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Shao C, Chen J, Stepien CA, Chu H, Ouyang Z, Bridgeman TB, Czajkowski KP, Becker RH, John R.  2015.  Diurnal to annual changes in latent, sensible heat, and CO2 fluxes over a Laurentian Great Lake: A case study in Western Lake Erie. Journal of Geophysical Research: Biogeosciences. 120(8):1587-1604.
Shade A, Read JS, Welkie DG, Kratz TK, Wu CH, McMahon KD.  2011.  Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance. Environmental Microbiology. 13(2752-2767)
Shade A, Jones SE, McMahon KD.  2008.  The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics. Environmental Microbiology. 10(1057-1067)
Shade A, Read JS, Youngblut ND, Fierer N, Knight R, Kratz TK, Lottig NR, Roden EE, Stanley EH, Stombaugh J et al..  2012.  Lake microbial communities are resilient after a whole-ecosystem disturbance. The ISME Journal. :2153-2167.
Shade A, Chiu CY, McMahon KD.  2010.  Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment. Environmental Microbiology. 12:455-66.
Shade A, Carey CC, Kara EL, Bertilsson S, McMahon KD, Smith MC.  2009.  Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies. The ISME Journal. 3:881-888.
Shade A, Chiu CY, McMahon KD.  2010.  Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics. Microbial Ecology. 59:546-554.
Schmidt SR, Gerten D, Hintze T, Lischeid G, Livingstone DM, Adrian R.  2018.  Temporal and spatial scales of water temperature variability as an indicator for mixing in a polymictic lake. Inland Waters.
Salonen K, Leppäranta M, Viljanen M, Gulati R.  2009.  Perspectives in winter limnology: closing the annual cycle of freezing lakes. Aquatic Ecology. 43:609-616.
Sadro S, Holtgrieve, G. W., Solomon CT, Koch GR.  2014.  Widespread variability in overnight patterns of ecosystem respiration linked to gradients in dissolved organic matter, residence time, and productivity in a global set of lakes. Limnology and Oceanography. 59(5)
Sadro S, Melack JM, MacIntyre S.  2011.  Spatial and Temporal Variability in the Ecosystem Metabolism of a High-elevation Lake: Integrating Benthic and Pelagic Habitats. Ecosystems. 14:1123-1140.
Sadro S, Melack JM, MacIntyre S.  2011.  Depth-integrated estimates of ecosystem metabolism in a high-elevation lake (Emerald Lake, Sierra Nevada, California). Limnology and Oceanography. 56:1764-1780.
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Ryder E, Jennings E, de Eyto E, Dillane M, NicAonghusa C, Pierson DC, Moore K, Rouen M, Poole R.  2012.  Temperature quenching of CDOM fluorescence sensors: temporal and spatial variability in the temperature response and a recommended temperature correction equation. Limnology and Oceanography: Methods. 10:1004-1010.
Ryder E, de Eyto E, Dillane M, Poole R, Jennings E.  2014.  Identifying the role of environmental drivers in organic carbon export from a forested peat catchment. Science of The Total Environment. 490:28-36.
Rueda FJ, MacIntyre S.  2009.  Flow paths and spatial heterogeneity of stream inflows in a small multibasin lake. Limnology and Oceanography. 54:2041-2057.
Rueda FJ, MacIntyre S.  2010.  Modelling the fate and transport of negatively buoyant storm–river water in small multi-basin lake. Environmental Modelling & Software. 25:146-157.
Rudorff CM, Milack JM, MacIntyre S, Barbosa CCF, Novo EMLM.  2011.  Seasonal and spatial variability of CO2 emission from a large floodplain lake in the lower Amazon. J. Geophys. Res. 116(G04007)
Ruan G., Hanson P.C., Dugan H.A., Plale B..  2017.   Mining lake time series using symbolic representation. Ecological Informatics. 39:10-22.
Rose KC, Winslow LA, Read JS, Read EK, Solomon CT, Adrian R, Hanson PC.  2014.  Improving the precision of lake ecosystem metabolism estimates by identifying predictors of model uncertainty. Limnology & Oceanography Methods. (12):303-312.
Rose KC, Williamson C.E., Kissman CEH, Saros JE.  2015.  Does allochthony in lakes change across an elevation gradient? Ecology. :150605123505009.
Rose KC, Williamson CE, Schladow SG, Winder M, Oris JT.  2009.  Patterns of spatial and temporal variability of transparency in Lake Tahoe, CA/NV. Journal of Geophysical Research. :114.
Rose KC, Williamson CE, Saros JE, Sommaruga R, Fischer JM.  2009.  Differences in UV transparency and thermal structure between alpine and subalpine lakes: implications for organisms. Photochemical & Photobiological Sciences. 8:1244-1256.
Rizk W, Kirillin G, Leppäranta M.  2014.  Basin-scale circulation and heat fluxes in ice-covered lakes. Limnol. Oceanogr. 59(2):455-464.
Rigosi A, Rueda FJ.  2012.  Propagation of uncertainty in ecological models of reservoirs: from physical to population dynamic predictions. Ecological Modelling. 247:199-209.
Rigosi A, Hanson PC, Hamilton DP, Hipsey MR, Rusak JA, Bois J, Sparber K, Chorus I, Watkinson AJ, Qin B et al..  2015.  Determining the probability of cyanobacterial blooms: the application of Bayesian networks in multiple lake systems. Ecological Applications. 25(1):186-199.

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