Faculty Publications

• Bal, T, Sharik T. 2019. Web content analysis of University forestry and related natural resources landing webpages in the United States in relation to student and faculty diversity.  Journal of Forestry doi:10.1093/jofore/fvz024. Read More
• Bal, T, Sharik T. 2019. Image content analysis of US natural resources-related professional society websites with respect to gender and racial/ethnic diversity.  Journal of Forestry doi:10.1093/jofore.fvs023.  Read More
• Bal, T, Raj, J, Richter, D. 2019. Influence of Chaga ( Inonotus obliquus) treatment of wood in decay tests. Current Research in Environmental & Applied Mycology 9(1): 85-91. Read More
• Cladas, K, Bal, T, Storer, A. 2018. Is success in detection of Agrilus planipennis related to forest edges?  Journal of Applied Entomology 143: 214-224   Read More
• Bal, TL, Storer, AJ, Jurgensen, MF. 2018. Evidence of damage from exotic invasive earthworm activity was highly correlated to sugar maple dieback in the Upper Great Lakes region. Biological Invasions 20 (1): 151-164. Read More
• Bal, TL, Storer, AJ, Jurgensen, MF, Doskey, PV, Amacher, MC, 2015. Nutrient stress predisposes and contributes to sugar maple dieback across its northern range: a review. Forestry 88 (1): 64-83. Read More
• Bal, T.L., 2014. Forest Health Detectives. The American Biology Teacher. 76 (8): 532-537 Read More
• Bal, T.L., Richter, D.L,. Storer, A.J., and Jurgensen, M.F. 2013. The relationship of the Sapstreak Fungus, Ceratocystis virescens, to Sugar Maple Dieback and Decay in North Michigan. American Journal of Plant Science 4(2A): 436-443. Read More
• Evaluation of Sugar Maple Dieback in the Upper Great Lakes Region and Development of a Forest Health Youth Education Program. PhD Dissertation. Michigan Technological University. 2013. Read More

• DeCandia, A. K. Brzeski, E. Heppenheimer, C. Carol, G. Camenisch, P. Wandeler, C. Driscoll, B. vonHoldt. 2019. Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited. Ecology and Evolution. DOI: 10.1002/ece3.4898

• Heppenheimer E. ^*, K. Brzeski*, R. Wooten, W. Waddell, Rutledge, M. Chamberlain, D. Stahler, J. Hinton, B. vonHoldt. 2018. Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast. Genes. 9(12):618. *co-lead & corresponding author.

• Heppenheimer,E., K. Brzeski, J. Hinton, B. Patterson, L. Rutledge, A. DeCandia, T. Wheeldon, S. Fain, P. Hohenlohe, R. Kays, B. White, B. vonHoldt. 2018. High genomic diversity and candidate genes under selection associated with range expansion in eastern coyote ( Canis latrans) populations. Ecology and Evolution. 8(24):12641-12655.

• vonHoldt, B., K. Brzeski, D. Wilcove, L. Rutledge. 2018. Redefining the impact of admixture and genomics in endangered species conservation. Conservation Letters. 11(2): e12371 doi:10.1111/conl.12371

• Heppenheimer E., D. Cosio, K. Brzeski, D. Caudill, M. Chamberlain, J. Hinton, B. vonHoldt. 2018. Demographic history influences spatial patterns of genetic diversity in recently expanded coyote ( Canis latrans) populations. Heredity. 120:183-195. doi:10.1038/s41437-017-0014-5.

• Brzeski, K., M. DeBiasse, D. Rabon, M. Chamberlain, S. Taylor. 2016.Mitochondrial DNA variation in Eastern pre-Columbian canids. Journal of Heredity, 107:287-293.

• Brzeski, K., J. Wolfe., J. Cooper, L. Powell. 2016. Camera sighting of Congo Clawless otter in the midst of rapid development on mainland Equatorial Guinea. IUCN Otter Specialist Group Bulletin. 33 (1), 96-101. 

• Hinton, J., K. Brzeski, D.Rabon, M. Chamberlain. 2016. Effects of anthropogenic mortality on red wolf breeding pairs: Implications for red wolf recovery, Oryx:1-8. doi:10.1017/S0030605315000770

• Crowther, T.W., C.W. Rowe, W.R. Wieder, J.C. Carey, M.B. Machmuller, K.E.O. Todd-Brown, L.B. Snoek, S. Fang, G. Zhou, S.D. Allison, J.M. Blair, S.D. Bridgham, A.J. Burton, et al. 2016. Quantifying global soil C losses in response to warming. Nature 540:104-108. Read More
• Carey, J.C., J. Tang, P.H. Templer, K.D. Kroeger, T.W. Crowther, A.J. Burton, J.S. Dukes, B. Emmett, S. Frey, et al. 2016. Temperature response of soil respiration largely unaltered with experimental warming. Proceedings National Academy of Sciences 113:13797-13802. Read More
• Ebanyenle, E., A.J. Burton, A.J. Storer, D.L. Richter, J.A. Glaeser. 2016. Elevated tropospheric CO2 and O3 may not alter initial wood decomposition rate or wood-decaying fungal community composition of northern hardwoods. International Biodeterioration and Biodegradation 111:74-77. Read More
• Ibanez, I., D. Zak, A.J. Burton, K. Pregtizer. 2016. Chronic nitrogen deposition alters allometric relationships in a dominant tree species: Implications for woody biomass production and ecosystem carbon storage. Ecological Applications 26:913-925. Read More
• Gahagan, A., C.P. Giardina, J.S. King, D. Binkley, K.S. Pregitzer, and A.J. Burton. 2015. Carbon fluxes, storage and harvest removals through 60 years of stand development in red pine plantations and mixed hardwood stands in Northern Michigan, USA. Forest Ecology and Management 337:88-97. Read More
• Frey, S.D., S. Ollinger, K. Nadelhoffer, R. Bowden, E. Brzostek, A. Burton, B.A. Caldwell, S. Crow, C.L. Goodale, A.S. Grandy, A. Finzi, M.G. Kramer, K. Lajtha, J. LeMoine, M. Martin, W.H. McDowell, R. Minocha, J.J. Sadowsky, P.H. Templer, and K. Wickings. 2014. Chronic nitrogen additions suppress decomposition and sequester soil carbon in temperate forests. Biogeochemistry 121:305-316. Read More
• Kaarakka, L., P. Tamminen, A. Saarsalmi, M. Kukkola, H.S. Helmisaari, and A.J. Burton. 2014. Effects of repeated whole-tree harvesting on soil properties and tree growth in a Norway spruce (Picea abies (L.) Karst.) stand. Forest Ecology and Management 313:180-187. Read More
• Talhelm, A.F., K.S. Pregitzer, M.E. Kubiske, D.R. Zak, C.E. Campany, A.J. Burton, R.E. Dickson, G.R. Hendrey, J.G. Isebrands, K.F. Lewin, J. Nagy, and D.F. Karnosky. 2014. Elevated carbon dioxide and ozone alter productivity and carbon storage in northern temperate forests. Global Change Biology 20:2492-2504. Read More
• Jarvi, M.P., and A.J. Burton. 2013. Acclimation and soil moisture constrain sugar maple root respiration in experimentally warmed soil. Tree Physiology 33:949-959. Read More
• Burton, A.J., J.C. Jarvey, M.P, Jarvi, D.R. Zak, and K.S. Pregitzer. 2012. Chronic N deposition alters root respiration-tissue N relationship in northern hardwood forests. Global Change Biology 18:258-266. Read More

