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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.
Huber PR, Thorne JH, Roth NE, McCoy MC.  2011.  Assessing ecological condition, vulnerability, and restorability of a conservation network under alternative urban growth policies. Natural Areas Journal. 31:12.
Larsen EW, Girvetz EH, Fremier AK.  2006.  Assessing the effects of alternative setback channel constraint scenarios employing a river meander migration model. ENVIRONMENTAL MANAGEMENT. 37:880--897. Abstract
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.
STOHLGREN TJ, Quinn JF.  1992.  AN ASSESSMENT OF BIOTIC INVENTORIES IN WESTERN UNITED-STATES NATIONAL-PARKS. NATURAL AREAS JOURNAL. 12:145--153. Abstract
Williams JN, Hollander AD, O'Geen TA, Thrupp AL, Hanifin R, Steenwerth K, McGourty G, Jackson LE.  2011.  Assessment of carbon in woody plants and soil across a vineyard-woodland landscape. Carbon Balance and Management. 6
Shilling F, Girvetz E.  2007.  Barriers to implementing a wildland network. Landscape and Urban Planning. 80:165-172.
Harrison S, Davies KF, Safford HD, Viers JH.  2006.  Beta diversity and the scale-dependence of the productivity-diversity relationship: a test in the Californian serpentine flora. JOURNAL OF ECOLOGY. 94:110--117. Abstract
Botsford LW, SMITH BD, Quinn JF.  1994.  BIMODALITY IN SIZE DISTRIBUTIONS - THE RED-SEA URCHIN STRONGYLOCENTROTUS-FRANCISCANUS AS AN EXAMPLE. ECOLOGICAL APPLICATIONS. 4:42--50. Abstract
Shilling F, Reed S, Boggs J, Lubell M.  0.  Bio-geographic and social optimization of National Forest recreational trails.
Culman S, Young-Mathews A, Hollander A, Ferris H, Sánchez-Moreno S, O’Geen A, Jackson L.  2010.  Biodiversity is associated with indicators of soil ecosystem functions over a landscape gradient of agricultural intensification. Landscape Ecology. 25:1333–1348.
Schwartz MW, Thorne JH, Viers JH.  2006.  Biotic homogenization of the California flora in urban and urbanizing regions. BIOLOGICAL CONSERVATION. 127:282--291. Abstract
Meynard CN, Quinn JF.  2008.  Bird metacommunities in the temperate forests of South America: direct and indirect effects of vegetation structure, area and climate. Ecology. 89:981-990.
Greenberg JA, Dobrowski SZ, Ramirez CM, and Ustin TJLSL.  2006.  A bottom-up approach to vegetation mapping of the Lake Tahoe Basin using hyperspatial image analysis. Photogrammetric Engineering & Remote Sensing.
Huber PR, Greco SE, Thorne JH.  2010.  Boundaries and baselines make a difference: The effects of spatial and temporal parameters on conservation planning. Professional Geographer. 62:17.
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
Viers JH, Thorne JH, Quinn JF.  2006.  CalJep: A Spatial Distribution Database of CalFlora and Jepson. San Francisco Estuary & Watershed Science. 4(1):1.
Jackson LE, Wheeler SM, Hollander AD, O’Geen AT, Orlove BS, Six J, Sumner DA, Santos-Martin F, Kramer JB, Horwath WR et al..  2011.  Case study on potential agricultural responses to climate change in a California landscape. Climatic Change. 109:407–427.
Meese RJ.  2012.  Cattle egret predation causing reproductive failures of nesting Tricolored Blackbirds.. California Fish and Game. 98:47-50.
Meese RJ.  2013.  Chronic low reproductive success of the colonial Tricolored Blackbird from 2006 to 2011.. Western Birds. 44:98-113.
Harrison S, Viers JH, Quinn JF.  2000.  Climatic and spatial patterns of diversity in the serpentine plants of California. Diversity & Distributions. 6:153-162.
Lubell M, Henry A, McCoy M.  2007.  Collaborative Policy in an Ecology of Games. Midwest Political Science Association.
Girvetz EH, Thorne JH, Jaeger JAG.  2007.  Comment on "Roadless Space of the Conterminous United States". Science. 5854 Abstract
Maynard CN, Howell CA, Quinn JF.  2009.  Comparing alternative systematic conservation planning strategies against a politically-driven conservation plan. Biodiversity and Conservation. 18:3061-3083.
Underwood EC, Ustin SL, Ramirez CM.  2007.  A comparison of spatial and spectral image resolution for mapping invasive plants in coastal California. Journal of Environmental Management . 39(1):63-83. Abstract