publications

2026

1. arXiv

   Three Centuries of the Laws of Cricket Reveal Core Principles of the Evolution of Regulatory Mechanisms

   Daniel Chia, Hyejin Youn, Jonny Singer, and 5 more authors

   arXiv preprint arXiv:2607.05586, 2026

   Bib PDF

   @article{chia2026three,
     title = {Three Centuries of the Laws of Cricket Reveal Core Principles of the Evolution of Regulatory Mechanisms},
     author = {Chia, Daniel and Youn, Hyejin and Singer, Jonny and Jeong, Dawoon and Kempes, Chris and Ogbunugafor, C Brandon and West, Geoffrey B and Holehouse, James},
     journal = {arXiv preprint arXiv:2607.05586},
     year = {2026},
     summary = {Shows that the Laws of Cricket have grown as a power law in system size over 300 years -- direct evidence for the Lab's claim that regulatory systems, biological or social, grow according to shared quantitative laws.}
   }

2. arXiv

   Branching under First-Passage Resetting

   Aanjaneya Kumar and James Holehouse

   arXiv preprint arXiv:2605.16693, 2026

   Bib PDF

   @article{kumar2026branching,
     title = {Branching under First-Passage Resetting},
     author = {Kumar, Aanjaneya and Holehouse, James},
     journal = {arXiv preprint arXiv:2605.16693},
     year = {2026},
     summary = {Introduces a framework where replication events (e.g. cell division, viral lysis) are triggered by internal first-passage dynamics rather than an external clock, showing that stochastic timing fluctuations actually enhance population growth relative to a deterministic clock. The Lab is building on this same branching-process math to model rule-making as a response to rule-breaking.}
   }

3. arXiv

   The Origins of Transient Bimodality

   Kaan Öcal, Augustinas Sukys, Aanjaneya Kumar, and 1 more author

   arXiv preprint arXiv:2607.16531, 2026

   arXiv Bib PDF

   @article{ocal2026origins,
     title = {The Origins of Transient Bimodality},
     author = {{\"O}cal, Kaan and Sukys, Augustinas and Kumar, Aanjaneya and Holehouse, James},
     journal = {arXiv preprint arXiv:2607.16531},
     year = {2026},
     summary = {Identifies a phase transition into transient bimodal behavior driven purely by noise and time-dependent kinetics -- core evidence for the Lab's claim that biology is fundamentally transient rather than steady-state.}
   }

4. bioRxiv

   Microbial Ecosystems Reveal a Universal Signature of Ecological Assembly

   James Holehouse, Geoffrey B West, Christopher P Kempes, and 1 more author

   bioRxiv, 2026

   DOI Bib Website

   @article{holehouse2026microbial,
     title = {Microbial Ecosystems Reveal a Universal Signature of Ecological Assembly},
     author = {Holehouse, James and West, Geoffrey B and Kempes, Christopher P and Swain, Anshuman},
     journal = {bioRxiv},
     year = {2026},
     doi = {10.64898/2026.07.10.737833},
     summary = {Extends the Lab's generative model of functional diversity to microbial ecosystems, showing they occupy a distinct region of the same parameter space that also describes proteomes and cities.}
   }

5. npj Comp.

   Quantifying broken detailed balance in transcription

   James Holehouse

   npj Complexity, 2026

   arXiv Bib PDF

   @article{holehouse2026quantifying,
     title = {Quantifying broken detailed balance in transcription},
     author = {Holehouse, James},
     journal = {npj Complexity},
     volume = {3},
     number = {1},
     pages = {10},
     year = {2026},
     publisher = {Nature Publishing Group UK London},
     summary = {Derives exact formulas for the thermodynamic irreversibility (entropy production rate) of a two-state gene, and finds that most real genes avoid kinetic regimes with high energy dissipation despite this not being required by thermodynamics alone. Also shows that cell-to-cell variability can make gene expression look more or less irreversible than a single "representative cell" would suggest.}
   }

6. Proc. B

   Do distinct subpopulations signify modes of behaviour in a noisy single cell?

