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Items: 32

1.

Coalescence modeling of intrainfection Bacillus anthracis populations allows estimation of infection parameters in wild populations.

Easterday WR, Ponciano JM, Gomez JP, Van Ert MN, Hadfield T, Bagamian K, Blackburn JK, Stenseth NC, Turner WC.

Proc Natl Acad Sci U S A. 2020 Feb 25;117(8):4273-4280. doi: 10.1073/pnas.1920790117. Epub 2020 Feb 13.

2.

Modeling R₀ for Pathogens with Environmental Transmission: Animal Movements, Pathogen Populations, and Local Infectious Zones.

Blackburn JK, Ganz HH, Ponciano JM, Turner WC, Ryan SJ, Kamath P, Cizauskas C, Kausrud K, Holt RD, Stenseth NC, Getz WM.

Int J Environ Res Public Health. 2019 Mar 17;16(6). pii: E954. doi: 10.3390/ijerph16060954. Review.

3.

Decoupling environmental effects and host population dynamics for anthrax, a classic reservoir-driven disease.

Gomez JP, Nekorchuk DM, Mao L, Ryan SJ, Ponciano JM, Blackburn JK.

PLoS One. 2018 Dec 12;13(12):e0208621. doi: 10.1371/journal.pone.0208621. eCollection 2018.

4.

An efficient extension of N-mixture models for multi-species abundance estimation.

Gomez JP, Robinson SK, Blackburn JK, Ponciano JM.

Methods Ecol Evol. 2018 Feb;9(2):340-353. doi: 10.1111/2041-210X.12856. Epub 2017 Jul 24.

5.

chromploid: An R package for chromosome number evolution across the plant tree of life.

Zenil-Ferguson R, Burleigh JG, Ponciano JM.

Appl Plant Sci. 2018 Apr 11;6(3):e1037. doi: 10.1002/aps3.1037. eCollection 2018 Mar.

6.

Ecological change points: The strength of density dependence and the loss of history.

Ponciano JM, Taper ML, Dennis B.

Theor Popul Biol. 2018 May;121:45-59. doi: 10.1016/j.tpb.2018.04.002. Epub 2018 Apr 26.

7.
8.

Compensatory mutations improve general permissiveness to antibiotic resistance plasmids.

Loftie-Eaton W, Bashford K, Quinn H, Dong K, Millstein J, Hunter S, Thomason MK, Merrikh H, Ponciano JM, Top EM.

Nat Ecol Evol. 2017 Sep;1(9):1354-1363. doi: 10.1038/s41559-017-0243-2. Epub 2017 Aug 7.

9.

Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots.

Zenil-Ferguson R, Ponciano JM, Burleigh JG.

Evolution. 2017 May;71(5):1138-1148. doi: 10.1111/evo.13226. Epub 2017 Mar 29.

PMID:
28295270
10.

Context-dependent landscape of fear: algal density elicits risky herbivory in a coral reef.

Gil MA, Zill J, Ponciano JM.

Ecology. 2017 Feb;98(2):534-544. doi: 10.1002/ecy.1668. Epub 2017 Jan 12.

PMID:
27870010
11.

Mutation Is a Sufficient and Robust Predictor of Genetic Variation for Mitotic Spindle Traits in Caenorhabditis elegans.

Farhadifar R, Ponciano JM, Andersen EC, Needleman DJ, Baer CF.

Genetics. 2016 Aug;203(4):1859-70. doi: 10.1534/genetics.115.185736. Epub 2016 Jun 22.

12.

Evaluating the role of genome downsizing and size thresholds from genome size distributions in angiosperms.

Zenil-Ferguson R, Ponciano JM, Burleigh JG.

Am J Bot. 2016 Jul;103(7):1175-86. doi: 10.3732/ajb.1500408. Epub 2016 May 10.

13.

An updated perspective on the role of environmental autocorrelation in animal populations.

Ferguson JM, Carvalho F, Murillo-García O, Taper ML, Ponciano JM.

Theor Ecol. 2016 Jun;9(2):129-148. Epub 2015 Aug 30.

14.

Functional Traits, Flocking Propensity, and Perceived Predation Risk in an Amazonian Understory Bird Community.

Martínez AE, Gomez JP, Ponciano JM, Robinson SK.

Am Nat. 2016 May;187(5):607-19. doi: 10.1086/685894. Epub 2016 Mar 29.

PMID:
27104993
15.

Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance.

Loftie-Eaton W, Yano H, Burleigh S, Simmons RS, Hughes JM, Rogers LM, Hunter SS, Settles ML, Forney LJ, Ponciano JM, Top EM.

Mol Biol Evol. 2016 Apr;33(4):885-97. doi: 10.1093/molbev/msv339. Epub 2015 Dec 14.

16.

Evidence and implications of higher-order scaling in the environmental variation of animal population growth.

Ferguson JM, Ponciano JM.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2782-7. doi: 10.1073/pnas.1416538112. Epub 2015 Feb 17.

17.

The red death meets the abdominal bristle: polygenic mutation for susceptibility to a bacterial pathogen in Caenorhabditis elegans.

Etienne V, Andersen EC, Ponciano JM, Blanton D, Cadavid A, Joyner-Matos J, Matsuba C, Tabman B, Baer CF.

Evolution. 2015 Feb;69(2):508-19. doi: 10.1111/evo.12585. Epub 2015 Jan 19.

18.
19.

Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series.

Ferguson JM, Ponciano JM.

Ecol Lett. 2014 Feb;17(2):251-9. doi: 10.1111/ele.12227. Epub 2013 Dec 5. Erratum in: Ecol Lett. 2014 Jun;17(6):769.

20.

The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics.

Tyerman JG, Ponciano JM, Joyce P, Forney LJ, Harmon LJ.

BMC Evol Biol. 2013 Jan 28;13:22. doi: 10.1186/1471-2148-13-22.

21.

Inherent variation in stable isotope values and discrimination factors in two life stages of green turtles.

Vander Zanden HB, Bjorndal KA, Mustin W, Ponciano JM, Bolten AB.

Physiol Biochem Zool. 2012 Sep-Oct;85(5):431-41. doi: 10.1086/666902. Epub 2012 Aug 3.

PMID:
22902371
22.

Assessing parameter identifiability in phylogenetic models using data cloning.

Ponciano JM, Burleigh JG, Braun EL, Taper ML.

Syst Biol. 2012 Dec 1;61(6):955-72. doi: 10.1093/sysbio/sys055. Epub 2012 May 30.

23.

First principles modeling of nonlinear incidence rates in seasonal epidemics.

Ponciano JM, Capistrán MA.

PLoS Comput Biol. 2011 Feb;7(2):e1001079. doi: 10.1371/journal.pcbi.1001079. Epub 2011 Feb 17.

24.

Replicated sampling increases efficiency in monitoring biological populations.

Dennis B, Ponciano JM, Taper ML.

Ecology. 2010 Feb;91(2):610-20.

PMID:
20392025
25.

Evolution of diversity in spatially structured Escherichia coli populations.

Ponciano JM, La HJ, Joyce P, Forney LJ.

Appl Environ Microbiol. 2009 Oct;75(19):6047-54. doi: 10.1128/AEM.00063-09. Epub 2009 Jul 31.

26.

Hierarchical models in ecology: confidence intervals, hypothesis testing, and model selection using data cloning.

Ponciano JM, Taper ML, Dennis B, Lele SR.

Ecology. 2009 Feb;90(2):356-62.

PMID:
19323219
27.

Adaptive plasmid evolution results in host-range expansion of a broad-host-range plasmid.

De Gelder L, Williams JJ, Ponciano JM, Sota M, Top EM.

Genetics. 2008 Apr;178(4):2179-90. doi: 10.1534/genetics.107.084475.

28.

Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship.

De Gelder L, Ponciano JM, Joyce P, Top EM.

Microbiology. 2007 Feb;153(Pt 2):452-463. doi: 10.1099/mic.0.2006/001784-0.

PMID:
17259616
29.

The population biology of bacterial plasmids: a hidden Markov model approach.

Ponciano JM, De Gelder L, Top EM, Joyce P.

Genetics. 2007 Jun;176(2):957-68. Epub 2006 Dec 6.

30.

Use of stochastic models to assess the effect of environmental factors on microbial growth.

Ponciano JM, Vandecasteele FP, Hess TF, Forney LJ, Crawford RL, Joyce P.

Appl Environ Microbiol. 2005 May;71(5):2355-64.

31.

Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution.

Joyce P, Abdo Z, Ponciano JM, De Gelder L, Forney LJ, Top EM.

J Math Biol. 2005 Jun;50(6):645-62. Epub 2004 Dec 20.

PMID:
15614551

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