Publications

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Pre-prints undergoing peer review

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. arXiv. https://doi.org/10.48550/arXiv.2407.03312

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. What can we learn from 100,000 freshwater forecasts? A synthesis from the NEON Ecological Forecasting Challenge. ESS Open Archive https://doi.org/10.22541/essoar.171458144.44104603/v1

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. Near-term lake water temperature forecasts can be used to anticipate the ecological dynamics of freshwater species. SSRN. http://dx.doi.org/10.2139/ssrn.4888712.

Accepted or In Press

Carey, C.C., R. S.D. Calder, R.J. Figueiredo, R.B. Gramacy, M.E. Lofton, M.E. Schreiber and R.Q. Thomas. 2024. A framework for developing a real-time lake phytoplankton forecasting system to support water quality management in the face of global change. Ambio: awaiting issue https://doi.org/10.1007/s13280-024-02076-7

Dalton, J.N. Miller, T.L. Greaver, R.D. Sabo, K. G. Austin, J.N. Phelan, R.Q. Thomas and C. Clark. 2024. Regional variation in growth and survival responses to atmospheric nitrogen and sulfur deposition for 140 tree species across the United States. Frontiers in Forests and Global Change 7:1426644. https://doi.org/10.3389/ffgc.2024.1426644

Dietze, M., E.P. White, A. Abeyta, C. Boettiger, N. Bueno Watts, C.C. Carey, R. Chaplin-Kramer, R.E. Emanuel, S.K. Morgan Ernest, R. Figueiredo, M.D, Gerst, L.R. Johnson, M.A. Kenney, J.S. McLachlan, I.C. Paschalidis, J.A. Peters, C.R. Rollinson, J. Simonis, K. Sullivan-Way, R. Q. Thomas, G.M. Wardle, A. Willson, J. Zwart. 2024. Near-term Ecological Forecasting for Climate Change Action. Nature Climate Change: Awaiting Issue. https://doi.org/10.1038/s41558-024-02182-0

Figueiredo, R.J., C.C. Carey, and R.Q. Thomas. Translational Edge and Cloud Computing to Advance Lake Water Quality Forecasting. Accepted at Computing in Science & Engineering.

Lofton, M.E., T.N. Moore, W.M. Woelmer, R.Q. Thomas, and C.C. Carey. 2024. A modular curriculum to teach undergraduates ecological forecasting improves student and instructor confidence in their data science skills. Bioscience: Awaiting issue. https://doi.org/10.1093/biosci/biae089

2024

McNellis, R., N. Smith, R.Q. Thomas, and N. van Gestel. 2024. Winter cover cropping increases albedo and latent heat flux in a Texas High Plains agro-ecosystem. Ecosphere 15:e4753 https://doi.org/10.1002/ecs2.4753

Meyer, M.F., M.E. Harlan, R.T. Hensley, Q. Zhan, N.S. Börekçi, T. Bucak, A.N. Cramer, J.Feldbauer, R. Ladwig, J.P. Mesman, I.A. Oleksy, R.M. Pilla, J.A. Zwart, E. Calamita, N.J. Gubbins, M.E. Lofton, D.A. Maciel, N.S. Marzolf, F. Olsson, A.N. Thellman, R.Q.Thomas, M.J. Vlah. 2024. Hacking Limnology Workshops and DSOS23: Growing a Workforce for the Nexus of Data Science, Open Science, and the Aquatic Sciences. Limnology and Oceanography Bulletin 33: 35-38. https://doi.org/10.1002/lob.10607

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

Park, S., R.Q. Thomas, C.C. Carey, A.D. Delany, Y.-J. Ku, M.E. Lofton, and R.J. Figueiredo. 2024. “FaaSr: Middleware for Serverless and Cross-Platform Function-as-a-Service Scientific Workflows in R” in 2024 IEEE 20th International Conference on e-Science (e-Science), Osaka, Japan, 2024 pp. 1-10. https://10.1109/e-Science62913.2024.10678660

Park, S., Y.-J. Ku, V. Daneshmand, R.Q. Thomas, C.C. Carey, R.J. Figuerido. 2024. FaaSr: R package for Function-as-a-Service. Journal of Open Source Software 9: 7027 https://doi.org/10.21105/joss.07027

