi

  • Gaussian Limits Associated with the Poisson-Dirichlet Distribution and the Ewens Sampling Formula
    (with P. Joyce and T.G. Kurtz). Annals of Applied Probability (2002) 12, 101-124.
    abstract | pdf

Markov Chain Monte Carlo

  • Small-World MCMC and Convergence to Multi-modal Distributions: From Slow Mixing to Fast Mixing
    (with Y. Guan). Annals of Applied Probability (2007) 17, 284-304.
    abstract | pdf

  • Markov Chain Monte Carlo in Small Worlds
    (with Y. Guan, R. Fleissner, P. Joyce). Statistics and Computing (2006) 16, 193-202.
    abstract | pdf

Random Networks

  • Application of Ecological Network Theory to the Human Microbiome
    (with J.A. Foster and L.J. Forney). Interdisciplinary Perspectives on Infectious Diseases (2008) Article ID 839501, 6 pages.
    abstract | pdf

  • On the Evolution of Structure in Ecological Networks
    (with M. Labrum, T. Soule, A. Blue). Proceedings of 5th International Conference on Complex Systems 2004.
    abstract | pdf | ps

Measure-Valued Diffusions

  • Representations for Continuous Additive Functionals of Super-Brownian and Super-Stable Processes
    Statistics and Probability Letters (1997) 34, 211-223.

  • Comparing Fleming-Viot and Dawson-Watanabe Processes
    (with S.N. Ethier). Stochastic Processes and their Applications (1995) 60, 171-190.

  • Conditioned Superprocesses and their Weighted Occupation Times
    Statistics and Probability Letters (1995) 22, 59-69.

  • Local Times for Superdiffusions
    Annals of Probability (1993) 21, 1599-1623.

For paper versions of the above, please email me (

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