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Beardsley K, Roth NE, Thorne JH, Huber PR, McCoy MC.  2007.  Environmental Impacts of Urban Growth in California’s San Joaquin Valley. Policy White Paper for the John Muir Institute for the Environment.
Beardsley K, Thorne JH, Roth NE, Gao S, McCoy MC.  2009.  Assessing the influence of rapid urban growth and regional policies on biological resources. Landscape and Urban Planning. 93:172-183.
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Girvetz EH, Thorne JH, Jaeger JAG.  2007.  Comment on "Roadless Space of the Conterminous United States". Science. 5854 Abstract
Girvetz EH, Thorne JH, Quinn JF, McCoy MC.  2008.  Early Biological Mitigation Needs Assessment: Elkhorn Slough Pilot Project.. Caltrans.
Girvetz EH, Thorne JH, Berry AM, Jaeger JAG.  2008.  Integration of landscape fragmentation analysis into regional planning: A statewide multi-scale case study from California, USA. Landscape and Urban Planning. (in press)
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Harrison S, Viers JH, Thorne JH, Grace JB.  2008.  Favorable Environments and the Persistence of Naturally Rare Species. Conservation Letters. 1:65-74.
Huber PR, Roth NE, Beardsley K, Thorne JH, McCoy MC, Meade R.  2007.  Potential impacts of urban growth on an ecological network in the San Joaquin Valley. Association for American Geographer’s (AAG) .
Huber GP l EH, Thorne JH, Hollander A, Quinn JF, McCoy. MC.  2008.  Early biological mitigation needs assessment: Pleasant Grove pilot project. Caltrans.
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Li T, Shilling F, Li F, Thorne JH, Schott H, Boynton R, Berry A.  0.  Fragmentation of China’s landscape by roads and land-use.
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Roth NE, Thorne JH, Johnston RA, Quinn JF, McCoy MC.  2012.  Modeling impacts to agricultural revenue and government service costs from urban growth.. Journal of Agriculture, Food Systems, and Community Development. 2
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Schmidt EE.  2010.  A New Method is Used to Evaluate the Strategic Value of Fresno County Farmland. California Agriculture. 64 Abstract
Schwartz MW, Thorne JH, Viers JH.  2006.  Biotic homogenization of the California flora in urban and urbanizing regions. BIOLOGICAL CONSERVATION. 127:282--291. Abstract
Seo C, Thorne JH, Hannah L, Thuiller W.  2008.  Scale effects in species distribution models – implications for planning under climate change.. Biology Letters.
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Thorne JH, Girvetz E, McCoy. MC.  2008.  Report on California state-wide mitigation needs forecasting database.
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, 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, 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, Girvetz EH, McCoy. M.  2009.  Evaluating aggregate terrestrial impacts of road construction projects for advanced regional mitigation.. Environmental Management. 43:936-948.
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, Viers JH, Price J, Stoms DM.  2009.  Spatial Patterns of Endemic Plants in California. Natural Areas Journal. 29:344-366.
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, Morgan BJ, Kennedy JA.  In Press.  Vegetation Change over 60 Years in the Central Sierra Nevada. Madroño.
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, McCoy MC, Hollander A, Roth NE, Quinn JF.  2005.  Regional analysis for transportation corridor planning. ICOET 2005.
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Vander Zanden MJ, Olden JD, Thorne JH, Mandrak NE.  2004.  Predicting occurrences and impacts of smallmouth bass introductions in north temperate lakes. ECOLOGICAL APPLICATIONS. 14:132--148. Abstract