Phelan J, G. Van Houtven, C Clark, J. Buckley, J. Cajka, A. Hargrave, K. Horn, R.Q. Thomas, and R. Sabo. 2024. Climate Change Could Negate U.S. Forest Ecosystem Services Benefits Gained Through Reductions in Nitrogen and Sulfur Deposition. Scientific Reports 14: 10767 https://doi.org/10.1038/s41598-024-60652-z

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

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, F. Olsson, B.G. Steele, K.C. Weathers, and C.C. Carey. 2024. Process-Based Forecasts of Lake Water Temperature and Dissolved Oxygen Outperform Null Models, with Variability Over Time and Depth. Ecological Informatics 83: 102825. https://doi.org/10.1016/j.ecoinf.2024.102825

2023

Clark, C.M., J. Phelan, J. Ash, J. Buckley, J. Cajka, K. Horn, R.Q. Thomas, R. Sabo. 2023. Future climate change effects on U.S. forest composition may offset benefits of reduced atmospheric deposition of N and S. Global Change Biology 29:4793-4810 http://doi.org/10.1111/gcb.16817

Clark, C.M., R.Q. Thomas, and K.J. Horn. 2023. Above-ground tree carbon storage in response to nitrogen deposition in the U.S. is heterogeneous and may have weakened. Communications Earth & Environment 4: 35 https://doi.org/10.1038/s43247-023-00677-w

Dietze, M., R.Q. Thomas, J. Peters, C. Boettiger, A. Shiklomanov, and J. Ashander. 2023. A community convention for ecological forecasting: output files and metadata v1.0. Ecosphere 14: e4686 https://doi.org/10.1002/ecs2.4686

Hounshell, A.G., B. M. D’Acunha, A. Breef-Pilz, M.S. Johnson, R. Quinn Thomas, C.C. Carey. 2023. Eddy covariance data reveal that a small freshwater reservoir emits a substantial amount of carbon dioxide and methane. Journal Geophysical Research - Biogeosciences 128: e2022JG007091 https://doi.org/10.1029/2022JG007091

Lofton, M.E., D.W. Howard, R.Q. Thomas, 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

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 28: 442–465 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 30: 385-419. https://doi.org/10.1007/s10651-023-00570-x

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, R.P. McClure, T.N. Moore, W.M. Woelmer, C. Boettiger, R.J. Figueiredo, R.T. Hensley, C.C. Carey. 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

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 14: e4628 https://doi.org/10.1002/ecs2.4628

Wynne, J. H., W. M. Woelmer, T. N. Moore, R.Q. Thomas, K C. Weathers, C. C. Carey. 2023. Uncertainty in projections of future lake thermal dynamics is differentially driven by global climate models and lake models. PeerJ 11:e15445 https://doi.org/10.7717/peerj.15445

2022

Carey, C.C., P.C. Hanson, R.Q. Thomas, A.B. Gerling, A.G. Hounshell, A.S.L Lewis, M.E. Lofton, R.P. McClure, H.L. Wander, W.M. Woelmer, B.R. Niederlehner, M.E. Schreider. 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

Moore, T.N., R.Q. Thomas, W.M. Woelmer, 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

Ahlswede, B.J., T.L. O’Halloran, and R.Q. Thomas. 2022. Combined carbon and albedo climate forcing from pine and switchgrass grown for bioenergy. Frontiers in Forests and Global Change 5:774067 https://doi.org/10.3389/ffgc.2022.774067

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., W. Woelmer, H. Wander, D. Howard, J. Smith, R. McClure, M. Lofton, N. Hammond, R. Corrigan, R.Q. Thomas, 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

Ahlswede, B.J., T.L. O’Halloran, J.D. Forsythe, and R.Q. Thomas. 2022. A minimally managed switchgrass ecosystem in a humid subtropical climate is a source of carbon to the atmosphere. GCB Bioenergy 14:24-36 https://doi.org/10.1111/GCBB.12897