   James Holehouse

   Proceedings of the Royal Society B: Biological Sciences, 2026

   Bib PDF

   @article{holehouse2026distinct,
     title = {Do distinct subpopulations signify modes of behaviour in a noisy single cell?},
     author = {Holehouse, James},
     journal = {Proceedings of the Royal Society B: Biological Sciences},
     volume = {293},
     number = {2070},
     year = {2026},
     publisher = {The Royal Society},
     summary = {Argues that counting subpopulations in single-cell data can be a misleading proxy for the true number of behavioral modes available to a cell, and constructs counterexamples where two apparent subpopulations actually arise from non-equilibrium transient dynamics rather than distinct stable states.}
   }

7. arXiv

   How is gene-regulatory evolution affected by cell-to-cell variability?

   Leonardo Ivan Estrella Dzib and James Holehouse

   arXiv preprint arXiv:2604.26082, 2026

   Submitted

   PDF
8. Nat. Sci. Data

   A Dataset Showing a Century of Evolution in the Complexity of the United States Legal Code

   Dawoon Jeong^*, James Holehouse^*, Jisung Yoon, and 3 more authors

   Scientific Data, 2026

   arXiv Bib PDF

   @article{jeong2025century,
     title = {A Dataset Showing a Century of Evolution in the Complexity of the United States Legal Code},
     author = {Jeong, Dawoon and Holehouse, James and Yoon, Jisung and Kempes, Chris and West, Geoffrey B and Youn, Hyejin},
     journal = {Scientific Data},
     year = {2026},
     publisher = {Nature Publishing Group UK London},
     summary = {Provides the century-long U.S. Code dataset that anchors the Lab's claim that legal and biological regulatory systems both grow as power laws in system size.}
   }

9. PNAS

   Scaling laws for function diversity and specialization across socioeconomic and biological complex systems

   Vicky Chuqiao Yang^*, James Holehouse^*, Hyejin Youn, and 4 more authors

   Proceedings of the National Academy of Sciences, 2026

   arXiv Bib PDF

   @article{yang2026scaling,
     title = {Scaling laws for function diversity and specialization across socioeconomic and biological complex systems},
     author = {Yang, Vicky Chuqiao and Holehouse, James and Youn, Hyejin and Arroyo, Jos{\'e} Ignacio and Redner, Sidney and West, Geoffrey B and Kempes, Christopher P},
     journal = {Proceedings of the National Academy of Sciences},
     volume = {123},
     number = {7},
     pages = {e2509729123},
     year = {2026},
     publisher = {National Academy of Sciences},
     summary = {Establishes the Lab's central scaling-law result: that function diversity and specialization scale similarly across socioeconomic and biological complex systems.}
   }

2025

1. arXiv

   A generative model of function growth explains hidden self-similarities across biological and social systems

   James Holehouse, S. Redner, V.C. Yang, and 5 more authors

   2025

   arXiv preprint arXiv:2509.14468

   arXiv Bib PDF

   @article{holehouse2025generative,
     title = {A generative model of function growth explains hidden self-similarities across biological and social systems},
     author = {Holehouse, James and Redner, S. and Yang, V.C. and Krapivsky, P.L. and Arroyo, J.I. and West, Geoffrey B. and Kempes, Chris and Youn, Hyejin},
     note = {arXiv preprint arXiv:2509.14468},
     year = {2025},
     summary = {The Lab's core generative model of functional diversity, showing that proteomes, federal agencies, and city occupations diversify through the same underlying stochastic process.}
   }

2024

1. JCP

   Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition

   Bingjie Wu, James Holehouse, Ramon Grima, and 1 more author

   The Journal of Chemical Physics, 2024

   Bib PDF Website

   @article{wu2024solving,
     title = {Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition},
     author = {Wu, Bingjie and Holehouse, James and Grima, Ramon and Jia, Chen},
     journal = {The Journal of Chemical Physics},
     volume = {160},
     number = {7},
     year = {2024},
     publisher = {AIP Publishing},
     summary = {Derives an exact time-dependent solution for autoregulated bursty gene expression, showing the eigenfunctions are Heun functions and the eigenvalues follow from a continued-fraction equation -- a genuinely transient, non-steady-state result in the same vein as the Lab's later work on regulatory transience.}
   }

