@article{gilpinevaluating,
  title={Evaluating the Risks of Domestic Radon Exposure},
  author={Gilpin, William}
}

@article{gilpinsurprising,
  title={Surprising Domestic Sources of Radioactivity},
  author={Gilpin, William}
}

@article{gilpin2016pypdb,
  title={PyPDB: a Python API for the protein data bank},
  author={Gilpin, William},
  journal={Bioinformatics},
  volume={32},
  number={1},
  pages={159--160},
  year={2016},
  publisher={Oxford University Press}
}

@article{gilpin2015worms,
  title={Worms under pressure: bulk mechanical properties of C. elegans are independent of the cuticle},
  author={Gilpin, William and Uppaluri, Sravanti and Brangwynne, Clifford P},
  journal={Biophysical journal},
  volume={108},
  number={8},
  pages={1887--1898},
  year={2015},
  publisher={Elsevier}
}

@article{gilpinengineering,
  title={Engineering the Charge Occupancy of Nitrogen Vacancies in Diamond},
  author={Gilpin, William}
}

@inproceedings{bayat2014formation,
  title={Formation of Nitrogen vacancy center ensembles in Diamond Nanowires},
  author={Bayat, Khadijeh and Sun, Won Kyu Calvin and Gilpin, William and Baroughi, Mhadi Farrokh and Loncar, Marko},
  booktitle={CLEO: QELS\_Fundamental Science},
  pages={JTu4A--104},
  year={2014},
  organization={Optica Publishing Group}
}

@article{gilpin2016ecocultural,
  title={An ecocultural model predicts Neanderthal extinction through competition with modern humans},
  author={Gilpin, William and Feldman, Marcus W and Aoki, Kenichi},
  journal={Proceedings of the National Academy of Sciences},
  volume={113},
  number={8},
  pages={2134--2139},
  year={2016},
  publisher={National Academy of Sciences}
}

@article{gilpin2017vortex,
  title={Vortex arrays and ciliary tangles underlie the feeding--swimming trade-off in starfish larvae},
  author={Gilpin, William and Prakash, Vivek N and Prakash, Manu},
  journal={Nature Physics},
  volume={13},
  number={4},
  pages={380--386},
  year={2017},
  publisher={Nature Publishing Group UK London}
}

@article{gilpin2017flowtrace,
  title={Flowtrace: simple visualization of coherent structures in biological fluid flows},
  author={Gilpin, William and Prakash, Vivek N and Prakash, Manu},
  journal={Journal of experimental biology},
  volume={220},
  number={19},
  pages={3411--3418},
  year={2017},
  publisher={The Company of Biologists Ltd}
}

@article{gilpin2017reply,
  title={Reply to'Boundary effects on currents around ciliated larvae'},
  author={Gilpin, William and Prakash, Vivek N and Prakash, Manu},
  journal={Nature Physics},
  volume={13},
  number={6},
  pages={521--522},
  year={2017},
  publisher={Nature Publishing Group UK London}
}

@article{gilpin2017phase,
  title={A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape},
  author={Gilpin, William and Feldman, Marcus W},
  journal={PLoS computational biology},
  volume={13},
  number={7},
  pages={e1005644},
  year={2017},
  publisher={Public Library of Science}
}

@article{gilpin2017dynamic,
  title={Dynamic vortex arrays created by starfish larvae},
  author={Gilpin, William and Prakash, Vivek N and Prakash, Manu},
  journal={Physical review fluids},
  volume={2},
  number={9},
  pages={090501},
  year={2017},
  publisher={American Physical Society}
}

@article{wakano2018ecocultural,
  title={Ecocultural range-expansion scenarios for the replacement or assimilation of Neanderthals by modern humans},
  author={Wakano, Joe Yuichiro and Gilpin, William and Kadowaki, Seiji and Feldman, Marcus W and Aoki, Kenichi},
  journal={Theoretical Population Biology},
  volume={119},
  pages={3--14},
  year={2018},
  publisher={Academic Press}
}

@inproceedings{gilpin2018low,
  title={Low-dimensional behavior and chaotic mixing by swimming starfish larvae},
  author={Gilpin, William and Nagendra Prakash, Vivek and Prakash, Manu},
  booktitle={APS March Meeting Abstracts},
  volume={2018},
  pages={K46--010},
  year={2018}
}

@article{gilpin2019cryptic,
  title={Cryptic selection forces and dynamic heritability in generalized phenotypic evolution},
  author={Gilpin, William and Feldman, Marcus W},
  journal={Theoretical Population Biology},
  volume={125},
  pages={20--29},
  year={2019},
  publisher={Academic Press}
}