Kyker-Snowman, E., D.L. Lombardozzi, G.B. Bonan, S.J. Cheng, J.S. Dukes, S.D. Frey, E.M. Jacobs, R. McNellis G, J.M. Rady G, N.G. Smith, R.Q. Thomas, W.R. Wieder, and A.S. Grandy. 2022. Increasing the spatial and temporal impact of ecological research: A roadmap for integrating a novel terrestrial process into an Earth system model. Global Change Biology 28: 665-684. https://doi.org/10.1111/gcb.15894

Woelmer, W., R.Q. Thomas, M. Lofton, R. McClure P, 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

2021

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

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

Graham, M.W., R.Q. Thomas, D.L. Lombardozzi, and M.E. O’Rourke. 2021. Modest capacity of no-till farming to offset emissions over 21st century. Environmental Research Letters 16: 054055 https://doi.org/10.1088/1748-9326/abe6c6

Meyer, M. F., R. Ladwig, H.A. Dugan, A. Anderson, A.R. Bah, B. Boehrer, L. Borre, R.J. Chapina, C. Doyle, E.J. Favot, G. Flaim, P. Forsberg, P.C. Hanson, B.W. Ibelings, P. Isles, F-P Lin, D. Lofton, T.N. Moore, S. Peel, J.A. Peters, D. Peirson, L.N. de Senerpont Domis, J.A. Schloss, M. Shikhani, A.P. Smagula, J.D. Stockwell, P. Thomas, R.Q. Thomas, T. Tietjen, and K.C. Weathers. 2021. Virtual Growing Pains: Initial Lessons Learned from Organizing Virtual Workshops, Summits, Conferences, and Networking Events during a Global Pandemic. Limnology and Oceanography Bulletin 30: 1- 11 https://doi.org/10.1002/lob.10431

Peters, J. and R.Q. Thomas. 2021. Going Virtual: What We Learned from the Ecological Forecasting Initiative Research Coordination Network Virtual Workshop. Bulletin of the Ecological Society of America 102: e01828 https://doi.org/10.1002/bes2.1828

Koplitz, S.N., C.G. Nolte, R.D. Sabo, C.M. Clark, K.J. Horn, R.Q. Thomas, and T.A. Newcomer-Johnson. 2021. The contribution of wildland fire emissions to nitrogen and sulfur deposition in the contiguous U.S.: Implications for tree growth and survival in the Northwest. Environmental Research Letters 16: 024028. https://doi.org/10.1088/1748-9326/abd26e

Thomas, V.A., R.H. Wynne, J. Kauffman, W. McCurdy, E.B. Brooks, R.Q. Thomas, and J. Rakestraw. 2021. Mapping thins to identify active forest management in southern pine plantations using Landsat time series stacks. Remote Sensing of Environment 252: 112127. https://doi.org/10.1016/j.rse.2020.112127

2020

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

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

Weaver, E.A., K. Kolivras, V.A. Thomas, R.Q. Thomas, and K. Abbas. 2020. Environmental factors affecting ecological niche of Coccidioides (spp.) and spatial dynamics of valley fever in the United States. Spatial and Spatio-temporal Epidemiology 32: 100317. https://doi.org/10.1016/j.sste.2019.100317

2019

Lawrence, D.M., et al. [52 authors including R.Q. Thomas]. 2019. The Community Land Model version 5: Description of new features, benchmarking, and impact of forcing uncertainty. Journal of Advances in Modeling Earth Systems 11: 4245-4287. https://doi.org/10.1029/2018MS001583

Thomas, R.Q., M. Williams, M.A. Cavaleri, J.-F. Exbrayat, T.L. Smallman, and L.E. Street. 2019. Alternate trait-based leaf respiration schemes evaluated at ecosystem-scale through carbon optimization modeling and canopy property data. Journal of Advances in Modeling Earth Systems 11: 4629-4644. https://doi.org/10.1029/2019MS001679

Wieder, W.R., D.M. Lawrence, R.A. Fisher, G.B. Bonan, S.J. Cheng, C.L. Goodale, C.D. Koven, D.L. Lombardozzi, K.W. Oleson, and R.Q. Thomas. 2019. Beyond static benchmarking: Evaluating model assumptions with experimental manipulations. Global Biogeochemical Cycles 33: 1289-1309. https://doi.org/10.1029/2018GB006141