2. Phys. Rev. E

   First passage on disordered intervals

   James Holehouse and S Redner

   Physical Review E, 2024

   Bib PDF Website

   @article{holehouse2024first,
     title = {First passage on disordered intervals},
     author = {Holehouse, James and Redner, S},
     journal = {Physical Review E},
     volume = {109},
     number = {3},
     pages = {L032102},
     year = {2024},
     publisher = {APS},
     summary = {Derives exact first-passage statistics for a random walk on a finite interval with disordered hopping rates, finding that different realizations of the disorder produce wildly different first-passage times, including genuinely bimodal first-passage-time distributions.}
   }

3. ESMTB Comms.

   Model reduction, mechanistic modelling and transience in models of stochastic chemical kinetics

   James Holehouse

   European Communications in Mathematical and Theoretical Biology, 2024

   Bib PDF Website

   @article{holehouse2024summary,
     title = {{Model reduction, mechanistic modelling and transience in models of stochastic chemical kinetics}},
     author = {Holehouse, James},
     journal = {European Communications in Mathematical and Theoretical Biology},
     year = {2024},
     volume = {26},
     pages = {6-14},
     summary = {Summarizes the PhD thesis work that seeded the Lab's research program on transience and model reduction in stochastic gene expression.}
   }

2023

1. Sci. Advances

   The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian

   Douglas E Weidemann, James Holehouse, Abhyudai Singh, and 2 more authors

   Science Advances, 2023

   Bib PDF Website

   @article{weidemann2023minimal,
     title = {The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian},
     author = {Weidemann, Douglas E and Holehouse, James and Singh, Abhyudai and Grima, Ramon and Hauf, Silke},
     journal = {Science Advances},
     volume = {9},
     number = {32},
     pages = {eadh5138},
     year = {2023},
     publisher = {American Association for the Advancement of Science},
     summary = {Identifies fission-yeast genes whose expression noise falls genuinely below the previously assumed Poissonian floor, and shows this "sub-Poissonian" regime arises from a higher mRNA export rate suppressing cytoplasmic noise.}
   }

2. Entropy

   Recurrence and Eigenfunction Methods for Non-Trivial Models of Discrete Binary Choice

   James Holehouse

   Entropy, 2023

   Bib PDF Website

   @article{holehouse2023recurrence,
     title = {Recurrence and Eigenfunction Methods for Non-Trivial Models of Discrete Binary Choice},
     author = {Holehouse, James},
     journal = {Entropy},
     volume = {25},
     number = {7},
     pages = {996},
     year = {2023},
     publisher = {MDPI},
     summary = {Derives a closed-form solution to the three-term recurrence relation that governs relaxation dynamics in binary-choice models like Kirman's ant-recruitment model, using the power-series structure of Heun functions.}
   }

2022

1. J. Phys. Complexity

   Exact time-dependent dynamics of discrete binary choice models

   James Holehouse and José Moran

   Journal of Physics: Complexity, 2022

   Bib PDF Website

   @article{holehouse2022exact,
     title = {Exact time-dependent dynamics of discrete binary choice models},
     author = {Holehouse, James and Moran, Jos\'e},
     journal = {Journal of Physics: Complexity},
     year = {2022},
     summary = {Derives exact time-dependent solutions for discrete binary-choice models with agent interactions -- including Kirman and Föllmer's ant-recruitment model for any finite population -- showing convergence to equilibrium depends only on the random switching rate, not on imitation rate or population size.}
   }

2. PLoS One

   Non-equilibrium time-dependent solution to discrete choice with social interactions

   James Holehouse and Hector Pollitt

   PLoS ONE, 2022

   Bib PDF Website

   @article{holehouse2021nonequilibrium,
     title = {Non-equilibrium time-dependent solution to discrete choice with social interactions},
     author = {Holehouse, James and Pollitt, Hector},
     year = {2022},
     journal = {PLoS ONE},
     summary = {Solves Brock and Durlauf's binary-decision model away from equilibrium, revealing metastable effects and path-dependent behavior for highly rational agents, and extends the model to altruistic as well as selfish decision-makers.}
   }

