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Journal Article
Xu X, Schimel JP, Thornton PE, Song X, Yuan F, Goswami S.  2014.  Substrate and environmental controls on microbial assimilation of soil organic carbon: a framework for Earth system models. Ecology Letters. 17(5):547-555.
Arain A, Yuan F, T. Black A.  2006.  Soil–plant nitrogen cycling modulated carbon exchanges in a western temperate conifer forest in Canada. Agricultural and Forest Meteorology. 140(1-4):171-192.
Chang K-H, Warland JS, Bartlett PA, Arain A, Yuan F.  2014.  A Simple Crop Phenology Algorithm in the Land Surface Model CN-CLASS. Agronomy Journal. 106(1):297.
Xu X, Yuan F, Hanson PJ, Wullschleger SD, Thornton PE, Riley WJ, Song X, Graham DE, Song C, Tian H.  2016.  Reviews and syntheses: Four decades of modeling methane cycling in terrestrial ecosystems. Biogeosciences. 13(12):3735-3755.
Fenn ME, Allen E.B., Weiss S.B., Jovan S., Geiser L.H., Tonnesen G.S., Johnson R.F., Rao L.E., Gimeno B.S., Yuan F et al..  2010.  Nitrogen critical loads and management alternatives for N-impacted ecosystems in California. Journal of Environmental Management. 91(12):2404-2423.
Grant R., Arain A, Arora VK, Barr A., Black AT, Chen J., Wang S., Yuan F, Zhang Y..  2004.  Modelling Temperature Effects on CO2 and Energy Exchange in Temperate and Boreal Coniferous Forests. AGU Spring Meeting Abstracts. :A3.
Yuan F, Arain A, BARR ALANG, Black AT, BOURQUE CHARLESP-A, COURSOLLE CAROLE, Margolis HA, McCaughey HJ, Wofsy SC.  2008.  Modeling analysis of primary controls on net ecosystem productivity of seven boreal and temperate coniferous forests across a continental transect. Global Change Biology. 14(8):1765-1784.
Hayes DJ, Kicklighter DW, A. McGuire D, Chen M, Zhuang Q, Yuan F, Melillo JM, Wullschleger SD.  2014.  The impacts of recent permafrost thaw on land–atmosphere greenhouse gas exchange. Environmental Research Letters. 9(4):045005.
Yuan F, Meixner T, Fenn ME, Šimůnek J.  2011.  Impact of transient soil water simulation to estimated nitrogen leaching and emission at high- and low-deposition forest sites in Southern California. Journal of Geophysical Research. 116(G3)
Yuan F, Arain A, Black AT, Morgenstern K.  2007.  Energy and water exchanges modulated by soil–plant nitrogen cycling in a temperate Pacific Northwest conifer forest. Ecological Modelling. 201(3-4):331-347.
Fenn ME, Jovan S., Yuan F, Geiser L., Meixner T., Gimeno B.S..  2008.  Empirical and simulated critical loads for nitrogen deposition in California mixed conifer forests. Environmental Pollution. 155(3):492-511.
Huang S, Arain A, Arora VK, Yuan F, Brodeur J, Peichl M.  2011.  Analysis of nitrogen controls on carbon and water exchanges in a conifer forest using the CLASS-CTEMN+ model. Ecological Modelling. 222(20-22):3743-3760.
Tang G, Yuan F, Bisht G, Hammond GE, Lichtner PC, Kumar J, Mills RT, Xu X, Andre B, HOFFMAN FORRESTM et al..  2016.  Addressing numerical challenges in introducing a reactive transport code into a land surface model: a biogeochemical modeling proof-of-concept with CLM–PFLOTRAN 1.0. Geoscientific Model Development. 9(3):927-946.