Publications

2026

[Pre-print] Pao, G.M., Deyle, E.R., Ye, H., Ogawa, J., Guaderrama, M., Ku, M., Tonnu, N, Khan,

N., Ke, E., Wittenberg, C., Verma, I.M., and Sugihara, G. Existence of Causation

without Correlation in Transcriptional Networks. bioRxiv, 2026.02.09.704821.

Ianniello, C. F., Large, S. I., Grace, J. B., Hyde, K. J., McManus, M. C., Smith, L. A., & Deyle, E. R. A multi-evidence causal investigation of water quality influences on Atlantic menhaden (Brevoortia tyrannus) habitat use and abundance in Narragansett Bay, USA. ICES Journal of Marine Science, 83(7), fsag117.

2025

Krasnow, R., Kaufman, L., and Deyle, E. Making the Most of Available Data: A Case Study of Converging Analyses to Model an Emerging Fishery for Jonah Crab (Cancer borealis). Fish and Fisheries, 26: 991-1003.

[Pre-print] Deyle, E.R., Pao, G., and Sugihara, G. Extending empirical dynamic modeling to cross-sectional data beyond traditional time series. bioRxiv, 2025.01.10.628762.

Ianiello,C. F., Beery, G., Chen, T.-H., Deyle, E., Heiger-Bernays, W., Motter, I., McAlister, J.S., and Rotjan, R.D. Stress in the City: Disentangling multi-stressor effects on an urbanized coral in a changing ocean. Marine Pollution Bulletin, in press.

Stallings, B., Edwards, C., Pedersen, N., Sandin, S., Deyle, E., Kaufman, L., Chidsey, T., and Rotjan, R. Examining the successional role of Montipora aequituberculata on remote, post-disturbance equatorial reefs. Marine Ecology Progress Series, 753: 37-54.

Carpenter, D., Saberski, E., Deyle, E., Park, J., and Sugihara, G. Repairing Gaps in Ecological Time Series. Methods in Ecology and Evolution, 16(3): 573-583.

2024

Saberski, E., Lorimer, T., Carpenter, D., Deyle, E., Merz, E., Park, J., Pao, G., and Sugihara, G. The impact of data resolution on dynamic causal inference in multiscale ecological networks. Communications Biology, 7, 1442.

White, C., Wang, Y.-H., Walter, R.K., Ruttenberg, B., Han, D., Newman, E., Deyle, E., Gopal, S., and Kaufman, L. Spatial planning offshore wind energy farms in California for mediating fisheries and wildlife conservation impacts. Environmental Development, 51: 101005.

Stern, B.D., Deyle, E.R., Munch, S.B., Saberski, E., and Hegedus, E.J. Stress drives soccer athlete wellness and movement: Using convergent cross-mapping to identify causal relationships in a dynamic environment. International Journal of Sports Physiology and Performance, 19(10): 1030-1040.

Gopal, S., Toshniwal, D., Kaufman, L., Deyle, E., and Pitts, J. Comparative Analysis of Generative Pre-Trained Transformers Responses to Coastal Ecosystem Questions: Implications for GenAI in Environmental Education. Research Square, rs.3.rs-4132837/v1.

2022

Deyle, E., Bouffard, B., Frossard, V., Schwefel, R., Melack, J., and Sugihara, G. A hybrid empirical and parametric approach to managing ecosystem complexity in a nonstationary world: capturing the combined effects of climate change and nutrients on water quality in Lake Geneva. Procceedings of the National Academy of Sciences of the United States of America, 119(26), e2102466119.

2021

Giron-Nava, A., Ezcurra, E., Brias, A., Velarde, E., Deyle, E., Cisnero-Montemayor, A.M., Munch, S., Sugihara, G., and Aburto-Oropeza, O. Environmental variability and fishing effects on the Pacific sardine fisheries in the Gulf of California. Canadian Journal of Fisheries and Aquatic Sciences, 78(5), pp. 623-630.

Natsukawa, H., Deyle, E.R., Pao, G.M., Koyamada, K., and Sugihara, G. A visual analytics approach for ecosystem dynamics based on Empirical Dynamic Modeling. IEEE Transactions on Visualization and Computer Graphics, 27(2): 506-516.

Nova, N., Deyle E.R., Shocket, M.S., MacDonald, A.J., Childs, M.L., Rypdal, M., Sugihara, G., and Mordecai, E.A. Susceptible host availability modulates climate effects on dengue dynamics. Ecology Letters, 24(3):415-425.