Song, J.J., S. Wan, S. Piao, A.K. Knapp, A.T. Classen, S. Vicca, P. Ciais, M. Hovenden, S. Leuzinger, C. Beier, P. Kardo, J, Xia, Q. Liu, J. Ru, Z. Zhou, Y. Luo, D. Guo, J. A. Langley, J. Zscheischler, J.S. Dukes, J. Tang, J. Chen, K.S. Hofmocke, L.M. Kueppers, L. Rustad, L. Liu, M.D. Smith, P.H. Templer, R. Q. Thomas, R.J. Norby, R.P. Phillips, S. Niu, S. Fatichi, Y. Wang, D. Wang, L. Lei, J. Wang, X. Li, Q. Zhang, H. Han, P. Shao, X. Li, F. Su, B. Liu, F. Yang, G. Ma, G. Li, Y. Liu, Y. Liu, Z. Yang, K. Zhang, Y. Miao, M. Hu, C. Yan, A. Zhang, M. Zhong, Y. Hui, Y. Li, M. Zheng. 2019. A meta-analysis of 1,119 manipulative experiments on terrestrial carbon-cycling responses to global change. Nature Ecology and Evolution 3: 1309–1320. https://doi.org/10.1038/s41559-019-0958-3

Cheng, S.J., P. Hess, W.R. Wieder, R.Q. Thomas, K.J. Nadelhoffer, and C.L. Goodale. 2019. Decadal fates and impacts of nitrogen additions on temperate forest carbon storage: a data–model comparison. Biogeosciences 16: 2771-2793. https://doi.org/10.5194/bg-16-2771-2019

Van Houtven, G., J.N. Phelan, C.M. Clark, R. Sabo, J. Buckley, R.Q. Thomas, K.J. Horn, and S.D. LeDuc. 2019. Nitrogen deposition and climate change effects on tree species composition and ecosystem services: A cohort analysis. Ecological Monographs 89: e01345. https://doi.org/10.1002/ecm.1345

2018

Jinshi, J., M.K. Steele, S. Day, and R.Q. Thomas. 2018. Future global soil respiration rates will swell despite regional decreases in temperature sensitivity caused by rising temperatures. Earth’s Future 6: 1539 – 1554. https://doi.org/10.1029/2018EF000937

Horn, K.J., R.Q. Thomas, C.M. Clark, L.H. Pardo, M.E. Fenn, G.B. Lawrence, S. Perakis, E.A.H. Smithwick, D. Baldwin, S. Braun, A. Nordin, C.H. Perry, J.N. Phelan, P.G. Schaberg, S.B. St.Clair, R. Warby, and S. Watmough. 2018. Growth and survival relationships of 94 tree species with nitrogen and sulfur deposition across the conterminous U.S. PLoS ONE 13(10): e0205296. https://doi.org/10.1371/journal.pone.0205296

Chu, H., D.D. Baldocchi, C. Poindexter, M. Abraha, A. Desai, G. Bohrer, A. Arain, T. Griffis, P. Blanken, T. O’Halloran, R.Q. Thomas, Q. Zhang, S. Burns, D. Christian, S. Brown, A. Black, C. Gough, B. E. Law, X. Lee, Ji. Chen, D. Reed, K. Clark, J. Hatfield, J. Prueger, R. Bracho, and T.A. Martin. 2018. Temporal dynamics of aerodynamic canopy height derived from eddy covariance momentum data collected across North American Flux Networks. Geophysical Research Letters 45: 9275-9287. https://doi.org/10.1029/2018GL079306

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

Jian, J., M.K. Steele, S.D. Day, R.Q. Thomas, and S.C. Hodges. 2018. Measurement strategies to account for soil respiration temporal heterogeneity across diverse regions. Soil Biology and Biochemistry 125: 167-177. https://doi.org/10.1016/j.soilbio.2018.07.003