@article{gilpin2018rapid,
  title={Rapid behavioral transitions produce chaotic mixing by a planktonic microswimmer},
  author={Gilpin, William and Prakash, Vivek N and Prakash, Manu},
  journal={arXiv preprint arXiv:1804.08773},
  year={2018}
}

@article{gilpin2018cryptographic,
  title={Cryptographic hashing using chaotic hydrodynamics},
  author={Gilpin, William},
  journal={Proceedings of the National Academy of Sciences},
  volume={115},
  number={19},
  pages={4869--4874},
  year={2018},
  publisher={National Academy of Sciences}
}

@article{gilpin2019cellular,
  title={Cellular automata as convolutional neural networks},
  author={Gilpin, William},
  journal={Physical Review E},
  volume={100},
  number={3},
  pages={032402},
  year={2019},
  publisher={American Physical Society}
}

@article{gilpin2019lagrange2d,
  title={Lagrange2D: A Mathematica package for Lagrangian analysis of two-dimensional fluid flows},
  author={Gilpin, William},
  journal={arXiv preprint arXiv:1908.00717},
  year={2019}
}

@inproceedings{gilpin2019cryptographic,
  title={Cryptographic analysis of chaotic fluid flows},
  author={Gilpin, William},
  booktitle={APS Division of Fluid Dynamics Meeting Abstracts},
  pages={M03--026},
  year={2019}
}

@article{gilpin2020multiscale,
  title={The multiscale physics of cilia and flagella},
  author={Gilpin, William and Bull, Matthew Storm and Prakash, Manu},
  journal={Nature Reviews Physics},
  volume={2},
  number={2},
  pages={74--88},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@article{gilpin2020cryptographic,
  title={Cryptographic analysis of chaotic systems},
  author={Gilpin, William},
  journal={Bulletin of the American Physical Society},
  volume={65},
  year={2020},
  publisher={American Physical Society}
}

@phdthesis{gilpin2019vortex,
  title={Vortex Arrays and Chaotic Mixing by Swimming Invertebrate Larvae},
  author={Gilpin, William Carl},
  year={2019},
  school={Stanford University}
}

@article{gilpin2020learning,
  title={Learning dynamics from large biological data sets: machine learning meets systems biology},
  author={Gilpin, William and Huang, Yitong and Forger, Daniel B},
  journal={Current Opinion in Systems Biology},
  volume={22},
  pages={1--7},
  year={2020},
  publisher={Elsevier}
}

@article{gilpin2020deep,
  title={Deep reconstruction of strange attractors from time series},
  author={Gilpin, William},
  journal={Advances in Neural Information Processing Systems},
  volume={33},
  year={2020}
}

@article{gilpin2021desynchronization,
  title={Desynchronization of jammed oscillators by avalanches},
  author={Gilpin, William},
  journal={Physical Review Research},
  volume={3},
  number={2},
  pages={023206},
  year={2021},
  publisher={American Physical Society}
}

@inproceedings{gilpin2021award,
  title={Award for Outstanding Doctoral Thesis Research in Biological Physics (2020): Vortex arrays and chaotic mixing by swimming invertebrate larvae},
  author={Gilpin, William},
  booktitle={APS March Meeting Abstracts},
  volume={2021},
  pages={A11--010},
  year={2021}
}

@inproceedings{gilpin2021detecting,
  title={Detecting coherent structures with automatic differentiation},
  author={Gilpin, William},
  booktitle={APS Division of Fluid Dynamics Meeting Abstracts},
  pages={N01--091},
  year={2021}
}

@article{gilpin2021chaos,
  title={Chaos as an interpretable benchmark for forecasting and data-driven modelling},
  author={Gilpin, William},
  journal={Advances in Neural Information Processing System},
  volume={34},
  year={2021}
}

@article{falk2024curiosity,
  title={Curiosity-driven search for novel nonequilibrium behaviors},
  author={Falk, Martin J and Roach, Finnegan D and Gilpin, William and Murugan, Arvind},
  journal={Physical review research},
  volume={6},
  number={3},
  pages={033052},
  year={2024},
  publisher={American Physical Society}
}

@article{gilpin2024generative,
  title={Generative learning for nonlinear dynamics},
  author={Gilpin, William},
  journal={Nature Reviews Physics},
  volume={6},
  number={3},
  pages={194--206},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

@article{gilpin2023model,
  title={Model scale versus domain knowledge in statistical forecasting of chaotic systems},
  author={Gilpin, William},
  journal={Physical Review Research},
  volume={5},
  number={4},
  pages={043252},
  year={2023},
  publisher={American Physical Society}
}

@inproceedings{falk2024curiosity,
  title={Curiosity-driven discovery of novel non-equilibrium behaviors},
  author={Falk, Martin and Murugan, Arvind and Gilpin, William and Roach, Finn},
  booktitle={APS March Meeting Abstracts},
  volume={2024},
  pages={S35--006},
  year={2024}
}

