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Shilling F, Harris R.  2007.  Effectiveness monitoring by California community watershed groups. IMPACT: (American Water Resources Association). 9:21-24.
Shilling F, Girvetz E.  2007.  Barriers to implementing a wildland network. Landscape and Urban Planning. 80:165-172.
Shilling F, Llevanos R, London J.  0.  Marginalization by collaboration: Environmental justice as a third party in and beyond CALFED.
Shilling F, Reed S, Boggs J, Lubell M.  0.  Bio-geographic and social optimization of National Forest recreational trails.
Shook CD, Madison ME, Willett KW, Quinn JF, McCoy MC.  1999.  Applied Geographic Information Systems in Cooperative Natural Resource Projects: A California Example. ESRI International Users Conference.
Springer NP, Garbach K, Guillozet K, Haden VR, Hollander AD, Huber PR, Ingersoll C, Langner M, Lipari G, Mohammadi Y et al..  2015.  Sustainable sourcing of global agricultural raw materials: assessing gaps in key impact and vulnerability issues and indicators. PLoS One.
STOHLGREN TJ, Quinn JF.  1992.  AN ASSESSMENT OF BIOTIC INVENTORIES IN WESTERN UNITED-STATES NATIONAL-PARKS. NATURAL AREAS JOURNAL. 12:145--153. Abstract
STOHLGREN TJ, Quinn JF, Ruggiero M, WAGGONER GS.  1995.  STATUS OF BIOTIC INVENTORIES IN US NATIONAL-PARKS. BIOLOGICAL CONSERVATION. 71:97--106. Abstract
Sze J, London J, Shilling F, Cadeanaso M.  0.  Defining and contesting environmental justice: Socio-natures and the politics of scale in the Delta.
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Thode A, van Wagtendonk J, Miller JD, Quinn JF.  2011.  Quantifying the Fire Regime Distributions for Severity in Yosemite National Park, California, USA. International Journal of Wildland Fire. 20:223-239.
Thorne JH, Viers JH, Price J, Stoms DM.  2009.  Spatial Patterns of Endemic Plants in California. Natural Areas Journal. 29:344-366.
Thorne JH, O Brien J, Forister ML, Shapiro AM.  2006.  Building phenological models from presence/absence data for a butterfly fauna. ECOLOGICAL APPLICATIONS. 16:1842--1853. Abstract
Thorne JH, Morgan BJ, Kennedy JA.  In Press.  Vegetation Change over 60 Years in the Central Sierra Nevada. Madroño.
Thorne JH, McCoy MC, Hollander A, Roth NE, Quinn JF.  2005.  Regional analysis for transportation corridor planning. ICOET 2005.
Thorne J, Bjorkman J, Boynton R, Thrasher S.  2008.  Observed Changes in Vegetation Patterns in California. California Energy Commission’s Second Annual Climate Change Conference.
Thorne JH, Huber PR, Harrison S.  2011.  Exploring tradeoffs among conservation goals in serpentine-rich landscapes. Serpentine: a Model for Evolution and Ecology.
Thorne JH, Huber P, Girvetz E, Quinn J, McCoy M.  2009.  Integration of regional mitigation assessment and conservation planning.. Ecology and Society. 14(1)
Thorne JH, Kennedy JA, Keeler-Wolf T, Quinn JF, Menke J, McCoy M.  2004.  A New Vegetation Map of Napa County Using the Manual of California Vegetation Classification and its Comparison to Other Digital Vegetation Map. Madroño . 51(4):343-363.
Thorne JH, Cameron D, Quinn JF.  2006.  A conservation design for the central coast of California and the evaluation of mountain lion as an umbrella species. NATURAL AREAS JOURNAL. 26:137--148. Abstract
Thorne JH, Girvetz E, McCoy. MC.  2008.  Report on California state-wide mitigation needs forecasting database.
Thorne JH, Girvetz EH, McCoy M.  2007.  A multi-scale and context sensitive state-wide environmental mitigation planning tool for transportation projects in California. Proceedings International Conference on the Environment and Transportation (ICOET).
Thorne JH, Gao SY, Hollander AD, Kennedy JA, McCoy M, Johnston RA, Quinn JF.  2006.  Modeling potential species richness and urban buildout to identify mitigation sites along a California highway. TRANSPORTATION RESEARCH PART D-TRANSPORT AND ENVIRONMENT. 11:277--291. Abstract
Thorne JH, Girvetz EH, McCoy. M.  2009.  Evaluating aggregate terrestrial impacts of road construction projects for advanced regional mitigation.. Environmental Management. 43:936-948.
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Underwood EC, Klausmeyer KR, Cox RL, Busby SM, Morrison SA, Shaw MR.  2009.  Expanding the global protected areas network to save the imperiled mediterranean biome. Conservation Biology. 23:43-52.
Underwood EC, Fisher BL.  2006.  The role of ants in conservation monitoring: If, when and how. Biological Conservation. 132:166-182. Abstract