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Jose Miguel Ponciano, Ph.D. - Publications

Affiliations: 
Biology University of Florida, Gainesville, Gainesville, FL, United States 
Area:
Statistical and theoretical ecology
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37 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Ponciano JM, Gómez JP, Ravel J, Forney LJ. Inferring stability and persistence in the vaginal microbiome: A stochastic model of ecological dynamics. Biorxiv : the Preprint Server For Biology. PMID 38464272 DOI: 10.1101/2024.03.02.581600  0.367
2022 Taper ML, Ponciano JM, Dennis B. Entropy, Statistical Evidence, and Scientific Inference: Evidence Functions in Theory and Applications. Entropy (Basel, Switzerland). 24. PMID 36141159 DOI: 10.3390/e24091273  0.757
2020 Easterday WR, Ponciano JM, Gomez JP, Van Ert MN, Hadfield T, Bagamian K, Blackburn JK, Stenseth NC, Turner WC. Coalescence modeling of intrainfection populations allows estimation of infection parameters in wild populations. Proceedings of the National Academy of Sciences of the United States of America. PMID 32054783 DOI: 10.1073/Pnas.1920790117  0.37
2019 Dennis B, Ponciano JM, Taper ML, Lele SR. Errors in Statistical Inference Under Model Misspecification: Evidence, Hypothesis Testing, and AIC. Frontiers in Ecology and Evolution. 7. PMID 34295904 DOI: 10.3389/fevo.2019.00372  0.781
2019 Ponciano JM, Taper ML. Model Projections in Model Space: A Geometric Interpretation of the AIC Allows Estimating the Distance Between Truth and Approximating Models. Frontiers in Ecology and Evolution. 7. PMID 33796541 DOI: 10.3389/fevo.2019.00413  0.749
2019 Ponciano JM, Taper ML. Model Projections in Model Space: A Geometric Interpretation of the AIC Allows Estimating the Distance Between Truth and Approximating Models Frontiers in Ecology and Evolution. 7. DOI: 10.3389/Fevo.2019.00413  0.76
2019 Dennis B, Ponciano JM, Taper ML, Lele SR. Errors in Statistical Inference Under Model Misspecification: Evidence, Hypothesis Testing, and AIC Frontiers in Ecology and Evolution. 7. DOI: 10.3389/Fevo.2019.00372  0.787
2018 Gomez JP, Nekorchuk DM, Mao L, Ryan SJ, Ponciano JM, Blackburn JK. Decoupling environmental effects and host population dynamics for anthrax, a classic reservoir-driven disease. Plos One. 13: e0208621. PMID 30540815 DOI: 10.1371/Journal.Pone.0208621  0.346
2018 Gomez JP, Robinson SK, Blackburn JK, Ponciano JM. An efficient extension of N-mixture models for multi-species abundance estimation. Methods in Ecology and Evolution. 9: 340-353. PMID 29892335 DOI: 10.1111/2041-210X.12856  0.396
2018 Zenil-Ferguson R, Burleigh JG, Ponciano JM. chromploid: An R package for chromosome number evolution across the plant tree of life. Applications in Plant Sciences. 6: e1037. PMID 29732267 DOI: 10.1002/Aps3.1037  0.739
2018 Ponciano JM, Taper ML, Dennis B. Ecological change points: The strength of density dependence and the loss of history. Theoretical Population Biology. PMID 29705062 DOI: 10.1016/J.Tpb.2018.04.002  0.778
2017 Ponciano JM. A parametric interpretation of Bayesian Nonparametric Inference from Gene Genealogies: Linking ecological, population genetics and evolutionary processes. Theoretical Population Biology. 122: 128-136. PMID 29174634 DOI: 10.1016/J.Tpb.2017.10.007  0.47
2017 Zenil-Ferguson R, Ponciano JM, Burleigh JG. Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots. Evolution; International Journal of Organic Evolution. PMID 28295270 DOI: 10.1111/Evo.13226  0.754
2016 Gil MA, Zill J, Ponciano JM. Context-dependent landscape of fear: algal density elicits risky herbivory in a coral reef. Ecology. PMID 27870010 DOI: 10.1002/Ecy.1668  0.313
2016 Zenil-Ferguson R, Ponciano JM, Burleigh JG. Evaluating the role of genome downsizing and size thresholds from genome size distributions in angiosperms. American Journal of Botany. PMID 27206462 DOI: 10.3732/Ajb.1500408  0.723
2016 Ferguson JM, Carvalho F, Murillo-García O, Taper ML, Ponciano JM. An updated perspective on the role of environmental autocorrelation in animal populations. Theoretical Ecology. 9: 129-148. PMID 27158281 DOI: 10.1007/S12080-015-0276-6  0.783
2016 Martínez AE, Gomez JP, Ponciano JM, Robinson SK. Functional Traits, Flocking Propensity, and Perceived Predation Risk in an Amazonian Understory Bird Community. The American Naturalist. 187: 607-19. PMID 27104993 DOI: 10.1086/685894  0.304
