Heinrich, P. L., P. G.  Flikkema, D.  F, B.  EP, and A.  AJ. 2023. Toward cyber-eco systems: networked sensing, inference and control for ecological and agricultural systems.. 397-417 in  Handbook of dynamic data driven applications systems,. Springer, Cham. . Springer, Cham.

Jarvis, K. J., G. J.  Allan, A. J.  Craig, R. K.  Beresic-Perrins, G.  Wimp, C. A.  Gehring, and T. G.  Whitham. 2017. Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones.. Ecology and evolution 7:5909 - 5921.

Jarvis, K. J., G. J.  Allan, A. J.  Craig, R. K.  Beresic-Perrins, G.  Wimp, C. A.  Gehring, and T. G.  Whitham. 2017. Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones.  . Ecology and Evolution 7.

Whitham, T. G., C. A.  Gehring, H. M.  Bothwell, H. F.  Cooper, J. B.  Hull, G. J.  Allan, K. C.  Grady, L.  Markovchick, S. M.  Shuster, J.  Parker, A. E.  Cadmus, D. H.  Ikeda, and R. K.  Bangert. 2017. IN PRESS: Using the Southwest Experimental Garden Array to enhance riparian restoration in response to global change: Identifying and deploying genotypes and populations for current and future environments.  . in  In Riparian research and management: Past, present, future. . Gen. Tech. Rep. RMRS-GTR-inpress Fort Collins U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station.Fort Collins, CO, USA.

Grady, K. C., T. E.  Wood, T. E.  Kolb, E.  Hersch-Green, S. M.  Shuster, C. A.  Gehring, S. C.  Hart, G. J.  Allan, and T. G.  Whitham. 2017. Local biotic adaptation of trees and shrubs to plant neighbors.  . Okios 126.

Andrews, L. V., and C. A.  Gehring. 2017. Root-associated microbes in pinyon pine: Implications for management.  In Symposium Proceedings for Piñon-juniper Habitats: Status and Management for Wildlife. In Symposium Proceedings for Piñon-juniper Habitats: Status and Management for Wildlife USFS.

Evans, L. M., S.  Kaluthota, D. W.  Pearce, G. J.  Allan, K.  Floate, S. B.  Rood, and T. G.  Whitham. 2016. Bud phenology and growth are subject to divergent selection across a latitudinal gradient in Populus angustifolia and impact adaptation across the distributional range and associated arthropods.. Ecology and evolution 6:4565 - 81.

Butterfield, B. J., J.  Bradford, C.  Armas, I.  Prieto, and F. I.  Pugnaire. 2016. Does the stress gradient hypothesis hold water? An assessment of vegetation effects on soil moisture and implications for plant-plant interactions.. Functional Ecology 30:10 - 19.

Zinkgraf, M. S., N.  Meneses, T. G.  Whitham, and G. J.  Allan. 2016. Genetic variation in NIN1 and C/VIF1 genes is significantly associated with Populus angustifolia resistance to a galling herbivore, Pemphigus betae.. Journal of insect physiology 84:50 - 59.

Ikeda, D. H., T. L.  Max, G. J.  Allan, M. K.  Lau, S. M.  Shuster, and T. G.  Whitham. 2016. Genetically informed ecological niche models improve climate change predictions. Global Change Biology.

Clark, J. S., L.  Iverson, C. W.  Woodall, C. D.  Allen, D. M.  Bell, D. C.  Bragg, A. W.  D'Amato, F. W.  Davis, M. H.  Hersh, I.  Ibanez, S. T.  Jackson, S.  Matthews, N.  Pederson, M.  Peters, M. W.  Schwartz, K. M.  Waring, and N. E.  Zimmermann. 2016. The impacts of increasing drought on forest dynamics, structure, and biodiversity in the United States.. Global change biology 22:2329 - 52.

Mau, R. L., C. M.  Liu, M.  Aziz, E.  Schwartz, P.  Dijkstra, J. C.  Marks, L. B.  Price, P.  Keim, and B. A.  Hungate. 2015. Linking soil bacterial biodiversity and soil carbon stability.. The ISME journal 9:1477 - 80.

Grady, K. C., D. C.  Laughlin, S. M.  Ferrier, T. E.  Kolb, S. C.  Hart, G. J.  Allan, and T. G.  Whitham. 2013. Conservative leaf economic traits correlate with fast growth of genotypes of a foundation riparian species near the thermal maximum extent of its geographic range .. Functional Ecology 27:427 - 438.

Compson, Z. G., K. J.  Adams, J. A.  Edwards, J. M.  Maestas, T. G.  Whitham, and J. C.  Marks. 2013. Leaf litter quality affects aquatic insect emergence: contrasting patterns from two foundation trees.. Oecologia 173:507 - 19.