• Yordanov YS, Ma C, Strauss SH, Busov VB (2014) Early Bud-Break 1 (EBB1) is a regulator of release from seasonal dormancy in poplar trees. Proc Natl Acad Sci U S A 111: 10001-10006 Read More
• Zawaski, Christine and Victor B. Busov. (2014) Roles of gibberellin catabolism and signaling in growth and physiological response to drought and short-day photoperiods in Populus trees. PLOS ONE, 9 (1), e86217 Read More
• Wei, Hairong, Yordan Yordanov, Tatyana Georgieva, Xiang Li, and Victor Busov (2013) Nitrogen deprivation promotes Populus root growth through global transcriptome reprogramming and activation of hierarchical genetic networks. New Phytol 200:483-497 Read More
• Elias, Ani A., Victor B. Busov, Kevin R. Kosola, Cathleen Ma, Elizabeth Etherington, Olga Shevchenko, Harish Gandhi, David W. Pearce, Stewart B. Rood, and Steven H. Strauss. (2012) Green revolution trees: Semi-dwarfism transgenes modify gibberellins, promote root growth, enhance morphological diversity, and reduce competitiveness in Populus. Plant Physiol 160: 1130-1144 Read More
• Yordanov Yordan, Sharon Regan and Victor Busov (2010) Members of the Lateral Organ Boundaries Domain (LBD) Transcription Factors Family are Involved in Regulation of Secondary Growth in Populus. The Plant Cell. 22: 3662-3677 Read More
• Gou, J., Strauss, S.H., Tsai, C.J., Fang, K., Chen, Y., Jiang, X., and Busov, V.B. (2010) Gibberellins Regulate Lateral Root Formation in Populus through Interactions with Auxin and Other Hormones. Plant Cell 22:623-639. Read More
• Busov VB, Brunner AM, Strauss SH. 2008. Genes for control of plant stature and form. New Phytologist 177: 589-607. 

• Cavaleri MA, Reed SC, Smith K, and Wood TE. (2015) Urgent need for warming experiments in tropical forests. Global Change Biology 21(6):2111-2121.
• Ma R-Y, Zhang J-L, Cavaleri MA, Sterck F, Strijk JS, and Cao K-F. (2015) Convergent evolution towards high net carbon gain efficiency contributes to the shade tolerance of palms (Arecaceae). PLoS ONE, doi:10.1371/journal.pone.0140384.
• Coble AP, and Cavaleri MA. (2015) Light acclimation optimizes leaf functional traits despite height-related constraints in a canopy shading experiment. Oecologia, 177:1131-1143.
• Cavaleri MA, Ostertag R, Cordell S, and Sack L. (2014) Native trees show conservative water use relative to invasive trees: results from a removal experiment in a Hawaiian wet forest. Conservation Physiology, 2(1): cou016. doi:10.1093/conphys/cou016.
• Coble AP, and Cavaleri MA. (2014) Light drives vertical gradients of leaf morphology in a sugar maple (Acer saccharum) forest. Tree Physiology, 34: 146-158.
• Coble AP, Autio A, Cavaleri MA, Binkley D, and Ryan MG. (2014) Converging patterns of vertical variability in leaf morphology and nitrogen across seven Eucalyptus plantations in Brazil and Hawaii, USA. Trees: Structure and Function, 28: 1-15.
• Reed SC, Wood TE, Cavaleri MA. (2012) Tropical forests in a warming world. New Phytologist, 193: 27-29.
• Wood TE, Cavaleri MA, and Reed SC. (2012) Tropical forest carbon balance in a warmer world: a critical review spanning microbial- to ecosystem-scale processes. Biological Reviews, 87: 912-927. 
• Cavaleri MA and Sack L. (2010) Comparative water use of native and invasive plants at multiple scales: a global meta-analysis. Ecology, 91: 2705-2715..
• Cavaleri MA, Oberbauer SF, Clark DB, Clark DA, and Ryan MG. (2010) Height is more important than light in determining leaf morphology in a tropical rain forest. Ecology, 91: 1730–1739. .
• Ryan MG, Cavaleri MA, Almeida de Campi A, Penchel R, Senock RS and Stape JL. (2009) Wood CO2 efflux and foliar respiration for Eucalyptus in Hawaii and Brazil. Tree Physiology, 29: 1213-1222.
• Cavaleri MA, Oberbauer SF, Ryan MG. (2008) Foliar and ecosystem respiration in an oldgrowth tropical rain forest. Plant, Cell and Environment, 31: 473-483.
• Cavaleri MA, Oberbauer SF, Ryan MG (2006) Wood CO2 efflux in a primary tropical rain forest. Global Change Biology, 12: 2442-2458.
• Cavaleri MA, Gilmore DW, Mozaffari M, Rosen CJ, Halbach TR. (2004) Hybrid poplar and forest soil response to municipal and industrial by-products: A greenhouse study. Journal of Environmental Quality, 33: 1055-1061. 

1. Gallego-Sala, A. and others. 2018. Latitudinal limits to the predicted increase of the peatland carbon sink with warming. Nature Climate Change 8(10), p.907. https://doi.org/10.1038/s41558-018-0271-1. 
2. Chimner, R.A., D.J. Cooper, M. Bidwell, A. Culpepper, Kay Zillich, Koren Nydick.  A new method for restoring ditches in peatlands: ditch filling with fiber bales. 2018.  Restoration Ecology. DOI: 10.1111/rec.12817.
3. Lilleskov, E., McCullough ^, K., Hergoualc’h, K., Castillo Torres, D.,  Chimner ^, R.A. , Murdiyarso, D., Kolka, R., Bourgeau-Chavez, L., Hribljan, J., Aguila Pasquel, J., Wayson, C., Warren, M. 2018. Is Indonesian peatland loss a cautionary tale for Peru? A two-country comparison of the magnitude and causes of tropical peatland degradation.  Mitigation and Adaptation Strategies for Global Change.DOI:10.1007/s11027-018-9790-3
4. Sánchez M.E.,  R.A. Chimner, J.A. Hribljan, E.A. Lilleskov, E. Suárez. 2017. Carbon dioxide and methane fluxes in grazed and ungrazed mountain peatlands in the Ecuadorian Andes.  Mires and Peat. 19(20), 1-18; 10.19189/MaP.2017.OMB.277
5. Hribljan J.A.,E Suarez, L. Bourgeau-Chavez, S. Endres,E.A. Lilleskov, S. Chimbolema, C. Wayson, E. Serocki,  R.A. Chimner. 2017. Multi-date, multi-sensor remote sensing reveals high density of carbon-rich mountain peatlands in the páramo of Ecuador.  Global Change Biology. 23:5412–5425. DOI:10.1111/gcb.13807.
6. Hribljan*J.A.,E.S. Kane, and  R.A. Chimner.2017. Implications of altered hydrology for substrate quality and trace gas production in a poor fen peatland.  Soil Science Society of America Journal. DOI:10.2136/sssaj2016.10.0322.
7. Comas X, N. Terry, J.A. Hribljan, E.A. Lilleskov, E. Suarez,  R.A. Chimner, and R.K. Kolka. 2017. Estimating belowground carbon stocks in peatlands of the Ecuadorian páramo using ground penetrating radar (GPR).  Journal of Geophysical Research – Biogeosciences.DOI: 10.1002/2016JG003550.
8. Chimner, R.A.,T.G. Pypker, J.A. Hribljan*, P.A. Moore and J.M. Waddington. 2017. Multi-decadal changes in water table levels alter peatland carbon cycling.   Ecosystems 20:1042–1057.  DOI:10.1007/s10021-016-0092-x.
9. Chimner, R.A.,D.J. Cooper, F.C. Wurster, L. Rochefort. 2017. An overview of peatland restoration in North America, where are we after 25 years.  Restoration Ecology 25:283-292. DOI: 10.1111/rec.12434.
10. Ott*, C.A. and  R.A. Chimner.Long Term Peat Accumulation in Temperate Forested Peatlands ( Thuja occidentalis Swamps) in the Great Lakes Region.2016.  Mires and Peat 18: Art. 01.; 10.19189/MaP.2015.OMB.182.
11. Hribljan J.A. E. Suarez, K. Heckman, E.A. Lilleskov, and  R.A. Chimner.2016. Peatland Carbon Stocks and Accumulation Rates in the Ecuadorian Páramo.   Wetland Ecology and Management 24: 113-127. 