2016 Taper ML, Ponciano JM. Evidential statistics as a statistical modern synthesis to support 21st century science Population Ecology. 58: 9-29. DOI: 10.1007/S10144-015-0533-Y  0.755
2015 Ferguson JM, Ponciano JM. Evidence and implications of higher-order scaling in the environmental variation of animal population growth. Proceedings of the National Academy of Sciences of the United States of America. 112: 2782-7. PMID 25730852 DOI: 10.1073/Pnas.1416538112  0.728
2015 Ferguson JM, Carvalho F, Murillo-García O, Taper ML, Ponciano JM. An updated perspective on the role of environmental autocorrelation in animal populations Theoretical Ecology. DOI: 10.1007/s12080-015-0276-6  0.748
2014 Dennis B, Ponciano JM. Density-dependent state-space model for population-abundance data with unequal time intervals. Ecology. 95: 2069-76. PMID 25230459 DOI: 10.1890/13-1486.1  0.667
2014 Ferguson JM, Ponciano JM. Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series. Ecology Letters. 17: 251-9. PMID 24304946 DOI: 10.1111/Ele.12227  0.712
2014 Ferguson JM, Ponciano JM. Corrigendum to Ferguson and Ponciano (2014) [Ecology Letters (2014) 17 769-769] Ecology Letters. 17: 769-769. DOI: 10.1111/Ele.12283  0.658
2014 Carvalho F, Ahrens R, Murie D, Ponciano JM, Aires-da-Silva A, Maunder MN, Hazin F. Incorporating specific change points in catchability in fisheries stock assessment models: An alternative approach applied to the blue shark (Prionace glauca) stock in the south Atlantic Ocean Fisheries Research. 154: 135-146. DOI: 10.1016/J.Fishres.2014.01.022  0.397
2013 Tyerman JG, Ponciano JM, Joyce P, Forney LJ, Harmon LJ. The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics. Bmc Evolutionary Biology. 13: 22. PMID 23356665 DOI: 10.1186/1471-2148-13-22  0.543
2013 Barbour AB, Ponciano JM, Lorenzen K. Apparent survival estimation from continuous mark-recapture/resighting data Methods in Ecology and Evolution. 4: 846-853. DOI: 10.1111/2041-210X.12059  0.436
2012 Vander Zanden HB, Bjorndal KA, Mustin W, Ponciano JM, Bolten AB. Inherent variation in stable isotope values and discrimination factors in two life stages of green turtles. Physiological and Biochemical Zoology : Pbz. 85: 431-41. PMID 22902371 DOI: 10.1086/666902  0.308
2012 Ponciano JM, Burleigh JG, Braun EL, Taper ML. Assessing parameter identifiability in phylogenetic models using data cloning. Systematic Biology. 61: 955-72. PMID 22649181 DOI: 10.1093/Sysbio/Sys055  0.778
2011 Ponciano JM, Capistrán MA. First principles modeling of nonlinear incidence rates in seasonal epidemics. Plos Computational Biology. 7: e1001079. PMID 21379320 DOI: 10.1371/Journal.Pcbi.1001079  0.405
2010 Dennis B, Ponciano JM, Taper ML. Replicated sampling increases efficiency in monitoring biological populations. Ecology. 91: 610-20. PMID 20392025 DOI: 10.1890/08-1095.1  0.784
2009 Ponciano JM, La HJ, Joyce P, Forney LJ. Evolution of diversity in spatially structured Escherichia coli populations. Applied and Environmental Microbiology. 75: 6047-54. PMID 19648364 DOI: 10.1128/Aem.00063-09  0.35
2009 Ponciano JM, Taper ML, Dennis B, Lele SR. Hierarchical models in ecology: confidence intervals, hypothesis testing, and model selection using data cloning. Ecology. 90: 356-62. PMID 19323219 DOI: 10.1890/08-0967.1  0.8
2007 Ponciano JM, De Gelder L, Top EM, Joyce P. The population biology of bacterial plasmids: a hidden Markov model approach. Genetics. 176: 957-68. PMID 17151258 DOI: 10.1534/Genetics.106.061937  0.468
2006 Dennis B, Ponciano JM, Lele SR, Taper ML, Staples DF. Estimating density dependence, process noise, and observation error Ecological Monographs. 76: 323-341. DOI: 10.1890/0012-9615(2006)76[323:Eddpna]2.0.Co;2  0.783
2005 Ponciano JM, Vandecasteele FP, Hess TF, Forney LJ, Crawford RL, Joyce P. Use of stochastic models to assess the effect of environmental factors on microbial growth. Applied and Environmental Microbiology. 71: 2355-64. PMID 15870322 DOI: 10.1128/Aem.71.5.2355-2364.2005  0.416
2005 Joyce P, Abdo Z, Ponciano JM, De Gelder L, Forney LJ, Top EM. Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution. Journal of Mathematical Biology. 50: 645-62. PMID 15614551 DOI: 10.1007/S00285-004-0300-8  0.371
2004 De Gelder L, Ponciano JM, Abdo Z, Joyce P, Forney LJ, Top EM. Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic-sensitive mutants in a population of resistant bacteria during experimental evolution. Genetics. 168: 1131-44. PMID 15579675 DOI: 10.1534/Genetics.104.033431  0.405
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