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2004
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.
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
2006
Viers, JH, Thorne JH, Quinn JF.  2006.  CalJep: A Spatial Distribution Database of CalFlora and Jepson. San Francisco Estuary & Watershed Science. 4(1):1.
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
Schwartz, MW, Thorne JH, Viers JH.  2006.  Biotic homogenization of the California flora in urban and urbanizing regions. BIOLOGICAL CONSERVATION. 127:282--291. Abstract
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, 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
2007
Girvetz, EH, Thorne JH, Jaeger JAG.  2007.  Comment on "Roadless Space of the Conterminous United States". Science. 5854 Abstract
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).
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) .
2008
Harrison, S, Viers JH, Thorne JH, Grace JB.  2008.  Favorable Environments and the Persistence of Naturally Rare Species. Conservation Letters. 1:65-74.
Thorne, JH, Girvetz E, McCoy. MC.  2008.  Report on California state-wide mitigation needs forecasting database.
Girvetz, EH, Thorne JH, Quinn JF, McCoy MC.  2008.  Early Biological Mitigation Needs Assessment: Elkhorn Slough Pilot Project.. Caltrans.
Huber, GP l EH, Thorne JH, Hollander A, Quinn JF, McCoy. MC.  2008.  Early biological mitigation needs assessment: Pleasant Grove pilot project. Caltrans.
In Press
Thorne, JH, Morgan BJ, and J. A K.  In Press.  Vegetation Change over 60 Years in the Central Sierra Nevada. Madroño.
Thorne, JH, Girvetz EH, McCoy. M.  In Press.  Evaluating aggregate terrestrial impacts of road construction projects for advanced regional mitigation.. Environmental Management.
Submitted
Thorne, JH, Viers JH, Price J, Stoms. DM.  Submitted.  Spatial patterns of endemic plants in California. Natural Areas Journal.
Beardsley, K, Thorne JH, Roth NE, McCoy M.  Submitted.  Impact of Rapid Human Population Growth on Biological Resources in the San Joaquin Valley of California. Landscape and Urban Planning.
Thorne, JH, Huber P, Girvetz E, Quinn J, McCoy M.  Submitted.  Integration of regional mitigation assessment and conservation planning.. Ecology and Society.