@article{gilpin2025optimization,
  title={Optimization hardness constrains ecological transients},
  author={Gilpin, William},
  journal={PLOS Computational Biology},
  volume={21},
  number={5},
  pages={e1013051},
  year={2025},
  publisher={Public Library of Science San Francisco, CA USA}
}

@inproceedings{zhang2024zero,
  title={Zero-shot forecasting of chaotic systems},
  author={Zhang, Yuanzhao and Gilpin, William},
  booktitle={The Thirteenth International Conference on Learning Representations},
  volume={13},
  year={2024}
}

@article{chen2024farewells,
  title={Farewells and hellos at Nature Reviews Physics},
  author={Chen, Xuelei and Aidelsburger, Monika and Economou, Sophia and Das, Sujit and Gilpin, William and Chen, Xuelei},
  journal={Nature Reviews Physics},
  volume={6},
  number={9},
  pages={525--525},
  year={2024},
  publisher={NATURE PORTFOLIO HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY}
}

@article{gilpin2025recurrences,
  title={Recurrences reveal shared causal drivers of complex time series},
  author={Gilpin, William},
  journal={Physical Review X},
  volume={15},
  number={1},
  pages={011005},
  year={2025},
  publisher={American Physical Society}
}

@article{yik2025neurobench,
  title={The neurobench framework for benchmarking neuromorphic computing algorithms and systems},
  author={Yik, Jason and Van den Berghe, Korneel and den Blanken, Douwe and Bouhadjar, Younes and Fabre, Maxime and Hueber, Paul and Ke, Weijie and Khoei, Mina A and Kleyko, Denis and Pacik-Nelson, Noah and others},
  journal={Nature Communications},
  volume={16},
  number={1},
  pages={1545},
  year={2025},
  publisher={Nature Publishing Group UK London}
}

@article{gilpin2025cell,
  title={The cell as a token: high-dimensional geometry in language models and cell embeddings},
  author={Gilpin, William},
  journal={Bioinformatics},
  volume={41},
  number={11},
  pages={btaf595},
  year={2025},
  publisher={Oxford University Press}
}

@inproceedings{zhang2025context,
  title={Context parroting: A simple but tough-to-beat baseline for foundation models in scientific machine learning},
  author={Zhang, Yuanzhao and Gilpin, William},
  booktitle={The Fourteenth International Conference on Learning Representations},
  volume={14},
  year={2025}
}

@article{krieger2025interpretable,
  title={Interpretable gene network inference with nonlinear causality},
  author={Krieger, Madison S and Gilpin, William},
  journal={bioRxiv},
  pages={2025--09},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

@article{chuckmused,
  title={MuSED-FM: A Benchmark for Evaluating Multivariate Time Series Foundation Models},
  author={Chuck, Caleb and Narasimhan, Sai Shankar and Agarwal, Shubhankar and Narayanan, Aditya and Gupta, Avantika and Mallampalli, Raghav and Feng, Fan and Bao, Anthony and Lai, Jeffrey B and Gilpin, William and others}
}

@inproceedings{lai2025panda,
  title={Panda: A pretrained forecast model for chaotic dynamics},
  author={Lai, Jeffrey and Bao, Anthony and Gilpin, William},
  booktitle={The Fourteenth International Conference on Learning Representations},
  volume={14},
  year={2025}
}

@article{bao2026transformers,
  title={Transformers for dynamical systems learn transfer operators in-context},
  author={Bao, Anthony and Lai, Jeffrey and Gilpin, William},
  journal={arXiv preprint arXiv:2602.18679},
  year={2026}
}

@article{bauer2026unifying,
  title={Unifying theories in high-dimensional biophysics: approaches, challenges and opportunities},
  author={Bauer, Marianne and Goyal, Akshit and Goyal, Sidhartha and Reddy, Gautam and Chakrabarti, Shaon and Desai, Michael M and Gilpin, William and Grilli, Jacopo and Husain, Kabir and Jain, Sanjay and others},
  journal={npj Systems Biology and Applications},
  volume={12},
  number={1},
  pages={43},
  year={2026},
  publisher={Nature Publishing Group UK London}
}

@inproceedings{mcvay2026information,
  title={Information Recovery Across Scales in Two-Dimensional Turbulence Using Fourier Neural Operators},
  author={McVay, Carson and Gilpin, William C},
  booktitle={APS Global Physics Summit 2026},
  year={2026}
}

@inproceedings{bao2026universal,
  title={Universal redundancies in time series foundation models},
  author={Bao, Anthony and Vattikuti, Hasith and Lai, Jeffrey and Gilpin, William},
  booktitle={Proceedings of the 43rd International Conference on Machine Learning},
  year={2026}
}