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Harter T, Lund JR, Darby JL, Fogg GE, Howitt R, Jessoe KK, Pettygrove SG, Quinn JF, Viers JH, Boyle DB et al..  2012.  Addressing Nitrate in California's Drinking Water with a Focus on Tulare Lake Basin and Salinas Valley Groundwater. Report for the State Water Resources Control Board Report to the Legislature.. :78p..
Huber PR, Girvetz EH, Thorne JH, Hollander A, Quinn JF, McCoy MC.  2008.  Early biological mitigation needs assessment: Pleasant Grove pilot project .
Huber PR, Springer NP, Hollander AD, Brodt S, Tomich TP, Quinn JF.  2015.  Indicators of global sustainable sourcing as a set covering problem: an integrated approach to sustainability. Ecosystem Health and Sustainability. 1:1–8. Abstract
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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.
McCoy MC, Quinn JF, Kalman NB.  2002.  Identifying environmental and agricultural values and opportunities for regional planning: a GIS approach. ESRI User Conference Proceedings.
Meynard CN, Quinn JF.  2007.  Predicting species distributions: a critical comparison of the most common statistical models using artificial species.. Journal of Biogeography. 34:1455-1469.
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Pettler A, Erickson G, Quinn JF, Meese RJ, Shilling F.  2007.  An Analytical Framework for Wildlife Crossing Policy in California. ICOET 2007 -- Little Rock, Arkansas.
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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.
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.
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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, McCoy MC, Hollander A, Roth NE, Quinn JF.  2005.  Regional analysis for transportation corridor planning. ICOET 2005.
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Underwood EC, Quinn JF.  2010.  Response of ants and spiders to prescribed fire in oak woodlands of California. Journal of Insect Conservation. 14:359-366.
Underwood EC, Olson D, Hollander AD, Quinn JF.  2014.  Ever-wet tropical forests as biodiversity refuges. Nature Climate Change. 4:740–741.
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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.
Viers JH, Liptzin D, Rosenstock TS, Jensen VB, Hollander AD, McNally A, King AM, Kourakos G, Lopez EM, De La Mora N et al..  2012.  Nitrogen Sources and Loading to Groundwater. Technical Report 2.
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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