Ferrier, S. M., R. K.  Bangert, E. I.  Hersch-Green, J. K.  Bailey, and G. J.  Allan. 2012. Unique arthropod communities on different host-plant genotypes results in greater arthropod diversity. Arthropod-Plant Interactions 6:187 - 195.

Grady, K. C., S. M.  Ferrier, T. E.  Kolb, S. C.  Hart, G. A.  Allan, and T. G.  Whitham. 2011. Genetic variation in productivity of foundation riparian species at the edge of their distribution: implications for restoration and assisted migration in a warming climate .. Global Change Biology 17:3724 - 3735.

Clark, J. S., P.  Agarwal, D. M.  Bell, P. G.  Flikkema, A.  Gelfand, X.  Nguyen, E.  Ward, and J.  Yang. 2011. Inferential ecosystem models, from network data to prediction.. Ecological applications : a publication of the Ecological Society of America 21:1523 - 36.

Axelsson, E. P., J.  Hjältén, T. G.  Whitham, R.  Julkunen-Tiitto, and G.  Pilate. 2011. Leaf ontogeny interacts with Bt modification to affect innate resistance in GM aspens. Chemoecology 21:161 - 169.

Bailey, J. K., J. A.  Schweitzer, F.  Ubeda, J.  Koricheva, C. J.  LeRoy, M. D.  Madritch, B. J.  Rehill, R. K.  Bangert, D. G.  Fischer, G. J.  Allan, and T. G.  Whitham. 2009. From genes to ecosystems: a synthesis of the effects of plant genetic factors across levels of organization.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 364:1607 - 16.

Woolbright, S. A., S. P.  Difazio, T.  Yin, G. D.  Martinsen, X.  Zhang, G. J.  Allan, T. G.  Whitham, and P.  Keim. 2008. A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree.. Heredity 100:59 - 70.

Whitham, T. G., S. P.  DiFazio, J. A.  Schweitzer, S. M.  Shuster, G. J.  Allan, J. K.  Bailey, and S. A.  Woolbright. 2008. Extending genomics to natural communities and ecosystems.. Science 320:492 - 5.

Bangert, R. K., E. V.  Lonsdorf, G. M.  Wimp, S. M.  Shuster, D.  Fischer, J. A.  Schweitzer, G. J.  Allan, J. K.  Bailey, and T. G.  Whitham. 2008. Genetic structure of a foundation species: scaling community phenotypes from the individual to the region.. Heredity 100:121 - 31.

Evans, L. M., G. J.  Allan, S. M.  Shuster, S. A.  Woolbright, and T. G.  Whitham. 2008. Tree hybridization and genotypic variation drive cryptic speciation of a specialist mite herbivore.. Evolution; international journal of organic evolution 62:3027 - 40.

Flikkema, P. G., P. K.  Agarwal, J. S.  Clark, C.  Ellis, and A.  Gelfand. 2007. From Data Reverence to Data Relevance: Model-Mediated Wireless Sensing of the Physical Environment. 988 - 994 in G.  Albada, Dongarra, J., and Sloot, P. ICCS 2007, 7th International Conference. Springer Berlin/HeidelbergBeijing, China.

Whitham, T. G., J. K.  Bailey, J. A.  Schweitzer, S. M.  Shuster, R. K.  Bangert, C. J.  LeRoy, E. V.  Lonsdorf, G. J.  Allan, S. P.  DiFazio, B. M.  Potts, D. G.  Fischer, C. A.  Gehring, R. L.  Lindroth, J. C.  Marks, S. C.  Hart, G. M.  Wimp, and S. C.  Wooley. 2006. A framework for community and ecosystem genetics: from genes to ecosystems.. Nature reviews. Genetics 7:510 - 23.

Bangert, R. K., G. J.  Allan, R. J.  Turek, G. M.  Wimp, N.  Meneses, G. D.  Martinsen, P.  Keim, and T. G.  Whitham. 2006. From genes to geography: a genetic similarity rule for arthropod community structure at multiple geographic scales.. Molecular ecology 15:4215 - 28.

Flikkema, P. G., P. K.  Agarwal, J. S.  Clark, C.  Ellis, and A.  Gelfand. 2006. Model-Driven Dynamic Control of Embedded Wireless Sensor Networks. 409 - 416 in V.  Alexandrov, van Albada, G., Sloot, P., and Dongarra, J. Computational Science - ICCS 2006, Lecture Notes in Computer Science, 6th International Conference. Springer Berlin/HeidelbergReading, UK.