1. Z. Chen and Juan A. Bonachela, Vegetation clump size and number as indicators for alternative stable states in semi-arid ecosystems, under review (2023).
  2.  
  3. B. Knowles*, Juan A. Bonachela*, et al., Altered growth and death in dilution-based viral predation assays, PLoS One 18, e0288114 (2023). (*Joint 1st authors)
  4.  
  5. G. Mukerjee, Juan A. Bonachela, M. A. Muñoz, and K. J. Wiese, Depinning in the quenched Kardar-Parisi-Zhang class I: Mappings, simulations and algorithm, Phys. Rev. E 107 , 054136 (2023).
  6.  
  7. Juan A. Bonachela, Viral plasticity facilitates host diversity in challenging environments, under review (2023).
  8.  
  9. R. Almeida, Juan A. Bonachela, and J. L. Lockwood, Multiple co-occurring bioeconomic drivers of overexploitation can accelerate rare species extinction risk, J. Appl. Ecol. 00 , 1 (2023). (Editor's Choice)
  10.  
  11. A. G. Garcia, W. Mesquita-Filho, C. A. H. Flechtmann, J. L. Lockwood, and Juan A. Bonachela, Alternative stable ecological states in a dung-beetle community arising from a human-caused biological invasion, Scientific Reports 12 , 20830 (2022).
  12.  
  13. R. Martinez-Garcia, C. Cabal, Juan A. Bonachela, J. M. Calabrese, E. Hernandez-Garcia, C. Lopez, C. E. Tarnita, Integrating theory and experiments to link local mechanisms and ecosystem-level consequences of vegetation patterns in drylands, Chaos, Solitons, and Fractals 166 , 112881 (2022).
  14.  
  15. H. Locke, K. D. Bidle, K. Thamatrakoln, C. Johns, Juan A. Bonachela, B. Ferrell, and K. E. Wommack, Virioplankton, the carbon cycle, and our future ocean, Advances in Virus Research 114 , 67-146 (2022).
  16.  
  17. R. Martinez-Garcia, C. E. Tarnita, and Juan A. Bonachela, Spatial patterns in ecological systems: from microbial colonies to landscapes, Emerging Topics in Life Sciences, ETLS20210282 (2022).
  18.  
  19. Juan A. Bonachela, M. Choua, and M. R. Heath, Unconstrained coevolution of bacterial size and the latent period of plastic phage, PLoS ONE 17 , e0268596 (2022).
  20.  
  21. J. Castillo-Vardaro*, Juan A. Bonachela*, C. C. M. Baker, M. L. Pinsky, D. F. Doak, R. Pringle, and C. Tarnita, The role of resource availability and heterogeneity on Odontotermes termite mound spatial distribution, Ecol. Lett. 24 , 1880 (2021). (*Joint 1st authors)
  22.  
  23. M. Choua, M. R. Heath, and Juan A. Bonachela, Evolutionarily stable coevolution between a plastic lytic virus and its microbial host, Front. Microbiol. 12 , 637490 (2021).
  24.  
  25. Juan A. Bonachela, M. Burrows, and M. Pinsky, Rate of community response to climate change depends on species traits and community composition, Ecol. Lett. 24 , 708 (2021).
  26.  
  27. V. Buendia, S. di Santo, Juan A. Bonachela, and M. A. Muñoz, Feedback mechanisms for self-organization to the edge of a phase transition: a review, Frontiers in Physics (Interdisciplinary Physics) 8 , 333 (2020).
  28.  
  29. B. Knowles, Juan A. Bonachela, et al., Temperate infection in a canonically virulent host-virus system, Nature Communications Nature Communications 11, 4626 (2020).
  30.  
  31. J. Pourtois, C. Tarnita, and Juan A. Bonachela, Impact of lytic phages on phosphorus- versus nitrogen-limited marine microbes, Frontiers in Microbiology, Frontiers in Microbiology 11, 221 (2020). (Editor's Choice)
  32.  
  33. P. Villegas, M. A. Muñoz, and Juan A. Bonachela, Evolution in the Debian GNU/Linux software network: analogies and differences with gene regulatory networks, J. Roy. Soc. Interface 17, 20190845 (2020).
  34.  