• Dickinson, Y.L., Battaglia, M.A. and Asherin, L.A. (2017) Evaluation of the FVS-CR Diameter Growth Model and Potential Modifications in Structurally-Complex Ponderosa Pine Forests. In: Keyser, C,E., Keyser, T.L. (eds.) Proceeding of the 2017 Forest vegetation simulator (FVS) e-Conference. e-Gen. Tech. Rep. SRS-224. Asheville, NC: U.S. Department of Agriculture Forest 
• Addington, R.N., Aplet, G.H., Battaglia, M.A., Briggs, J.S., Brown, P.M., Cheng, T.S., Dickinson, Y., Feinstein, J.A., Fornwalt, P.J., Gannon, B., Julian, C., Pelz, K.A., Regan, C.M., Thinnes, J., Truex, R., Underhill, J. and Wolk, B. (2017) Principles and Practices for the Restoration of Ponderosa Pine and Dry Mixed-Conifer Forests of the Colorado Front Range . RMRS General Technical Report 373, US Forest Service. 
• Tinkham, W.T., Dickinson, Y., Hoffman, C.M., Battaglia, M.A., Ex, S., Smith, F. and Underhill, J.  (2017) Visualization guide to heterogeneous forest structures following treatment in the southern Rocky Mountains.   RMRS General Technical Report 365, US Forest Service.
• Dickinson, Y.L. and Cadry, J.* (2017) Evaluation of tree designation methods for implementing spatially heterogeneous restoration: a mixed methods study.  Journal of Sustainable Forestry 36(1):47-64
• Gauthier, R.* and Dickinson, Y. (2016) The effect of deer browse on a northern hardwood forest in Baraga County, MI. Partners News, April 2016.  Partners in Forestry Landowner Cooperative. Conover, WI.
• Vakili, E.*, Hoffman, C. M., Keane, R. E., Tinkham, W. T., & Dickinson, Y. (2016). Spatial variability of surface fuels in treated and untreated ponderosa pine forests of the southern Rocky Mountains. International Journal of Wildland Fire 25(11): 1156-1168
• Dickinson, Y.L., Giles, E.*, Pelz, K.* and Howie, J.* (2016) Have we been successful? Monitoring horizontal forest complexity for forest restoration projects.  Restoration Ecology 24(1): 8-17
• Dickinson, Y. (2014) Landscape restoration of a forest with a historically mixed-severity fire regime: What was the historical landscape pattern of openings and canopy? Forest Ecology and Management 331:264-271
• Underhill, J., Dickinson, Y.L., Rudney, A. and Thinnes, J. (2014) Silviculture of the Colorado Forest Restoration Initiative. Journal of Forestry 112(5):484-493Dickinson, Y.L. and Giles, E. (2014) Monitoring landscape-scale forest heterogeneity: A protocol. CFRI-TB-1404. Colorado Forest Restoration Institute, Ft Collins, CO. 24p.
• Dickinson, Y.L. and the Front Range Roundtable Spatial Heterogeneity Subgroup. (2014) Stand- and Landscape-Scale Desirable Forest Structures for a Restored Front Range. Colorado Forest Restoration Institute, Colorado State University, Technical Brief CFRI-TB-1402, Fort Collins, CO. 18 p.
• Dickinson, Y.L. Zenner, E.K., and Miller, D.A. (2014) Examining the effect of diverse management strategies on landscape scale patterns of forest structure in Pennsylvania using novel remote sensing techniques. Canadian Journal of Forest Research 44: 301-312
• Pelz, K.A. and Dickinson, Y.L. (2014) Monitoring forest cover spatial patterns with aerial imagery: A tutorial. CFRI-TB-1401. Colorado Forest Restoration Institute, Ft Collins, CO
• Zenner, E.K., Dickinson, Y.L. and Peck, J. E. (2013) Recovery of forest structure and composition to harvesting in different strata of mixed even-aged central Appalachian hardwoods. Annals of Forest Science 70(2): 151-159
• Young, N., Reeder, C., Addington, R., Dickinson, Y., Evangelista, P. and Cheng, T. (2013) Colorado Front Range Collaborative Forest Landscape Restoration Project: 2011-2012 Pre- and post-treatment stand structure analyses for the Pike and San Isabel and Arapaho and Roosevelt National Forests. Colorado Forest Restoration Institute, Ft Collins, CO. 
• Dickinson, Y. L. and Norton, D. A. (2011) Divergent fine-scale spatial patterns in New Zealand’s short tussock grasslands. New Zealand Journal of Ecology 35(1): 76-82
• Dickinson, Y. L. and Zenner, E. K. (2010) Allometric equations for the aboveground biomass of selected common eastern hardwood understory species. Northern Journal of Applied Forestry 27(4): 160-165
• Norton, D.A., Dickinson, Y. and Van Leuween, M. (2007) Ecology of a Ranunculus lyallii population at its eastern distributional limit in Canterbury. New Zealand Journal of Botany 45(1):81-85
• Miller, R.M., Dickinson, Y. and A. Reid. (2005) Maori Connections to Forestry in Feary, S. (ed.) Forestry for Indigenous Peoples: Learning from Experiences. Fenner School of Environment & Society, ANU College of Science, p. 13-22 

• Haskell, D. D.J. Flaspohler, C. Webster, and M. Meyer. 2010 (accepted, in press). Variation in soil temperature, moisture, and plant growth with the addition of down woody material on lakeshore restoration sites. Restoration Ecology.
• Webster, C.R., D.J. Flaspohler, R.D. Jackson, T. Meehan, C. Gratton. 2010 (accepted, in press). Diversity, productivity and landscape-level effects of grasslands managed for biomass production. Biofuels.
• Ford, M. and D. Flaspohler. 2010 (accepted, in press). Scale-dependent response by breeding songbirds to residential development along Lake Superior. Wilson Bulletin of Ornithology.
• Flaspohler, D., C. Giardina, G. Asner, P. Hart, J. Price, C. Ka’apu, and X. Castaneda. 2010. Long-term effects of fragmentation and fragment properties on bird species richness in Hawaiian forests. Biological Conservation 143:280-288.
• Fargione, J.E., T.R. Cooper, D.J. Flaspohler, J. Hill, C.L. Lehman, T. McCoy, S. McLeod, E. J. Nelson, K. S. Oberhauser, and D. Tilman. 2009. Bioenergy and wildlife: Threats and opportunities for grassland conservation. BioScience 59(9):767-778.
• Holmes, S., C. Webster, D. Flaspohler and R. Froese. 2009. Death and Taxus: the cost of high palatability in an era of population decline. Canadian Journal of Forest Research 39:1366-1374.
• Corace, R.G., III, D.J. Flaspohler, L.M. Shartell. 2009. Geographic patterns in openland cover and hayfield mowing in the Upper Great Lakes region: implications for grassland bird conservation. Landscape Ecology 24:309-324. 