2021

1. J. R. Soc. Interface

   Distinguishing between models of mammalian gene expression: telegraph-like models versus mechanistic models

   Svitlana Braichenko^*, James Holehouse^*, and Ramon Grima

   Journal of the Royal Society Interface, 2021

   Bib PDF Website

   @article{braichenko2021distinguishing,
     title = {Distinguishing between models of mammalian gene expression: telegraph-like models versus mechanistic models},
     author = {Braichenko, Svitlana and Holehouse, James and Grima, Ramon},
     journal = {Journal of the Royal Society Interface},
     year = {2021},
     publisher = {The Royal Society},
     summary = {Compares simplified telegraph-like models against a detailed mechanistic model of mammalian transcription, finding the two are practically indistinguishable from mRNA count distributions alone but can be told apart from their waiting-time distributions.}
   }

2020

1. Biophysical Journal

   Stochastic modeling of autoregulatory genetic feedback loops: A review and comparative study

   James Holehouse, Zhixing Cao, and Ramon Grima

   Biophysical journal, 2020

   Bib PDF Website

   @article{holehouse2020stochastic1,
     title = {Stochastic modeling of autoregulatory genetic feedback loops: A review and comparative study},
     author = {Holehouse, James and Cao, Zhixing and Grima, Ramon},
     journal = {Biophysical journal},
     volume = {118},
     number = {7},
     pages = {1517--1525},
     year = {2020},
     publisher = {Elsevier},
     summary = {A review comparing the major stochastic models of autoregulatory genetic feedback loops used in the literature, summarizing what is and isn't known about how they relate to one another.}
   }

2. J. Phys. A

   Steady-state fluctuations of a genetic feedback loop with fluctuating rate parameters using the unified colored noise approximation

   James Holehouse, Abhishek Gupta, and Ramon Grima

   Journal of Physics A: Mathematical and Theoretical, 2020

   Bib PDF Website

   @article{holehouse2020steady,
     title = {Steady-state fluctuations of a genetic feedback loop with fluctuating rate parameters using the unified colored noise approximation},
     author = {Holehouse, James and Gupta, Abhishek and Grima, Ramon},
     journal = {Journal of Physics A: Mathematical and Theoretical},
     volume = {53},
     number = {40},
     pages = {405601},
     year = {2020},
     publisher = {IOP Publishing},
     summary = {Uses the unified colored noise approximation to show how fluctuations in a gene circuit's own rate parameters reshape its protein distribution, and identifies when this approximation breaks down.}
   }

3. JCP

   Stochastic time-dependent enzyme kinetics: closed-form solution and transient bimodality

   James Holehouse, Augustinas Sukys, and Ramon Grima

   The Journal of Chemical Physics, 2020

   Bib PDF Website

   @article{holehouse2020stochastic2,
     title = {Stochastic time-dependent enzyme kinetics: closed-form solution and transient bimodality},
     author = {Holehouse, James and Sukys, Augustinas and Grima, Ramon},
     journal = {The Journal of Chemical Physics},
     volume = {153},
     number = {16},
     pages = {164113},
     year = {2020},
     publisher = {AIP Publishing LLC},
     summary = {Derives a closed-form solution for stochastic Michaelis-Menten enzyme kinetics and shows the substrate distribution can become transiently bimodal at intermediate times -- a behavior with no deterministic counterpart.}
   }

2019

1. Biophysical Journal

   Revisiting the reduction of stochastic models of genetic feedback loops with fast promoter switching

   James Holehouse and Ramon Grima

   Biophysical journal, 2019

   Bib PDF Website

   @article{holehouse2019revisiting,
     title = {Revisiting the reduction of stochastic models of genetic feedback loops with fast promoter switching},
     author = {Holehouse, James and Grima, Ramon},
     journal = {Biophysical journal},
     volume = {117},
     number = {7},
     pages = {1311--1330},
     year = {2019},
     publisher = {Elsevier},
     summary = {Shows that the standard fast-promoter-switching approximation for stochastic gene feedback loops breaks down whenever the protein-DNA binding rate greatly exceeds the unbinding rate, meaning commonly used reduced models are only accurate in part of the relevant parameter space.}
   }