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Huber PR, Greco SE, Thorne JH.  2010.  Spatial scale effects on conservation network design: trade-offs and omissions in regional versus local scale planning. Landscape Ecology. 25:13.
Huber PR, Shilling FM, Thorne JH, Greco SE.  2012.  Municipal and regional habitat connectivity planning. Landscape and Urban Planning. 105
Huber PR, Thorne JH, Madison ME.  2010.  Marxan analysis for the Elkhorn Slough watershed: mitigation planning and “ideal” reserves.
Huber PR, Cameron DR, Thorne JH, Frink TM.  2009.  Regional advance mitigation planning: a pilot study integrating multi-agency mitigation needs and actions within a comprehensive ecological framework. International Conference on Ecology and Transportation.
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.
Huber PR, Thorne JH, Siepel N.  2013.  Convergence of green- and blueprints: integrating long-range transportation planning and landscape connectivity. International Conference on Ecology and Transportation.
Huber PR, Girvetz EH, Thorne JH, Hollander A, Quinn JF, McCoy MC.  2008.  Early biological mitigation needs assessment: Pleasant Grove pilot project .
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.
Huber PR, Thorne JH, Williams A, Loeffler R, McCoy MC, Erickson G, Roth NE, Holgiun AJ, Boynton RM, Le NT.  2011.  A statewide Caltrans mitigation needs assessment in support of the Statewide Advance Mitigation Initiative (SAMI). International Conference on Ecology and Transportation.
Huber PR, Shilling FM, Thorne JH, Greco SE, Roth NE.  2010.  Safe Passages and the City of Riverbank: wildlife connectivity in the San Joaquin Valley, California .
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Schmidt EE, Thorne JH, Huber PR, Roth NE, Thompson E, McCoy MC.  2010.  A new method is used to evaluate the strategic value of Fresno County farmland. California Agriculture. 64:6.
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Thorne JH, Huber PR, Harrison S.  2011.  Exploring tradeoffs among conservation goals in serpentine-rich landscapes. Serpentine: a Model for Evolution and Ecology.
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Viers JH, Fremier AK, Hutchinson RA, Quinn JF, Thorne JH, Vaghti MG.  2012.  Multiscale Patterns of Riparian Plant Diversity and Implications for Restoration. Restoration Ecology. 20:160-169.
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Waetjen DP, Thorne JH, Hollander AH, Shapiro AM, Quinn JF.  2010.  The Butterfly Effect: An Approach to Web-Based Scientific Data Distribution and Management with Linkages to Climate Data and the Semantic Web. e-Research Collaboration. :pp.133-151. Abstract