• Banskota, A., N. Kayastha, M.J. Falkowski, M.A. Wulder, R.E. Froese and J.C. White. 2015. Forest monitoring using Landsat time-series data – A review. Canadian Journal of Remote Sensing 40:362-384. Read More
• Vance, E.D., W.M. Aust, R.E. Froese, R.B. Harrison, L.A. Morris and B.D. Strahm. 2014. Biomass harvesting and soil productivity: is the science meeting our policy needs? Soil Science Society of America Journal 78:S95-S104.
• Pond, N.C., R.E. Froese, R.K. Deo and M.J. Falkowksi. 2014. Multiscale validation of an operational model of forest inventory attributes developed with constrained remote sensing data. Canadian Journal of Remote Sensing 40:51-67. Read More
• Pond, N.C., R.E. Froese and L.M. Nagel. 2014. Sustainability of the selection system in northern hardwood forests. Forest Science 60(2):374:381. Read More
• Pond, N.C. and R.E. Froese. 2014. Evaluating published approaches for modelling diameter at breast height from stump dimensions. Forestry 87(5):683-696. Read More
• Brosofske, K.D., R.E. Froese, M.J. Falkowski and A. Banskota. 2014. A review of methods for mapping and prediction of inventory attributes for operational forest management. Forest Science 60(4):733-756. Read More
• Witt, J.C., C.R. Webster, R.E. Froese, T.D. Drummer and J.A. Vucetich. 2012. Scale-dependent drivers of ungulate patch use along a temporal and spatial gradient of snow depth. Canadian Journal of Zoology. 90: 972-83. Read More
• Barnes, D., R.E. Froese, R.G. Mannes and B. Warner. 2011. Combined sustainable biomass feedstock combustion, CO2/EOR, and saline reservoir geological carbon sequestration in Northern Lower Michigan, USA: towards negative CO2 emissions. Energy Procedia 4:2955-2962. Read More
• Froese, R.E., D.R. Shonnard, C.A. Miller, K.P. Koers and D.M. Johnson. 2010. Greenhouse gas emissions from coal-fired power plants in the US Great Lakes States. Biomass & Bioenergy 34(3): 251-262. Read More
• Pokharel, B and R.E. Froese. 2009. Representing site productivity in the basal area increment model for FVS-Ontario. Forest Ecology and Management 258: 657-666.
• Holmes, S.A., Webster, C.R., Flaspohler, D.J., and R.E. Froese. 2009. Death and Taxus: the cost of high palatability in an era of population decline. Canadian Journal of Forest Research 39: 1366-1374.
• Johnson, D.M, R.E. Froese, J. Waterstraut, A. Martin-Garcia J.H. Whitmarsh and C.A. Miller. 2009. Business viability of biomass co-firing and gasification for electricity generation. International Journal of Environmental Engineering 1: 405-431.
• Webster, C.R., J.H. Rock, R.E. Froese and M.A. Jenkins. 2008. Drought-herbivory interaction disrupts competitive displacement of native plants by Microstegium vimineum, 10 year results. Oecologia 157: 497-508.
• Pokharel, B. and R.E. Froese. 2008. Evaluating alternative implementations of the Lake States FVS diameter increment model. Forest Ecology and Management 255(5-6): 1759-1771.
• Froese, R.E. and A.P. Robinson. 2007. A validation and evaluation of the Prognosis individual-tree basal area increment model. Canadian Journal of Forest Research 37: 1438-1449.
• Robinson, A.P. and R.E. Froese. 2004. Model validation using equivalence tests. Ecological Modelling 176: 349-358. 

• Banerjee*, A., K.E. Halvorsen, A. Eastmond-Spencer, and S.R. Sweitz. 2017. Sustainable development for whom and how? Exploring the gaps between popular discourses and ground reality using the Mexican Jatropha biodiesel case. Environmental Management 59:912-923.
• Banerjee*, A., C. Schelly, and K.E. Halvorsen. 2017. Understanding public perceptions of wood-based electricity production in Wisconsin, United States: Place-based dynamics and social representations. Environmental Sociology Online First. DOI 10.1080/23251042.2016.1272181. 
• Halvorsen, K.E., J.L. Knowlton, A.S. Mayer, C.C. Phifer, T. Martins, E.C. Pischke*, T.S. Propato, C. Garcia, M. Chiappe, A. Eastmond, J. Licata, M. Kuhlberg, R. Medeiros, V. Picasso, G. Mendez, P. Primo, A. Frado, S. Veron, J. Dunn. 2016. Assessing the Success of an International, Interdisciplinary Energy-related Research Project. Journal of Environmental Science and Studies. 6(2)313-323.
• Norris, P., M. O’Rourke, A. Mayer, and K.E. Halvorsen. 2016. Doubling Down: Transdisciplinary Research Team Formation as a Wicked Problem. Invited Manuscript for Special Issue\Wicked Problems. Landscape and Urban Planning. 151(7).
• Solomon Barry D., Aparajita Banerjee*, Alberto Acevedo, Kathleen E. Halvorsen, and Amarella Eastmond. 2015. Policies for the Sustainable Development of Biofuels in Pan America: A Review and Synthesis of Five Countries. Special Issue of Environmental Management on Bioenergy across the Americas. 56(6)1276-1294.
• NRC-NAS Committee on Economic and Environmental Impacts of Increasing Biofuels Production (Lave, L.B. (chair), I.C. Burke (co-chair), W.E. Tyner (co-chair), V.H. Dale, K.E. Halvorsen, J.D. Hill, S.R. Kaffka, K.C. Klasing, S.J. McGovern, J.A. Miranowski, A. Patrinos, J.L. Schnoor, D.R. Schweikhardt, T.L. Selfa, B.L. Sohngen, and J.A. Soria). 2011. Renewable Fuel Standard: Potential Economic and Environmental Effects of U.S. Biofuel Policy. Natural Research Council of the National Academies.  

• Auer, M.T., Auer, N.A., Barkdoll, B.B., Bornhorst, T.J., Brooks, C., Dempsey, D., Doskey, P.V., Green, S.A., Hyslop, M.D., Kerfoot, W.K., Mayer, A.S., Perlinger, J.A., Shuchman, R., Urban, N.R. and Watkins, Jr., D.W. 2012. The Great Lakes: Foundations of Physics, Hydrology, Water Chemistry, and Biodiversity. In, J. Schnoor (ed.), Water Quality and Sustainability, Elsevier Publishers, London.
• Auer, M.T., Auer, N.A., Barkdoll, B.B., Bornhorst, T.J., Brooks, C., Dempsey, D., Doskey, P.V., Green, S.A., Hyslop, M.D., Kerfoot, W.K., Mayer, A.S., Perlinger, J.A., Shuchman, R., Urban, N.R. and Watkins, Jr., D.W. 2012. The Great Lakes: Nutrients, Sediments, Persistent Pollutants, and Policy Perspectives for a Sustainable Future. In, J. Schnoor (ed.), Water Quality and Sustainability, Elsevier Publishers, London.
• Hyslop, M.D., A.J. Storer, S. Brodeur-Campbell and J. Metzger. 2009. Michigan Ash Monitoring Plot System Upper Peninsula Plot Atlas. School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI.
• Storer, A.J., M.D. Hyslop, N.D. Windmuller, J.C. Witter, J. Stoyenoff. 2009. Southeastern Michigan Recreation Site Ash Survey Maps. School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI.
• Hyslop, M.D., A.J. Storer and J. Oisten. 2009. Upper Peninsula Recreation Site Ash Survey Maps. School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI.
• Storer A.J., M.F. Jurgensen, A.C. Risch, J. Delisle and M.D. Hyslop. 2008. The fate of an intentional introduction of Formica lugubris to North America from Europe. Journal of Applied Entomology 2008 132:4 276.
• Risch, A.C., M.F. Jurgensen, A.J. Storer, M.D. Hyslop and M. Schutz. 2008. Abundance and distribution of organic mound-building ants of the Formica rufa-group in Yellowstone National Park. Journal of Applied Entomology 2008 132:4 326.
• Froese, R.E., M.D. Hyslop, C.A. Miller, B. Garmon, H. McDiarmid, Jr., A. Shaw, L. Leefers, M. Lorenzo, S. Brown and M. Shy. 2007. Large-tract Forestland Ownership Change: Land Use, Conservation, and Prosperity in Michigan's Upper Peninsula. National Wildlife Federation, Ann Arbor, MI. 

