All Publications

2026

Chia, D., Youn, H., Singer, J., Jeong, D., Kempes, C., Ogbunugafor, C. B., ... & Holehouse, J. (2026). Three Centuries of the Laws of Cricket Reveal Core Principles of the Evolution of Regulatory Mechanisms. arXiv preprint arXiv:2607.05586. In press at PNAS.

Dzib, L. I. E., & Holehouse, J. (2026). How is gene-regulatory evolution affected by cell-to-cell variability? arXiv preprint arXiv:2604.26082. In revision at Evolution.

Holehouse, J. (2026). Do distinct subpopulations signify modes of behaviour in a noisy single cell? Proc. R. Soc. B; 293 (2070): 20260134.

Holehouse, J. (2026). Quantifying broken detailed balance in transcription. npj Complexity, 3(1), 10.

Holehouse, J., West, G. B., Kempes, C. P., & Swain, A. (2026). Microbial Ecosystems Reveal a Universal Signature of Ecological Assembly. bioRxiv, 2026-07. Under review at Ecology Letters.

Jeong*, D., Holehouse*, J., Yoon, J., Kempes, C. P., West, G. B., & Youn, H. (2026). A Dataset Showing a Century of Evolution in the Complexity of the United States Legal Code. Scientific data, 13(1), 13.

Kumar, A., & Holehouse, J. (2026). Branching under First-Passage Resetting. arXiv preprint arXiv:2605.16693. In revision at Physical Review Letters.

Öcal, K., Sukys, A., Kumar, A., & Holehouse, J. (2026). The Origins of Transient Bimodality. arXiv preprint arXiv:2607.16531. Under review at Journal of the Royal Society Interface.

Yang*, V. C., Holehouse*, J, Youn, H., Arroyo, J. I., Redner, S., West, G. B., & Kempes, C. P. (2026). Scaling laws for function diversity and specialization across socioeconomic and biological complex systems. Proceedings of the National Academy of Sciences, 123(7), e2509729123.

2025

Holehouse, J., Redner, S., Yang, V. C., Krapivsky, P. L., Arroyo, J. I., West, G. B., ... & Youn, H. (2025). A generative model of function growth explains hidden self-similarities across biological and social systems. arXiv preprint arXiv:2509.14468. Under review at Journal of the Royal Society Interface.

2024

Holehouse, J. (2024). Model reduction, mechanistic modelling and transience in models of stochastic chemical kinetics. European Communications in Mathematical and Theoretical Biology, 26, 6–14.

Holehouse, J., & Redner, S. (2024). First passage on disordered intervals. Physical Review E, 109(3), L032102.

Wu, B., Holehouse, J., Grima, R., & Jia, C. (2024). Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition. The Journal of Chemical Physics, 160(7). 

2023

Holehouse, J. (2023). Recurrence and Eigenfunction Methods for Non-Trivial Models of Discrete Binary Choice. Entropy, 25(7), 996.

Weidemann, D. E., Holehouse, J., Singh, A., Grima, R., & Hauf, S. (2023). The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. Science Advances, 9(32), eadh5138. 

2022

Holehouse, J., & Moran, J. (2022). Exact time-dependent dynamics of discrete binary choice models. Journal of Physics: Complexity, 3(3), 035005.

Holehouse, J., & Pollitt, H. (2022). Non-equilibrium time-dependent solution to discrete choice with social interactions. PLoS ONE, 17(5), e0267083.

2021

Braichenko*, S., Holehouse*, J., & Grima, R. (2021). Distinguishing between models of mammalian gene expression: telegraph-like models versus mechanistic models. Journal of the Royal Society Interface, 18(183), 20210510.

2020

Holehouse, J., Cao, Z., & Grima, R. (2020). Stochastic modeling of autoregulatory genetic feedback loops: A review and comparative study. Biophysical Journal, 118(7), 1517-1525.

Holehouse, J., Gupta, A., & Grima, R. (2020). Steady-state fluctuations of a genetic feedback loop with fluctuating rate parameters using the unified colored noise approximation. Journal of Physics A: Mathematical and Theoretical, 53(40), 405601.

Holehouse*, J., Sukys*, A., & Grima, R. (2020). Stochastic time-dependent enzyme kinetics: Closed-form solution and transient bimodality. The Journal of Chemical Physics, 153(16).

2019

Holehouse, J., & Grima, R. (2019). Revisiting the reduction of stochastic models of genetic feedback loops with fast promoter switching. Biophysical Journal, 117(7), 1311-1330.

2018

Holehouse, J., & Blythe, R. A. (2018). Cross-situational learning of large lexicons with finite memory. arXiv preprint arXiv:1809.11047.