Publications

Carey, C.C., P.C. Hanson, R.Q. Thomas, A.B. Gerling, A.G. Hounshell, A.S.L Lewis, M.E. Lofton P, R.P. McClure, H.L. Wander, W.M. Woelmer, B.R. Niederlehner, M.E. Schreiber. 2022. Anoxia decreases the magnitude of the carbon, nitrogen, and phosphorus sink in freshwater ecosystems. Global Change Biology 28:4861-4881 https://doi.org/10.1111/gcb.16228

McClure, R.P, R.Q. Thomas, M.E. Lofton, W.M. Woelmer and C.C. Carey. 2021. Iterative forecasting improves near-term predictions of methane ebullition rates. Frontiers in Environmental Science 9:756603. https://doi.org/10.3389/fenvs.2021.756603

Olsson, F, T.N. Moore, C.C. Carey, A. Breef-Pilz, and R.Q. Thomas. 2024. A multi-model ensemble of baseline and process-based models improves the predictive skill of near-term lake forecasts. Water Resources Research 60: e2023WR035901 https://doi.org/10.1029/2023WR035901

Olsson, F., C.C. Carey, C. Boettiger, G. Harrison, R. Ladwig, M.F. Lapeyrolerie, A.S.L. Lewis, M.E. Lofton, F. Motealegre-Mora, J.S. Rebaey, C.J. Robbins. X. Yang, and R.Q. Thomas. 2025. What can we learn from 100,000 freshwater forecasts? A synthesis from the NEON Ecological Forecasting Challenge. Ecological Applications 35:e70004 https://doi.org/10.1002/eap.70004

Paíz, R., R.Q. Thomas, C. C. Carey, E. de Eyto, A. Delany, R. Poole, P. Nixon, M. Dillane, I.D. Jones, D.C. Pierson, V. McCarthy, S. Linnane, E. Jennings. 2025. Near-term lake water temperature forecasts can be used to anticipate the ecological dynamics of freshwater species. Ecosphere 16: e70335  http://dx.doi.org/10.1002/ecs2.70335

Thomas, R.Q. , C. Boettiger, C.C. Carey, M.C. Dietze, L.R. Johnson, M.A. Kenney, J.S. McLachlan, J.A Peters, E.R. Sokol, J.F. Weltzin, A. Willson, W.M. Woelmer, and Challenge Contributors. 2023. The NEON Ecological Forecasting Challenge. Frontiers in Ecology and Environment 21: 112-113. https://doi.org/10.1002/fee.2616

Thomas. R.Q., A.L. Jersild, E.B. Brooks, V.A. Thomas, and R.H. Wynne. 2018. A mid-century ecological forecast with partitioned uncertainty predicts increases in loblolly pine forest productivity. Ecological Applications. 28: 1503-1519. https://doi.org/10.1002/eap.1761

Thomas, R.Q, R.P. McClure, T.N. Moore, W.M. Woelmer, C. Boettiger, R.J. Figueiredo, R.T. Hensley, and C.C. Carey. 2023. Near-term forecasts of NEON lakes reveal gradients of environmental predictability across the U.S. Frontiers in Ecology and Environment 21: 220–226. https://doi.org/10.1002/fee.2623

Wheeler, K., M. Dietze, D. LeBauer, J. Peters, A.D. Richardson, R.Q. Thomas, K. Zhu, U. Bhat, S. Munch, R.F Buzbee, M. Chen, B. Goldstein, J.S. Guo, D. Hao, C. Jones, M. Kelly-Fair, H. Liu, C. Malmborg, N. Neupane. D. Pal, A. Ross, V. Shirey, Y. Song, M. Steen, E.A. Vance, W.M. Woelmer, J. Wynne and L. Zachmann. 2024. Predicting Spring Phenology in Deciduous Broadleaf Forests: An Open Community Forecast Challenge. Agricultural and Forest Meteorology 345: 09810 https://doi.org/10.1016/j.agrformet.2023.109810

Woelmer, W.M, R.Q. Thomas, M. Lofton, R. McClure, and C.C Carey. 2022. Near-term phytoplankton forecasts reveal the effects of model time step and forecast horizon on predictability. Ecological Applications 32: e2642. https://doi.org/10.1002/eap.2642