• Shashank K. Pandey, Nookaraju Akula, Takeshi Fujino, Sivakumar Pattathil, and Chandrashekhar P. Joshi* (2016) Virus Induced Gene Silencing (VIGS) Mediated Functional Characterization of Two Genes Involved in Lignocellulosic Secondary Cell Wall Formation. Plant Cell Reports, 35:2353-2367.
• Puranik Swati, Kavitha S. Kumar, Oliver Gailing and Chandrashekhar P. Joshi* (2014) Modifying plant cell walls for bioenergy production. CAB Reviews 9, 017, pp 1-10.
• Nookaraju Akula, Shashank K. Pandey, Takeshi Fujino, Ju Young Kim, Mi Chung Suh, and Chandrashekhar P. Joshi* (2014) Enhanced Accumulation of Fatty Acids and Triacylglycerols in Transgenic Tobacco Stems for Enhanced Bioenergy Production. Plant Cell Reports 33 (7) 1041-1052.
• Sera Jung, Dae-Seok Lee, Yeon-Ok Kim, Chandrashekhar P. Joshi, and Hyeun-Jong Bae (2013) Improved recombinant cellulase expression in chloroplast of tobacco through promoter engineering and 5′ amplification promoting sequence. Plant Molecular Biology 83: 317–328. Published online in June 2013. DOI 10.1007/s11103-013-0088-2.
• Nookaraju A, Pandey SP, Bae HJ and Joshi CP* (2013) Designing cell walls for better bioenergy production. Molecular Plant 6 (1):8-10. doi: 10.1093/mp/sss111 First published online: October 5, 2012.
• Liu Y, Xu F, Gou J, Al-Haddad J, Telewski FW, Bae HJ and C. P. Joshi* (2012) Importance of Two Consecutive Methionines at the N-terminus of a Cellulose Synthase (PtdCesA8) for Normal Wood Cellulose Synthesis in Transgenic Aspen. Tree Physiology 32(11): 1403-1412 first published online October 17, 2012
• Chandrashekhar P. Joshi*, Shivegowda Thammannagowda, Takeshi Fujino, Jiqing Gou, Utku Avci, Candace H. Haigler, Lisa M. McDonnell, Shawn D. Mansfield, Bemnet Menghesa, Nicholas C. Carpita, Darby Harris, Seth DeBolt and Gary F. Peter (2011) Perturbation of wood cellulose synthesis causes pleiotropic effects in transgenic aspen. Molecular Plant 4(2) 331-345.
• Zhu X, Pattahil S, Mazumdar K, Brehm A, Hahn MG. Dinesh-Kumar SP and C. P. Joshi* (2010) Virus-induced gene silencing offers a functional genomics platform for studying plant cell wall formation. Molecular Plant 3 (5): 818-833.
• Fuyu Xu and Chandrashekhar P. Joshi* (2010) Overexpression of Aspen Sucrose Synthase Gene Promotes Growth and Development of Transgenic Arabidopsis Plants. Advances in Biosciences and Biotechnology 1: 426-438.
• Manoj Kumar, Shivegowda Thammannagowda, Vincent Bulone, Vincent Chiang, Kyung-Hwan Han, Chandrashekhar P. Joshi, Shawn D. Mansfield, Ewa Mellerowicz, Björn Sundberg, Tuula Teeri, and Brian E. Ellis. An update on the nomenclature for the cellulose synthases genes from Populus. Trends in Plant Science 14(5):248-254, 2009.
• Shanfa Lu, Laigeng Li, Xiaoping Yi, Chandrashekhar P. Joshi, and Vincent L. Chiang: Differential expression of three eucalyptus secondary cell wall- related cellulose synthase genes in response to tension stress. Journal of Experimental Botany 59: 681-695, 2008.
• (Invited presentation) C.P. Joshi: Genetic engineering of poplars for biofuel production via altered synthesis of cellulose. Presented at Tree Biotechnology meeting at Whistler, BC, Canada during June 28-July 2, 2009.
• C. P. Joshi, Brunner A, Busov V, Meilan R, Thammanagowda S, Tsai C.: Poplars. In: Compendium of transgenic crop plants: Transgenic forest tree species. C. Kole and T. Hall (Eds). Wiley-Blackwell Publishing, Oxford, UK. PP 1-34. 2008.
• C.P. Joshi* and S.D. Mansfield: The cellulose paradox: simple molecule, complex biosynthesis. Current Opinion in Plant Biology. 10: 220-226, 2007.

• Page-Dumroese, D.S., M.F. Jurgensen, and T. Terry. 2010. Maintaining Soil Productivity during Forest or Biomass-to-Energy Thinning Harvests in the Western United States. Western Journal of Applied Forestry 25: 5-10.
• Kilpeläinen, J., L. Finér, S. Neuvonen, P. Niemelä, T. Domisch, A.C. Risch, M.F. Jurgensen, M. Ohashi, L. Sundström. 2009. Does the mutualism between wood ants (Formica rufa group) and Cinara aphids affect Norway spruce growth? Forest Ecology and Management 257: 238–243.
• Storer, A.J., M.F. Jurgensen, A.C. Risch, J. Delisle, and M.D. Hyslop. 2008. The fate of an intentional introduction of Formica lugubris to North America from Europe. Journal of Applied Entomology 132: 276-280.
• Tarpey, R.A., M.F. Jurgensen, B.J. Palik, and R. K. Kolka. 2008. The long-term effects of silvicultural thinning and partial cutting on soil compaction in red pine ( Pinus resinosa Ait.) and northern hardwood stands in the northern Great Lakes Region of the United States. Canadian Journal of Soil Science 88: 849-857.
• Page-Dumroese, D.S., Dumroese, R.K., Jurgensen, M.F., Abbott, A., Hensiek, J.J. 2008. Effect of nursery storage and site preparation techniques on field performance of high-elevation Pinus contorta seedlings. Forest Ecology and Management 256: 2065–2072.
• Risch, A.C., M.F. Jurgensen, D.S. Page-Dumroese, O. Wildi, and, M. Schutz. 2008. Long-term development of above- and below-ground carbon stocks following land-use change in subalpine ecosystems of the Swiss National Park. Canadian Journal of Forest Research 38: 1590 – 1602.
• Jurgensen, M.F., L. Finér, T. Domisch, J. Kilpeläinen, P. Punttila, M. Ohashi, P. Niemelä, L. Sundström, S. Neuvonen, and A.C. Risch. 2008. Organic mound-building ants: their impact on soil properties in temperate and boreal forests. Journal of Applied Entomology 132: 266-275. 