Jian, J., M.K. Steele, R.Q. Thomas, S. Day, and S. Hodges. 2018. Constraining global soil respiration by quantifying sources of uncertainty. Global Change Biology 24: 4143- 4159. https://doi.org/10.1111/gcb.14301

2017

Ahlswede, B.J., and R.Q. Thomas. 2017. Community Earth system model simulations reveal the relative importance of afforestation and forest management to surface temperature in eastern North America. Forests 8: 499. https://doi.org/10.3390/f8120499

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

2016

Niu, S., A.T. Classen, J. Dukes, P. Kardol, L. Liu, Y. Luo, L. Rustad, J. Tang, P.H. Templer, R.Q. Thomas, D. Tian, S. Vicca, Y.-P. Wang, J. Xia, and S. Zaehle. 2016. Global Patterns and Fundamental Mechanisms of the Terrestrial Nitrogen Cycle. Ecology Letters 19: 697-709. https://doi.org/10.1111/ele.12591

Hurtt, G.C., R.Q. Thomas, J. Fisk, R. Dubayah, and S. Sheldon. 2016. The impact of fine-scale disturbances on the predictability of vegetation dynamics and carbon flux. PLoS ONE 11: e0152883. https://doi.org/10.1371/journal.pone.0152883

2015

Burd, A.B., S. Frey, A. Cabre, T. Ito, N.M. Levine, C. Lønborg, M. Long, M. Mauritz, R.Q. Thomas, B. Stevens, T. Vanwallenghem, and N. Zeng. 2016. Terrestrial and marine perspectives on modeling organic matter degradation pathways and controls. Global Change Biology 22, 121–136. https://doi.org/10.1111/gcb.12987

Bracco, A.B., M.C. Long, N.M. Levine, R.Q. Thomas, C. Deutsch, and G.A. McKinley. 2016. The NCAR advanced study program summer colloquium on carbon-climate connections in the Earth system: capacity building in cross-disciplinary research. Bulletin of the American Meteorological Society 96: 1381–1384. https://doi.org/10.1175/BAMS-D-13-00246.1

Thomas, R.Q., E.N.J. Brookshire, S. Gerber. 2015. Nitrogen limitation on land: how can it occur in Earth system models? Global Change Biology 21: 1777–1793. https://doi.org/10.1111/gcb.12813

2014

Thomas, R.Q., and M. Williams. 2014. A model using marginal efficiency of investment to analyze carbon and nitrogen interactions in terrestrial ecosystems (ACONITE Version 1). Geoscientific Model Development 7: 2015-2037. https://doi.org/10.5194/gmd-7-2015-2014

2013

Thomas, R.Q, G.A. McKinley, and M.C. Long. 2013. Examining Uncertainties in Representations of the Carbon Cycle in Earth System Models. EOS, Transactions American Geophysical Union 94: 460. https://doi.org/10.1002/2013EO480006

Thomas, R.Q., S. Zaehle, P.H. Templer, and C.L. Goodale. 2013. Global patterns of nitrogen limitation: Confronting two global biogeochemical models with observations. Global Change Biology 19: 2986–2998. https://doi.org/10.1111/gcb.12281

Bell, R.C., A. Belmaker, C.S. Couch, K.M. Marchetto, J.L. Simonis, R.Q. Thomas, J.P. Sparks, J.M. Brown, K.S. Franscisco, and M.E. Manuel. 2013. Effectiveness of Erythrina gall wasp bio-control and implications for the recovery of threatened Wiliwili trees (Fabaceae: Erythrina sandwicensis). Journal of the Torrey Botanical Society 140:215–224. https://doi.org/10.3159/TORREY-D-12-00069.1

Thomas, R.Q., J.R. Kellner, D.B. Clark, and D.R. Peart. 2013. Low mortality in tall tropical trees. Ecology 94:920–929. https://doi.org/10.1890/12-0939.1

Thomas, R.Q., G.B. Bonan, and C.L. Goodale. 2013. Insights into mechanisms governing forest carbon response to nitrogen deposition: a model-data comparison using observed responses to nitrogen addition. Biogeosciences 10: 3869–3887. https://doi.org/10.5194/bg-10-3869-2013