Wander, H.L., R.Q. Thomas, T.N. Moore, M.E. Lofton, A. Breef-Pilz, C.C. Carey. 2024. Data assimilation experiments inform monitoring needs for near-term ecological forecasts in a eutrophic reservoir. Ecosphere 15: e4752. https://doi.org/10.1002/ecs2.4752

Wander, H.L., M.E. Lofton, J.P. Doubek, D.W. Howard, M.R. Hipsey, R.Q. Thomas, and C.C. Carey. 2025. Warming air temperatures alter the timing and magnitude of reservoir zooplankton biomass. Ecological Modeling 509: 111272. https://doi.org/10.1016/j.ecolmodel.2025.111272. Open Access version at ESS Open Archive

Daneshmand, V., A. Breef-Pilz, C.C. Carey, Y. Jin, Y.-J. Kun, K.C., R.Q. Thomas, R.J. Figueiredo. 2021 “Edge-to-cloud Virtualized Cyberinfrastructure for Near Real-time Water Quality Forecasting in Lakes and Reservoirs” in 2021 IEEE 17th International Conference on eScience (eScience), Innsbruck, Austria, 2021 pp. 138-148. https://doi.org/10.1109/eScience51609.2021.00024

Daw, A., R.Q. Thomas, C.C. Carey, J.S. Read, A.P. Appling, and A. Karpatne. 2020. “Physics-guided architecture (PGA) of neural networks for quantifying uncertainty in lake temperature modeling” in Proceedings of the 2020 SIAM International Conference on Data Mining: 532-540. https://doi.org/10.1137/1.9781611976236.60

Hipsey, M.R., L.C. Bruce, C. Boon, B. Busch, C.C. Carey, D.P. Hamilton, P.C. Hanson, J.S. Read, E. de Sousa, M. Weber, and L.A. Winslow. 2019. A General Lake Model (GLM 3.0) for linking with high-frequency sensor data from the Global Lake Ecological Observatory Network (GLEON). Geoscientific Model Development. 12: 473-523. https://doi.org/10.5194/gmd-12-473-2019

Holthuijzen, M.F., R.B. Gramacy, C.C. Carey, D.M. Higdon, and R.Q. Thomas. Synthesizing data products, mathematical models, and observational measurements for lake temperature forecasting. Annals of Applied Statistics19: 1127-1146 https://doi.org/10.1214/25-AOAS2027. Also available on arXiv.

Lofton, M.E., J.A. Brentrup, W. Beck, J.A. Zwart, R. Bhatttacharya, L. Brighenti, S.H. Burnet, I. McCullough, B. Steele, C.C. Carey, K.L. Cottingham, M.C. Dietze, H.A. Ewing, K.C. Weathers, and S. LaDeau. 2022. Using near-term forecasts and uncertainty partitioning to improve prediction of oligotrophic lake cyanobacterial density. Ecological Applications. 32: e2590. https://doi.org/10.1002/eap.2590

Thomas R.Q, R.J. Figueiredo, V. Daneshmand, B.J. Bookout, L.K. Puckett, and C.C. Carey. 2020. A near‐term iterative forecasting system successfully predicts reservoir hydrodynamics and partitions uncertainty in real time. Water Resources Research 56: e2019WR026138. https://doi.org/10.1029/2019WR026138

Thomas, R.Q., E.B. Brooks, A.L. Jersild, E.J. Ward, R.H. Wynne, T.J. Albaugh, H.D. Aldridge, H.E. Burkhart, J.-C. Domec, T.R. Fox, C.A. Gonzalez-Benecke, T.M. Martin, A. Noormets, D.A. Sampson, and R.O. Teskey. 2017. Leveraging 35 years of Pinus taeda research in the southeastern US to constrain forest carbon cycle predictions: regional data assimilation using ecosystem experiments. Biogeosciences 14: 3525-3547. https://doi.org/10.5194/bg-14-3525-2017

Smith, J.W., L.R. Johnson, and R.Q. Thomas. 2023. Assessing Ecosystem State Space Models: Identifiability and Estimation. Journal of Agriculture, Biological and Environmental Statistics. https://doi.org/10.1007/s13253-023-00531-8

Smith, J.W., L.R. Johnson, and R.Q. Thomas. 2023. Parameterizing Lognormal state space models using moment matching. Environmental and Ecological Statistics. https://doi.org/10.1007/s10651-023-00570-x