Herndon EM, Kinsman‐Costello L, Duroe KA, Mills J, Kane ES, Sebestyen SD, Thompson AA, Wullschleger SD. 2019. Iron (oxyhydr)oxides serve as phosphate traps in tundra and boreal peat soils. Journal of Geophysical Research- Biogeosciences. doi.org/10.1029/2018JG004776.

*McPartland MY, Kane ES, Falkowski MJ, Kolka R, Turetsky MR, Palik B, Montgomery RA. 2019. The response of boreal peatland community composition and NDVI to hydrologic change, warming, and elevated carbon dioxide. Global Change Biology, DOI: 10.1111/gcb.14465.

Marcarelli AM, *Coble AS, *Meingast KM, Kane ES, Brooks C, Buffam I, Green S, Huckins C, Toczydlowski D, Stottlemyer R. 2018. Of small streams and Great Lakes: integrating tributaries to understand the ecology and biogeochemistry of Lake Superior. Journal of the American Water Resources Association, 1-17, DOI: 10.1111/1752-1688.12695.

*Richard R, Potvin LR, Kane ES, Handler S, Smith P, Peterson D. 2018. Biochar and wood ash amendments for forestry in the Lake States: field report and initial results. Journal of Forestry, 116(3):222–227.

*Houle GP, Kane ES, Kasischke ES, *Gibson CM, Turetsky MR. 2018. Recovery of carbon pools a decade after wildfire in black spruce forests of interior Alaska: effects of soil texture and landscape position. Canadian Journal of Forest Research, 48(1): 1-10.

*Mosier SL, Kane ES, Richter DL, Lilleskov EA, Jurgensen MF, Burton AJ, Resh SC. 2017. Interactive effects of climate change and fungal communities on wood-derived carbon in forest soils. Soil Biology and Biochemistry, 115: 297-309.

*Hribljan JA, Kane ES, Chimner RA. 2017. Implications of Altered Hydrology for Substrate Quality and Trace Gas Production in a Poor Fen Peatland. Soil Science Society of America Journal, 81(3): 633-646.

Haynes KM, Kane ES, Potvin L, Lilleskov E, Kolka RK, Mitchell CPJ. 2017. Mobility and transport of mercury and methylmercury in peat as a function of changes in water table regime and plant functional groups, Global Biogeochem. Cycles, 31, doi:10.1002/2016GB005471.

*Wiedermann M, Kane ES, Potvin LR, Lilleskov E. 2017. Interactive plant functional group and water table effects on decomposition and extracellular enzyme activity in Sphagnum peatlands. Soil Biology and Biochemistry, 108: 1-8.

Olefeltd D, Euskirchen SE, Harden J, Kane ES, McGuire AD, Waldrop M, Turetsky MR. 2017. Greenhouse gas fluxes and their cumulative response to inter-annual variability and experimental manipulation of the water table position in a boreal fen. Global Change Biology, DOI: 10.1111/gcb.13612.

• Naidoo S, Christie N , AcostaJ J, Mphahlele M, Payn K, Myburg AA,  Külheim C(2018) Terpenes associated with resistance against the gall wasp,  Leptocybeinvasa, in  Eucalyptus grandis.  Plant, Cell & Environment  In print [ Jo urnal impact factor:6.17]
• Hsieh J-F, Chuah A, Patel H, Sandhu K, Foley WJ,  Külheim C(2018) Transcriptome profiling of resistant and susceptible  Melaleucaquinquenervia reveals defense mechanisms against the exotic pathogen myrtle rust( Austropucciniapsidii).  Phytopathology:108 :495-509 [ Journ al impact factor:2.90]
• Tobias PA, Guest DI,  Külheim C, Park RF(2018) Identification of candidate genes involved in resistance to  Austropucciniapsidii(myrtlerust) in  Sy zygiumluehmannii(riberry).  Phytopathology:108 :627-640 [ Journ al impact factor:2.90]
• Ranjard L,Wong TKF,  Külh e im  C, Rodrigo AG, Ragg NLC, Dunphy BJ(2018) Complete mitochondrial genome of the green-lipped mussel,  Pernacanaliculus(Mollusca:Mytiloidea), from long nanoporesequencing reads.  Mitochondrial DNA Part B: Resources 3 :175-176
• Padovan A, Keszei A, Hassan Y, Krause ST, Köllner TG, Degenhardt J, Gershenzon J,  Külheim C, Foley WJ(2017) Fourterpenesynthases contribute to the generation of different chemotypes in teatree( Melaleucaalternifolia).  BMC Plant Biology 17 :160 [ Journ al impact factor:3.96;citations:1]
• Bustos-Segura C, Padovan A, Kainer D, Foley WJ,  Külheim C(2017) Transcriptome analysis of terpene chemotypes of  Melaleucaalternifolia across different tissues.  Plant,Cell & Environment  DOI:10.1111/pce.13048 [ Journ al impact factor:6.17;citations:1]
• PadovanA,WebbH,MazenekR,GraylingP,FoleyWJ, KülheimC(2017)Associationgeneticsofessentialoiltraitsin Eucalyptusloxophleba:explainingvariationinoilyield. MolecularBreeding37: 73[ Journ alimpactfactor:2.11]
• Bustos-Segura C, Dillon S, Keszei A, Foley WJ,  KülheimC(2017) Intraspecific diversity of terpenes of  Eucalyptuscamaldulensis at a continental scale. Australian Journal of Botany 65: 257-269[ Journ al impact  factor:1.87;citations:1]
• Tobias PA, Christie N, Naidoo S,  Külheim C(2017) Identification of the  Eucalyptus grandis chitinasegene family and expression characterization under different biotic stress challenges. Tree Physiology37: 565-582 [ Journ al impact factor:3.66;citations:1]
• Kainer D, Bush D, Foley WJ,  Külheim C(2017) Components of oil yield in a commercial plantation of  Eucalyptus polybractea(bluemalee). Industrial Crops and Products 102: 32-44[ Journ al impact factor:3.45;citations: 2]

• Augilar, F.X. and M.C. Kelly. 2019. US family forest management coupling natural and human systems: Role of markets and public policy instruments. Landscape and Urban Planning. Read More
• Kelly, M.C., R.H. Germain, and S. Bick. 2017 Impacts of forestry best management practices on logging costs and productivity in the Northeast U.S.A. Journal of Forestry. 115(6): 503-512. Read More
• Kelly, M.C., R.H. Germain, and S.A. Mack. 2016. Forest conservation programs and the landowners who prefer them: Profiling family forest owners in the New York City Watershed. Land Use Policy. 50 (17-28). Read More
• Kelly, M.C. and R.H. Germain. 2016. Is it efficient to single-handedly run a multi-machine harvesting operation? A case study from the Northeast United States. International Journal of Forest Engineering. 27(3): 140-150. Read More
• Germain, R.H., Bick, S., Kelly, M.C., Benjamin, J. and W. Ferrand. 2016. A case study of three high-performing contract loggers with distinct harvest systems: Are they thriving, striving or just surviving? Forest Products Journal 66(1/2):97–105. Read More
• Kelly, M.C., R.H. Germain, and S.V. Stehman. 2015. Family forest owner preferences for forest conservation programs: A New York case study. Forest Science. 61(3):597-603. Read More

US family forest management coupling natural and human systems: Role of markets and public policy instruments

• Robinson, S.C., Laks, P.E. and Richter, D.L. 2011. Stimulating Spalting in Sugar Maple Using Sub-lethal Doses of Copper. European Journal of Wood and Wood Products 69(4): 527-532.
• G.M. Larkin, P.E. Laks, M. Mankowski, D. Schubert, N. Miller. 2010. Zinc-Boron-Silicate Wood Preservative Systems. Proceedings of the AWPA Annual Conference, pp.278-286.
• P.E. Laks, D.L. Richter, G.M. Larkin, J.O. Eskola. 2010. A Survey of the Biological Resistance of Commercial WPC Decking. Proceedings of the 10th Pacific Rim Bio-Based Composites Symposium, pp. 193-201.
• Robinson, S.C., Laks, P.E. 2010. The Effects of Sub-threshold Loadings of Tebuconazole, DDAC and Boric Acid on Wood Decay by Postia placenta. Holzforschung 64(4):537-543.
• P.E. Laks, P. I. Morris, G.M. Larkin, and J.K. Ingram. 2008. Field Tests of naturally Durable North American Wood Species. International Research Group on Wood Preservation Doc. IRG/WP 08-10675. 

