Publications

Publications

Bold: Lab members; Italics: Students or Post-docs in Lab

Submitted or Pre-prints

Daw, A., R. Q. Thomas, C. C. Carey and J. S. Read and A. P. Appling and A. Karpatne.  2019. Physics-Guided Architecture (PGA) of Neural Networks for Quantifying Uncertainty in Lake Temperature Modeling. arXiv:1911.02682. [link]

Thomas, R. Q., R. J. Figueiredo, V. Daneshmand, B.  J. Bookout, L. K. Puckett, and C. C. Carey. A near-term iterative forecasting system successfully predicts reservoir hydrodynamics and partitions uncertainty. In Revision.

Thomas, R.Q., M. Williams, M.A. Cavaleri, J.-F. Exbrayat, T. L. Smallman, and L.E. Street. Alternate trait-based leaf respiration schemes evaluated at ecosystem-scale through carbon optimization modeling and canopy property data. In Review.

2019

Lawrence, DM, et al. [50 authors including R. Q. Thomas].  The Community Land Model version 5: Description of new features, benchmarking, and impact of forcing uncertainty.  In Press at Journal of Advances in Modeling Earth Systems.  [link]

Weaver, E.A., K. Kolivras, , V. A. Thomas, R. Q. Thomas, and K. Abbas. Environmental factors affecting ecological niche of Coccidioides (spp.) and spatial dynamics of valley fever in the United States . In Press at Spatial and Spatio-temporal Epidemiology.

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. Beyond static benchmarking: Evaluating model assumptions with experimental manipulations. In Press at Global Biogeochemical Cycles. [link]

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 [link]

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 [link]

Van Houtven, G., J. Phelan, C.  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 [link]

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 [link]

Horn, K. J., R. Q. Thomas, C. M. Clark, L. H. Pardo, M. E. Fenn, G. B. Lawrence, S. 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. Growth and survival relationships of 94 tree species with nitrogen and sulfur deposition across the conterminous U.S.  PLoS ONE 13(10): e0205296.[link]

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 [link]

Thomas. R. Q., A. Jersild, E. 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 [link]

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 [link]

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 [link]

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 [link]

Thomas, R. Q., E. Brooks, A. Jersild, E. Ward, R. H. Wynne, T.J. Albaugh, H. D. Aldridge, H. E. Burkhart, J-C Domec, T. R. Fox, C. A. Gonzalez-Benecke, 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 [link]

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. [link]

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 [link]

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. 2015. Terrestrial and marine perspectives on modeling organic matter degradation pathways. Global Change Biology 22, 121–136 [link]

Bracco, A.B, M.C. Long, N.M. Levine, R.Q. Thomas, C. Deutsch, and G.A. McKinely. 2015. NCAR’s Summer Colloquium: Capacity building in Cross-disciplinary Research of  Earth System Carbon-climate Connections.  Bulletin of the American Meteorological Society 96: 1381–1384. [link]

Thomas, R.Q., E.N.J. Brookshire, and S. Gerber. 2015. Nitrogen limitation on land: How can it occur in Earth system models? Global Change Biology 21: 1777–1793 [link]

2014

Thomas, R. Q. and Williams, M. 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. [link]

2013

Thomas, R.Q, G.A. McKinley, M.C. Long. 2013. Examining Uncertainties in Representations of the Carbon Cycle in Earth System Models. EOS, Transactions American Geophysical Union 94: 460 [link]

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. [link]

Bell, R.C., A. Belmaker, J. M. Brown, C. S. Couch, K. S. Francisco, M. E. Manuel, K. M. Marchetto, J. L. Simonis, R. Q. Thomas, and J. P. Sparks. 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. [link]

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. [link]

Thomas, R. Q., J. R. Kellner, D. B. Clark, and D. Peart. 2013. Low mortality in tall tropical trees. Ecology 94:920–929.  [link]

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. [link]

2012

C.C. Carey, H.A. Ewing, K.L. Cottingham, K.C. Weathers, R.Q. Thomas, and J.F. Haney. 2012. Occurrence and toxicity of the cyanobacterium Gloeotrichia echinulata in low-nutrient lakes in the northeastern United States.  Aquatic Ecology 46: 395–409 [link]

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, G. Wilson.  2012.  Local-Scale Carbon Budgets and Mitigation Opportunities for the Northeastern United States.  Bioscience 62: 23-38. [link]

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.  [link]

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. [link]

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. [link]

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. [link]

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. [link]

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.  [link]