2020

Chang, C.-W., Ye, H., Miki,. T., Deyle, E.R., Souissi, S., Anneville, O., Adrian, R., Chiang, Y.-R., Ichise, S., Kumagai, M., Matsuzaki, S.S., Shiah, F.-K., Wu, J.-T.,

Hsieh, C.-H., and Sugihara, G. Long-term warming destabilizes aquatic ecosystems through weakening biodiversity-mediated causal networks. Global Change Biology, 6: 6413-6423.

Giron-Nava, A., Munch, S.B., Johnson, A.F., Deyle, E., James, C.C., Saberski, E., Pao, G.M., Aburto-Oropeza, O. and Sugihara, G. Circularity in fisheries data weakens real world prediction. Scientific Reports, 10(1): 1-6.

2019

Runge, J., Bathiany, S., Bollt, E., Camps-Valls, G., Coumou, D., Deyle, E., Glymour, C., Kretschmer, M., Mahecha, M., Mu˜noz-Mar´ı, J., Van Nes, E., Peters, J., Quax, R., Reichstein, M., Scheffer, M., Schoelkopf, B., Spirtes, P., Sugihara, G., Sun, J., Zhang, K, and Zscheischler, J. Inferring causation from time series in Earth system sciences. Nature Communications,10: 2553.

Sguotti, C., Sakia, O., Werner, K.-M., Deyle, E., Sugihara, G., and M¨ollmann, C. Nonlinearity in stock-recruitment relationships of Atlantic cod: insights from a multi-model approach. ICES Journal of Marine Science, fsz113.

2018

Deyle, E. R., Schueller, A., Ye, H., and Sugihara, G. Ecosystem-based forecasts of recruitment in two menhaden species. Fish and Fisheries 19(5): 769-781.

Ushio, M., Hsieh, C.-H., Masuda, R., Deyle, E. R., Ye, H. Chang, C.W-., Sugihara, G., and Kondoh, M. Fluctuating interaction network and time-varying stability of a natural fish community. Nature 554(7692):360-363.

2017

McGowan, J.A., Deyle, E.R., Ye, H., Carter, M.L., Perretti, C.T., Seger, K.D., Verneil, A. and Sugihara, G. Predicting coastal algal blooms in southern California. Ecology 98:1419-1433.

2016

Deyle, E. R., Maher, M. C., Hernandez, R. D., Basu, S., and Sugihara, G. Global environmental drivers of influenza. Proceedings of the National Academy of Sciences of the United States of America 113 13081-13086.

Deyle E., May R.M., Munch S., and Sugihara G. Tracking and forecasting ecosystem interactions in real time. Proceedings of the Royal Society B 283: 20152258.

van Nes E., Scheffer M., Brovkin V., Lenton T.M., Ye H., Deyle E., and Sugihara G. Causal feedbacks in climate change. Nature Climate Change 5: 445-448.

2015

Clark A., Ye H., Isbell F., Deyle E., Cowles J., Tilman D., and Sugihara G. Spatial ’convergent cross mapping’ to detect causal relationships from short time-series. Ecology 96: 1174-1181.

Ye H., Deyle E.R., Gilarranz L.J., Sugihara G. Distinguishing time-delayed causal interactions using convergent cross mapping. Scientific Reports 5: 14750.

Tsonis A.A., Deyle E.R., May R.M., Sugihara G., Swanson K., Verbeten J.D., Wang G. Dynamical evidence for causality between galactic cosmic rays and interannual variation in global temperature. Proceedings of the National Academy of Science USA 112: 3253-3256.

2014

Liu H., Fogarty M.J., Hare J.A., Hsieh C.H., Glaser S.M., Ye H., Deyle E., and Sugihara G. Modeling dynamic interactions and coherence between marine zooplankton and fishes linked to environmental variability. Journal of Marine Systems 131: 120-129.

2013

Deyle E., Fogarty M.J., Hsieh C.H., Kaufman L., MacCall A., Munch S., Perretti C., Ye H., and Sugihara G. Predicting climate effects on Pacific sardine. Proceedings of the National Academy of Sciences USA 110: 6430-6435.

2012

Sugihara G., May R., Ye H., Hsieh C.H., Deyle E., Fogarty M.J., and Munch S.B. Detecting causality in complex ecosystems. Science 338: 496-500.

2011

Sugihara G., Beddington J., Hsieh C.H., Deyle E., Fogarty M., Glaser S.M., Hewitt R., Hollowed A., May R.M., Munch S.B., Perretti C., Rosenberg A., Sandin S., and Ye H. Are exploited fish populations stable? Proceedings of the National Academy of Sciences USA 108: E1224-E1225.

Deyle, E., Sugihara G. Generalized Theorems for Nonlinear State Space Reconstruction. PLoS 6: e18295.