• Thistle, J. and N. Langston. 2015. “Entangled histories: Iron ore mining in Canada and the United States. ” Extractive Industries and Society Pre-print publication 14 July 2015; 10.1016/j.exis.2015.06.00 Read More
• Mårald, E., N. Langston, A. Stens, and J. Moen. 2015. “Changing ideas in forestry: a comparison of concepts in Swedish and American forestry journals during the early 20th and 21st centuries.” Ambio. Read More
• Steen-Adams, M. M., Langston, N., Adams, M. D., & Mladenoff, D. J. 2015. “Historical framework to explain long-term coupled human and natural system feedbacks: application to a multiple-ownership forest landscape in the northern Great Lakes region, USA.” Ecology and Society, 20(1). Read More
• Nancy Langston. 2013. Mining the Boreal North. American Scientist. April
• Nancy Langston. 2010. Toxic Bodies: Hormone Disruptors and the Legacy of DES. New Haven: Yale University Press. Read More
• Langston, N. 2015. “Thinking Like A Microbe: Borders and Environmental History.” Canadian Historical Review. 95(4): 592-603 Read More
• Michelle Steen-Adams, David J. Mladenoff, Nancy E. Langston, Feng Liu, and Jun Zhu. 2011. “Influence of Biophysical Factors and Differences in Ojibwe Reservation Versus Euro-American Social Histories on Forest Landscape Change in Northern Wisconsin, USA.” Landscape Ecology 26 (8) (August 21): 1165-1178. Read More
• Michelle Steen-Adams, N. Langston, and D. J. Mladenoff. 2010. “Logging the Great Lakes Indian Reservations: The Case of the Bad River Band of Ojibwe.” American Indian Culture and Research Journal 34: 41-66. Read More

• Andrew, C. J., Lilleskov, E. A. (2009) Productivity and community structure of ectomycorrhizal fungal sporocarps under increased atmospheric CO2 and O3, Ecology Letters, 12, 813-822, Published.
• Lilleskov, E. A., Bruns, T. D., Dawson, T. E., Camacho, F. J. (2009) Water sources and controls on water-loss rates of epigeous ectomycorrhizal fungal sporocarps during summer drought, New Phytologist, 182, 483-494, Published.
• Lilleskov, E. A., Mattson, W. J, Storer, A. J. (2008) Divergent biogeography of native and introduced soil macroinvertebrates in North America north of Mexico, Diversity and Distributions, 14, 893-904, Published.
• Lilleskov, E. A., Wargo, P. M, Vogt, K. M., Vogt, D. J. (2008) Mycorrhizal fungal community relationship to root nitrogen concentration over a regional atmospheric nitrogen deposition gradient in the northeastern USA, Canadian Journal of Forest Research, 38, 1260-1266, Published.
• Karberg, N. J., Lilleskov, E. A. (2008) White-tailed deer (Odocoileus virginianus) fecal pellet decomposition is accelerated by the invasive earthworm Lumbricus terrestris, Biological Invasions, 11, 761-767, Published.
• van Diepen, L.T.A, Lilleskov, E. A., Pregitzer, K. S., Miller, R. M. (2007) Decline of arbuscular mycorrhizal fungi in northern hardwood forests exposed to chronic nitrogen additions, New Phytologist, 176, 175-183, Published.
• Lilleskov, E. A., J.L. Parrent (2007) Can we develop general predictive models of mycorrhizal fungal community-environment relationships?, New Phytologist, , In Press. 

Liu, F., M. Conklin, and G. Shaw (2017), Insights into concentration-discharge and endmember mixing analyses in the mid Merced River basin, Water Resources Research, 53, doi:10.1002/2016WR019437. 

Al-Qudah, M. O., F. Liu, R. N. Lerch, N. Kitchen, and J. Yang (2016), Controls on nitrate-N concentrations in groundwater in a Missourian claypan watershed, Earth and Space Science, 3: 90-105, doi: 10.1002/2015EA000117.

Shaw, G., M. H. Conklin, G. Nimz, and F. Liu (2014), Groundwater and surface water flow to the Merced River, Yosemite Valley, California: ³⁶Cl and Cl ^- evidence, Water Resources Research, 10.1002/2013WR014222.

Liu, F., C. Hunsaker, and R. C. Bales (2013), Controls of streamflow generation in small catchments across snow/rain transition in the Southern Sierra, California, Hydrological Processes, 27, 1959-1972, DOI: 10.1002/hyp.9304.

Frisbee, M. D., F. M. Phillips, A. R. Campbell, F. Liu, and S. A. Sanchez (2011), Streamflow generation in a large, alpine watershed in the southern Rocky Mountains of Colorado: Is streamflow generation simply the aggregation of hillslope runoff responses? Water Resources Research, 47, W06512, doi: 10.1029/2010WR009391.

Liu, F., R. C. Bales, M. H. Conklin, and M. E. Conrad (2008), Stream flow generation from snowmelt in semi-arid, forested and seasonally snow-covered catchments, Valles Caldera, New Mexico, Water Resources Research, 44, W12443, doi:10.1029/2007WR006278.

Liu, F., R. Parmenter, P. Brooks, M. Conklin, and R. C. Bales (2008), Intra- and inter-annual variation of streamflow pathways in semiarid, forested catchments, Valles Caldera, New Mexico, Ecohydrology, 1(3), 239-252, doi: 10.1002/eco.22.

Liu, F., M. Williams, and N. Caine (2004), Source waters and flow paths in an alpine catchment, Colorado Front Range, USA, Water Resources Research, Vol. 40, W09401, doi: 10.1029/2004WR003076. 

