@article{21985,
  abstract     = {Upon infecting a bacterial cell, temperate phages make a decision between lysis and lysogeny. While research has previously explored how phages sense environmental information to make this choice, most studies have focused on modelling known mechanisms that impact the decision. These mechanisms tell us what environmental information the phage does respond to, but not what it should respond to, as the signals sensed by the phage may serve as proxies for other sources of information. Here, using a mechanism-agnostic population dynamics model, we find that irreversible phage binding to lysogens protects sensitive host cells from infection. This results in lysogens being an additional environmental factor that the phage should sense while making its decision to undergo lysis or lysogeny. Using this model, we derive a responsive lysogeny probability for phages that respond to both cell and lysogen densities optimized towards invading phage-occupied systems, and show that it is more capable of invading and resisting invasion than phage with fixed lysogeny probabilities across different environmental conditions.},
  author       = {Wu, Bryan and Guet, Calin C},
  issn         = {1558-5646},
  journal      = {Evolution},
  number       = {6},
  pages        = {1365--1373},
  publisher    = {Oxford University Press},
  title        = {{Responsive lysogeny under nonproductive phage binding}},
  doi          = {10.1093/evolut/qpag061},
  volume       = {80},
  year         = {2026},
}

@phdthesis{20470,
  abstract     = {Systems design has classically relied on composable systems, in which individual subsystems
have defined inputs, outputs, and interactions with each other; however, attempts at
designing complex systems in synthetic biology has often run in to issues of crosstalk and
interference, given that these systems must function within the context of the host. In nature,
mobile genetic elements are systems that have evolved to travel between hosts, and thus
appear to be a good candidate with which to evaluate composability. Selecting temperate
phages as a model system, I used mathematical modelling to identify sources of information
that temperate phages should respond to. I found that essential proteins of temperate phages
can interfere with potential hosts, indicating limitations to composability. I also designed a
lysogeny reporter construct and characterize its behavior across various laboratory and
environmental strains, finding differences in phage lambda lysogens, and potential
interference from prophages that already exist within the environmental strains. Although
the information gathered is not conclusive, it suggests that composability is not a key property
of temperate phages, implying that biological systems may not be composable, and that other
system design principles should be considered when designing synthetic systems.},
  author       = {Wu, Bryan},
  issn         = {2663-337X},
  pages        = {102},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{An examination on phages as a naturally composable system}},
  doi          = {10.15479/AT-ISTA-20470},
  year         = {2025},
}