  35. M. Choua, M. R. Heath, D. C. Speirs, and Juan A. Bonachela, The effect of viral plasticity on the persistence of host-virus systems, J. Theor. Biol. 498, 110263 (2020).
  36.  
  37. M.T. Wortel, H. Peters, Juan A. Bonachela, and N.Chr. Stenseth, Coupled fast and slow feedbacks lead to continual evolution: a general modeling appoach, PNAS 117, 4234 (2020).
  38.  
  39. Juan A. Bonachela, Book review: ``Natural Complexity'', by Paul Charbonneau, The Quarterly Review of Biology 94, 289 (2019).
  40.  
  41. C. Caceres, S. Spatharis, E. Kaiserli, E. Smeti, H. Flowers, and Juan A. Bonachela, Temporal phosphate gradients reveal diverse acclimation responses in phytoplankton phosphate uptake, ISME J. 13, 2834 (2019).
  42.  
  43. S. M. Vallina, R. Martinez-Garcia, S. L. Smith, Juan A. Bonachela, Models in Microbial Ecology, in ``Encyclopedia of Microbiology, 4th Edition'' Elsevier, USA (2019).
  44.  
  45. M. Choua and Juan A. Bonachela, Ecological and evolutionary consequences of viral plasticity, The American Naturalist 193, 346 (2019).
  46.  
  47. R. Martínez-García, C.D. Nadell, R. Hartmann, K. Drescher, and Juan A. Bonachela, Cell adhesion and fluid flow jointly initiate biofilm genetic structure, PLoS Comp. Biol. 14, e1006094 (2018).
  48.  
  49. Juan A. Bonachela, M.T. Wortel, and N.Chr. Stenseth, Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system, Sci. Rep. 7, 17655 (2017).
  50.  
  51. C.E. Tarnita*, Juan A. Bonachela*, E. Sheffer, J.A. Guyton, T.C. Coverdale, R.A. Long, and R.M. Pringle, A theoretical foundation for multi-scale regular vegetation patterns, Nature 541, 398 (2017). (*Joint 1st authors) (Cover article)
  52.  
  53. N.S. Garcia, Juan A. Bonachela, and A.C. Martiny, Interactions between growth-dependent cell size, nutrient supply and cellular elemental stoichiometry of marine Synechococcus, ISME J. 10, 2715-2724 (2016).
  54.  
  55. Juan A. Bonachela, C.A. Klausmeier, K.F. Edwards, E. Litchman, and S.A. Levin, The role of phytoplankton diversity in the emergent oceanic stoichiometry, J. Plankton Res. 38, 1021-1035 (2016).
  56.  
  57. P. Villa, Juan A. Bonachela, S.A. Levin, and M.A. Muñoz, Eluding catastrophic shifts, PNAS Plus 112, E1828 (2015).
  58.  
  59. Juan A. Bonachela, R.M. Pringle, E. Sheffer, T.C. Coverdale, J.A. Guyton, K.K. Caylor, S.A. Levin, and C.E. Tarnita, Termite mounds can increase the robustness of dryland ecosystems to climatic change, Science 345, 651 (2015). (Cover article)
  60.  
  61. C. Mouginot, A.E. Zimmerman, Juan A. Bonachela, H. Fredricks, S.D. Allison, B.A.S. Van Mooy, and A.C. Martiny, Resource allocation by the marine cyanobacterium Synechococcus WH8102 in response to different nutrient supply ratios, Limnol.Oceanogr. 60, 1634-1641 (2015).
  62.  
  63. M.W. Lomas, Juan A. Bonachela, S.A. Levin, and A.C. Martiny, Impact of ocean phytoplankton diversity on phosphate uptake, PNAS 111, 17540 (2014).
  64.  
  65. A.F.A. Pellegrini, J.R. Watson, C.Torney, L. McManus, Juan A. Bonachela, C. Chang, and A.P. Dobson, Poaching and climate change: Interacting stochastic drivers of elephant population dynamics across Africa, under review (2018).
  66.  
  67. Juan A. Bonachela and S.A. Levin, Evolutionary Comparison Between Viral Lysis Rate and Latent Period, J.Theor.Biol. 345, 32 (2014).
  68.  
  69. P. Villa, Juan A. Bonachela and M.A. Muñoz, Quenched disorder forbids discontinuous transitions in non-equilibrium low-dimensional systems, Phys. Rev. E 89, 012145 (2014).