Carey, C.C., R. S.D. Calder, R.J. Figueiredo, R.B. Gramacy, M.E. Lofton, M.E. Schreiber and R.Q. Thomas. 2025. A framework for developing a real-time lake phytoplankton forecasting system to support water quality management in the face of global change. Ambio 25: 475–487. https://doi.org/10.1007/s13280-024-02076-7

Carey, C.C., N.K. Ward, K.J. Farrell, M.E. Lofton, A.I. Krinos, R.P. McClure, K. Subratie, R.J. Figueiredo, J.P. Doubek, P.C. Hanson, P. Papadopoulos, and P. Arzberger. 2019. Enhancing collaboration between ecologists and computer scientists: lessons learned and paths forward. Ecosphere. 10:e02753. https://doi.org/10.1002/ecs2.2753

Carey C.C., W.M. Woelmer, M.E. Lofton, R.J. Figueiredo, B.J. Bookout, R.S. Corrigan, V. Daneshmand, A.G. Hounshell, D.W. Howard, A.S. Lewis, R.P. McClure, H.L. Wander, N.K. Ward, and R.Q. Thomas. 2022. Advancing lake and reservoir water quality management with near-term, iterative ecological forecasting. Inland Waters 12: 107-120 https://doi.org/10.1080/20442041.2020.1816421

Lewis, A.G, W. Woelmer G, H. Wander G, D. Howard, J. Smith G, R. McClure P, M. Lofton, N. Hammond, R. Corrigan, R.Q. Thomas, and C.C. Carey. 2022. Increased adoption of best practices in ecological forecasting enables comparisons of forecastability across systems. Ecological Applications 32: e02500. https://doi.org/10.1002/eap.2500

Lofton, M.E., D.W. Howard, R.Q. Thomas, and C. C Carey. 2023. Progress and opportunities in advancing near-term forecasting of freshwater quality. Global Change Biology 29: 1691-1714 https://doi.org/10.1111/gcb.16590

Ward, N.K., M.G. Sorice, M.S. Reynolds, K.C. Weathers, W. Weng, and C.C. Carey. 2022. Can interactive data visualizations promote waterfront best management practices? Lake and Reservoir Management. 38: 95–108. https://doi.org/10.1029/2020WR027296

Carey, C.C., K.J. Farrell, A.G. Hounshell, and K. O’Connell. Macrosystems EDDIE teaching modules significantly increase ecology students’ proficiency and confidence working with ecosystem models and use of systems thinking. Ecology & Evolution. 10: 12515–12527. https://doi.org/10.1002/ece3.6757

Farrell, K.J., and C.C. Carey. 2018. Power, pitfalls, and potential for integrating computational literacy into undergraduate ecology courses. Ecology and Evolution. 8:7744-7751. https://doi.org/10.1002/ece3.4363

Hounshell, A.G., K.J. Farrell, and C.C. Carey. 2021. Macrosystems EDDIE teaching modules increase students’ ability to define, interpret, and apply concepts in macrosystems ecology. Education Sciences. 11: 382. https://doi.org/10.3390/educsci11080382

Lofton, M.E., T.N. Moore, W.M. Woelmer, R.Q. Thomas, and C.C. Carey. 2025. A modular curriculum to teach undergraduates ecological forecasting improves student and instructor confidence in their data science skills. Bioscience 75: 127-138 https://doi.org/10.1093/biosci/biae089. Also available on ESS Open Archive

Moore, T.N. , R.Q. Thomas, W.M. Woelmer, and C.C Carey. 2022. Integrating ecological forecasting into undergraduate ecology curricula with an R Shiny application-based teaching module. Forecasting 4:604-633. https://doi.org/10.3390/forecast4030033

Willson, A.M., H. Gallo, J.A. Peters, A. Abeyta, N. Bueno Watts, C.C. Carey, T.N. Moore, G. Smies, R.Q. Thomas, W.M. Woelmer, and J.S. McLachlan. 2023. Assessing opportunities and inequities in undergraduate ecological forecasting education. Ecology and Evolution 13: e10001. https://doi.org/10.1002/ece3.10001

Woelmer, W.M., T.N. Moore, M.E. Lofton, R.Q. Thomas, and C.C. Carey. 2023. Embedding communication concepts in forecasting training increases students’ understanding of ecological uncertainty. Ecosphere https://doi.org/10.1002/ecs2.4628