Rastetter, E.B., R.D. Yanai, R.Q. Thomas, M.A. Vadeboncoeur, T.J. Fahey, M.C. Fisk, B.L. Kwiatkowski, and S.P. Hamburg. 2013. Recovery from disturbance requires resynchronization of ecosystem nutrient cycles. Ecological Applications 23:621–642. https://doi.org/10.1890/12-0751.1

2012

Carey, C.C., H.A. Ewing, K.L. Cottingham, K.C. Weathers, R.Q. Thomas, and J.F. Haney. 2012. Occurrence, toxicity, and potential ecological consequences of the cyanobacterium Gloeotrichia echinulata for low-nutrient lakes in the northeastern United States. Aquatic Ecology 46: 395–409. https://doi.org/10.1007/s10452-012-9409-9

Raciti, S.M., T.J. Fahey, R.Q. Thomas, P.B. Woodbury, C.T. Driscoll, F.J. Carranti, D.R. Foster, P.S. Gwyther, B.R. Hall, S.P. Hamburg, J.C. Jenkins, C. Neill, B.W. Peery, E.E. Quigley, R. Sherman, M.A. Vadeboncoeur, D.A. Weinstein, and G. Wilson. 2012. Local scale carbon budgets and mitigation opportunities for the northeastern United States. Bioscience 62: 23-38. https://doi.org/10.1525/bio.2012.62.1.7

2011

Leuzinger, S., and R.Q Thomas. 2011. How do we improve Earth system models? Integrating Earth system models, ecosystem models, experiments and long-term data. New Phytologist 191: 15–18. https://doi.org/10.1111/j.1469-8137.2011.03778.x

2010

Thomas, R.Q., C.D. Canham, K.C. Weathers, and C.L. Goodale. 2010. Increased tree carbon storage in response to nitrogen deposition in the U.S. Nature Geosciences 3: 13-17. https://doi.org/10.1038/ngeo721

Hurtt, G.C., J. Fisk, R.Q. Thomas, R. Dubayah, P. Moorcroft, and H. Shugart. 2010. Linking models and data on vegetation structure: data requirements and a modeling framework for future space-borne missions. Journal of Geophysical Research 115: G00E10. https://doi.org/10.1029/2009JG000937

Canham, C.D. and R.Q. Thomas. 2010. Local frequency but not relative abundance of temperate tree species varies along climate gradients in eastern North America. Ecology 91: 3433 – 3440. https://doi.org/10.1890/10-0312.1

2008

Thomas, R.Q., G.C. Hurtt, R. Dubayah, and M. Schilz. 2008. Using lidar data and a height structured ecosystem model to improve estimates forest carbon stocks and fluxes over mountainous terrain. Canadian Journal of Remote Sensing 34: S351-S363. https://doi.org/10.5589/m08-036

Fisher, J., G.C. Hurtt, R.Q. Thomas, and J.Q. Chambers. 2008. Clustered disturbances lead to bias in large-scale estimates based on forest sample plots. Ecology Letters 11: 554-563. https://doi.org/10.1111/j.1461-0248.2008.01169.x

Book Chapters

Daw, A., R.Q. Thomas, C.C. Carey, J.S. Read, A.P. Appling, and A. Karpatne. 2023. Physics-Guided Architecture (PGA) of LSTM Models for Uncertainty Quantification in Lake Temperature Modeling. In A. Karpatne, R. Kannan, V. Kumar (editors). Knowledge Guided Machine Learning, 1st edition, Chapman and Hall/CRC.

Pace, M.L., G.M. Lovett, C.C. Carey, and R.Q. Thomas. 2021. Primary production: the foundation of ecosystems. In K.C. Weathers, D.L. Strayer, and G.E. Likens (editors). Fundamentals of Ecosystems Science, 2nd edition. Academic Press.

Data Sets

Seyednasrollah, B. et al. [115 authors included R.Q. Thomas]. 2019. PhenoCam Dataset v2.0: Vegetation Phenology from Digital Camera Imagery, 2000-2018. ORNL DAAC, Oak Ridge, Tennessee, USA. https://doi.org/10.3334/ORNLDAAC/1674