  70.  
  71. Juan A. Bonachela, S.D. Allison, A.C. Martiny, and S.A. Levin, A model for variable phytoplankton stoichiometry based on cell protein regulation, Biogeosciences 10, 4341 (2013).
  72.  
  73. S.A. Levin, Juan A. Bonachela, and C.D. Nadell, Mathematical and Computational Challenges in the Study of Complex Adaptive Microbial Systems, ``The Social Biology of Microbial Communities'' Institute of Medicine of the National Academies Workshop Summary Report, National Academies Press, USA (2012).
  74.  
  75. Juan A. Bonachela, M.A. Muñoz, and S.A. Levin, Patchiness and Demographic Noise in Three Ecological Examples, J.Stat.Phys. 148, 723 (2012).
  76.  
  77. Juan A. Bonachela, M. Raghib, and S.A. Levin, Acclimation or Starvation: Dynamic Model of Flexible Phytoplankton Nutrient Uptake, PNAS 108, 20633 (2011).
  78.  
  79. M.A. Fortuna, Juan A. Bonachela, and S.A. Levin, Evolution of a Modular Software Network, PNAS 108, 19985 (2011).
  80.  
  81. F. Vázquez, Juan A. Bonachela, C. López, and M.A. Muñoz, Temporal Griffiths Phases, Phys. Rev. Lett. 106, 235702 (2011).
  82.  
  83. Juan A. Bonachela, C.D. Nadell, J.B. Xavier, S.A. Levin, Universality in Bacterial Colonies, J. Stat. Phys. 144, 303 (2011).
  84.  
  85. Juan A. Bonachela, S. de Franciscis, J.J. Torres, and M.A. Muñoz, Self-Organization Without Conservation: Are Neuronal Avalanches Generically Critical?, J. Stat. Mech. P02015 (2010).
  86.  
  87. Juan A. Bonachela and M.A. Muñoz, Self-Organization Without Conservation: True or Just Apparent Scale-Invariance?, J. Stat. Mech. P09009 (2009).
  88.  
  89. A.C. Barato, C.E. Fiore, Juan A. Bonachela, H. Hinrichsen, and M. A. Muñoz, The Simplest Nonequilibrium Phase Transition into an Absorbing State, Phys. Rev. E 79, 041130 (2009).
  90.  
  91. Juan A. Bonachela and M.A. Muñoz, Boundary-Induced Heterogeneous Absorbing States, in Modeling and Simulation of New Materials: Tenth Granada Lectures, Eds. P. L. Garrido, J. Marro and P. I. Hurtado, American Institute of Physics Conference Proceedings 1091, 204 (2009).
  92.  
  93. Juan A. Bonachela, M. Alava, and M.A. Muñoz, Cusps, Self-Organization, and Absorbing States, Phys. Rev. E 79, R050106 (2009).
  94.  
  95. Juan A. Bonachela and M.A. Muñoz, Confirming and Extending the Hypothesis of Universality in Sandpiles, Phys. Rev. E 78, 041102 (2008).
  96.  
  97. Juan A. Bonachela, H. Hinrichsen, and M.A. Muñoz, Entropy Estimates of Small Data Sets, J. Phys. A 41, 202001 (2008).
  98.  
  99. Juan A. Bonachela and M.A. Muñoz, How to discriminate easily between directed-percolation and Manna scaling , Physica A 384 89 (2007).
  100.  
  101. Juan A. Bonachela, H. Chaté, I. Dornic, and M.A. Muñoz, Absorbing States and Elastic Interfaces in Random Media: Two Equivalent Descriptions of Self-Organized Criticality, Phys. Rev. Lett. 98, 155702 (2007).
  102.  
  103. O. Al Hammal, Juan A. Bonachela, and M.A. Muñoz, Absorbing State Phase Transitions with a Non-Accessible Vacuum, J. Stat. Mech. P12007 (2006).
  104.  
  105. Juan A. Bonachela, J. J. Ramasco, H. Chaté, I. Dornic, and M.A. Muñoz, Sticky Grains do not Change the Universality Class of Isotropic Sandpiles, Phys. Rev. E 74, 050102(R) (2006).
  106.