Data Sets

Seyednasrollah, B., A.M. Young, K. Hufkens, T. Milliman, M.A. Friedl, S. Frolking, A.D. Richardson, M. Abraha, D.W. Allen, M. Apple, M.A. Arain, J. Baker, J.M. Baker, C.J. Bernacchi, J. Bhattacharjee, P. Blanken, D.D. Bosch, R. Boughton, E.H. Boughton, R.F. Brown, D.M. Browning, N. Brunsell, S.P. Burns, M. Cavagna, H. Chu, P.E. Clark, B.J. Conrad, E. Cremonese, D. Debinski, A.R. Desai, R. Diaz-Delgado, L. Duchesne, A.L. Dunn, D.M. Eissenstat, T. El-Madany, D.S.S. Ellum, S.M. Ernest, A. Esposito, L. Fenstermaker, L.B. Flanagan, B. Forsythe, J. Gallagher, D. Gianelle, T. Griffis, P. Groffman, L. Gu, J. Guillemot, M. Halpin, P.J. Hanson, D. Hemming, A.A. Hove, E.R. Humphreys, A. Jaimes-Hernandez, A.A. Jaradat, J. Johnson, E. Keel, V.R. Kelly, J.W. Kirchner, P.B. Kirchner, M. Knapp, M. Krassovski, O. Langvall, G. Lanthier, G.l. Maire, E. Magliulo, T.A. Martin, B. McNeil, G.A. Meyer, M. Migliavacca, B.P. Mohanty, C.E. Moore, R. Mudd, J.W. Munger, Z.E. Murrell, Z. Nesic, H.S. Neufeld, T.L. O’Halloran, W. Oechel, A.C. Oishi, W.W. Oswald, T.D. Perkins, M.L. Reba, B. Rundquist, B.R. Runkle, E.S. Russell, E.J. Sadler, A. Saha, N.Z. Saliendra, L. Schmalbeck, M.D. Schwartz, R.L. Scott, E.M. Smith, O. Sonnentag, P. Stoy, S. Strachan, K. Suvocarev, J.E. Thom, R.Q. Thomas, A.K. Van den berg, R. Vargas, C.S. Vogel, J.J. Walker, N. Webb, P. Wetzel, S. Weyers, A.V. Whipple, T.G. Whitham, G. Wohlfahrt, J.D. Wood, S. Wolf, J. Yang, X. Yang, G. Yenni, Y. Zhang, Q. Zhang, and D. Zona. 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

Milliman, T., B. Seyednasrollah, A.M. Young, K. Hufkens, M.A. Friedl, S. Frolking, A.D. Richardson, M. Abraha, D.W. Allen, M. Apple, M.A. Arain, J. Baker, J.M. Baker, C.J. Bernacchi, J. Bhattacharjee, P. Blanken, D.D. Bosch, R. Boughton, E.H. Boughton, R.F. Brown, D.M. Browning, N. Brunsell, S.P. Burns, M. Cavagna, H. Chu, P.E. Clark, B.J. Conrad, E. Cremonese, D. Debinski, A.R. Desai, R. Diaz-Delgado, L. Duchesne, A.L. Dunn, D.M. Eissenstat, T. El-Madany, D.S.S. Ellum, S.M. Ernest, A. Esposito, L. Fenstermaker, L.B. Flanagan, B. Forsythe, J. Gallagher, D. Gianelle, T. Griffis, P. Groffman, L. Gu, J. Guillemot, M. Halpin, P.J. Hanson, D. Hemming, A.A. Hove, E.R. Humphreys, A. Jaimes-Hernandez, A.A. Jaradat, J. Johnson, E. Keel, V.R. Kelly, J.W. Kirchner, P.B. Kirchner, M. Knapp, M. Krassovski, O. Langvall, G. Lanthier, G.l. Maire, E. Magliulo, T.A. Martin, B. McNeil, G.A. Meyer, M. Migliavacca, B.P. Mohanty, C.E. Moore, R. Mudd, J.W. Munger, Z.E. Murrell, Z. Nesic, H.S. Neufeld, W. O echel, A.C. Oishi, W.W. Oswald, T.D. Perkins, M.L. Reba, B. Rundquist, B.R. Runkle, E.S. Russell, E.J. Sadler, A. Saha, N.Z. Saliendra, L. Schmalbeck, M.D. Schwartz, R.L. Scott, E.M. Smith, O. Sonnentag, P. Stoy, S. Strachan, K. Suvocarev, J.E. Thom, R.Q. Thomas, A.K. Van den berg, R. Vargas, C.S. Vogel, J.J. Walker, N. Webb, P. Wetzel, S. Weyers, A.V. Whipple, T.G. Whitham, G. Wohlfahrt, J.D. Wood, J. Yang, X. Yang, G. Yenni, Y. Zhang, Q. Zhang, and D. Zona. 2019. PhenoCam Dataset v2.0: Digital Camera Imagery from the PhenoCam Network, 2000-2018. ORNL DAAC, Oak Ridge, Tennessee, USA. https://doi.org/10.3334/ORNLDAAC/1689