• Mason, L.A., A.L. Maclean and R.E. Froese. 2009. GIS Modeling Of Riparian Zones Utilizing Digital Elevation Models And Flood Height Data. Environmental Modeling and Assessment. (in revision).
• S. Saunders, M. Mislivets, K.Brosofske, D. Cleland, and A. Maclean. 2009. Predicting burns in subregional ecological and climatic units of the northern Great Lakes Region. Internationational Journal of Wildland Fire. (in review).
• Shonnard, D.R., J.R. Jensen, J.D. Naber, Q. Zhang, A.L. Maclean, K.E. Halvorsen, T.L. Jenkins, C. Polonowski, and J.W. Sutherland. 2008. Wood-to-Wheels: A Multidisciplinary Research Initiative in Sustainable Transportation Utilizing Fuels and Co-Products from Forest Resources. In: Proceedings from Convergence 2008, SAE International, October 20-22, 2008, Detroit, MI USA 2008-21-0026.
• Cleland, David T., Thomas R. Crow, Sari C. Saunders, Donald I Dickmann, Ann L. Maclean James K. Jordan, Richard L. Watson, Alyssa Sloan, Kimberly Brosofske. 2004. “Characterizing Historical and Modern Fires Regimes in Michigan: A Landscape Ecosystem Approach.” Forest Ecology. 19(3):311-325.
• VanLuven, D.M., J.E. Huntoon, and A.L. Maclean. 1999. Determination of the Influence of Wind on the Keweenaw Current in the Lake Superior Basin as Identified by Advanced Very High Resolution Radiometer (AVHRR) Imagery. Journal of Great Lakes Research. 25 (3):631- 647.
• Owens, K.E., A.J. Londo, D.D. Reed., A.L. Maclean and G.D. Mroz. 1999. A landscape level comparison of pre-European settlement and current soil carbon storage of a forested landscape in upper Michigan. Forest Ecology and Management. Vol. 113, pp. 179-189.
• Budd, J.W., W.C. Kerfoot and A.L. Maclean. 1998. Documenting complex surface temperature patterns from Advanced Very High Resolution Radiometer (AVHRR) imagery of Saginaw Bay, Lake Huron. Journal of Great Lakes Research 24(2): 582-594. 

• Editorial for 2019 special issue on Landscape-scale Dynamics of Family Forest Owners in  Landscape and Urban Planning
• Mayer AL. 2019. Family forest owners and landscape-scale interaction: A review.  Landscape and Urban Planning doi: 10.1016/j.landurbplan.2018.10.017
• Tortini R, AL Mayer, T Hermosilla, NC Coops, MA Wulder. 2019. Using annual Landsat imagery to identify harvesting over a range of intensities for non-industrial family forests. Landscape & Urban Planning. https://doi.org/10.1016/j.landurbplan.2018.04.012
• Mayer AL and AM Wellstead. 2018. Questionable survey methods generate a questionable list of recommended articles. Nature Ecology & Evolution [online]: DOI: 10.1038/s41559-018-0637-9
• Rahman SMM*, C Schelly, AL Mayer, ES Norman. 2018. Uncovering discursive framings of the Bangladesh shipbreaking industry. Social Sciences 7(1):14.
• Mu B, HW Li, AL Mayer, RZ He, GH Tian. 2017. Dynamic changes of green-space connectivity based on remote sensing and graph theory: a case study in Zhengzhou, China. Acta Ecologica Sinica 37(14):13pp. [In Chinese]
• Mayer AL. 2017. A scientist on any schedule. Science 355(6323):426. Read More

• Goyke, N.*, and B. Orr. 2018. The local migration of plant-based medicines from rural communities to Gral. E. Aquino, Paraguay. Natural Resources. 9:429- 447.

• Preston, K. T.G. Pypker, and B. Orr. 2017. Women and fuelwood in Lupeta, Tanzania: constraints to alternative fuels and fuelwood management strategies. J. of Sustainable Forestry. 36(6):555-567.  online: http://dx.doi.org/10.1080/10549811.2017.1313165

• Mejia, G.A., and B. Orr. 2015. Forest management plans in Los Planes de La Palma, El Salvador. Natural Resources 6:527-533.

• Sterling, S.J., and B. Orr.  2014. Patterns of tree distribution in small communities of the Sudanian Savana-Sahel. Land 3(4):1284-1292.

• Kenny, A.L., J.B. Pickens, and B. Orr. 2014. Modeling Teak Introduction on Smallholder Farms in Southern Togo. Journal of Sustainable Forestry.
• Cisz, M.E., M.J. Falkowski, and B. Orr. 2013. Small-scale spatial patterns of Copernicia alba Morong near Bahia Negra, Paraguay. Natural Resources 4:369-377. Read More
• Earnshaw, K.M., and B. Orr. 2013. Soil moisture, field-scale toposequential position, and slope effects on yields in irrigated rice (Oryza sativa L.) fields in Honduras. Agricultural Science. 4(8A):1-8. (Special issue on Water Management in Agriculture.) http://dx.doi.org/10.4236/as.2013.48A001
• Williams, R., T. Kuzmic, and B. Orr. 2013. The Student-Citizen and Study Abroad. J. of Forestry. 111(4):300-302.
• Fox, M.M., S.J. Trull, and B. Orr. 2013. Suitability of Cardamine concatenata (Michx.) Sw. as an Indicator Species on the Ottawa National Forest. Michigan Botanist. 51(4):121-132. (dated 2012, published 2013)
• Fox, M.M., S.J. Trull, and B. Orr. 2012, Effect of Selection Logging on Carex assiniboinensis W. Boott in a Northern Hardwood Stand Michigan Botanist. 51(3):110-116.
• Seib, M.D., K.C. Arnold, and B. Orr. 2012. Effectiveness of 3MTM PetrifilmTM as a Teaching Tool in Rural Mali. Development in Practice. 22(2):267-271.
• Aragona, F.B., and B. Orr. 2011. Agricultural intensification, monoculture and economic failure: The case of onion production in the Tipajara Watershed on the eastern slope of the Bolivian Andes. Journal of Sustainable Agriculture. 35(5):467-492.   
• Lincoln, K. and B. Orr. 2011. The use and cultural significance of the pita plant (Aechmea magdalenae) among Ngöbe women of Chalite, Panama. . Economic Botany. 65(1):13-26.
• Rhoades, J.L,. M.S. Demeyan, and B. Orr. 2011. Impacts of Deforestation and Land Cover Change on Mountain Soils in Hrazdan, Armenia. Journal of Sustainable Forestry. 30(7):677-696.
• Paulete, F.E., B. Orr. 2010. Combining Technical Competence and Stakeholder Impact in Environmental Education: The Gambia All Schools Nursery Competition. Applied Environmental Education and Communication. 9(1):18-27.
• Satterlee, B.M., M. Yemefack, and B.D. Orr. 2009. Maize yield and soil property responses to Entada abyssinica (Steud. ex A. Rich.) cuttings in the Adamawa Lowlands, Cameroon. J.of Food, Agriculture and Environment 7(1):192-196.
• Slatton, R., and B. Orr. 2008. A Smorgasbord of Agricultural Technologies: Farmers’ Choices and Lessons from Chalite, Panama. Development in Practice. 18(1):125-130.
• Orr, B. 2007. Cross-Country Skiing USSA Points as a Predictor of Future Performance among Junior Skiers. The Sports Journal. Online. Vol 10, No. 4.
• Jones, Michael J., and B. Orr. 2007. Resin Tapping and Forest Cooperatives in Honduras. J.of Sustainable Forestry 22(3/4):135-169.
• Cohen, M.E., J. B. Pickens, J. Cardenas Castillo, and B. Orr 2005. Ecological suitability and tree seedling survival in the Bolivian Altiplano. Ecologia Austral 15:207-215.
• Jarvis, MC, AM Miller, J Sheahan, K Ploetz, J Ploetz, RR Watson, MP Ruiz, CAP Villapan, JG Alvarado, AL Ramirez, & B Orr. 2005. Edible wild mushrooms of the Cofre de Perote Region, Veracruz, Mexico: an ethnomycological study of common names and uses. Economic Botany. 58(Supplement):S111-S115.
• Ploetz, K., and B. Orr. 2004. Wild herb use in Bulgaria. Economic Botany 58(2):231-241. 

• Wilmers, C, E. Post, R. Peterson, & J. Vucetich. 2006. Disease-mediated switch from top-down to bottom-up control increases moose population response to climate. Ecology Letters, in press.
• Wright, G.J., R.O. Peterson, D.W. Smith, and T.O. Lemke. 2005. Selection of northern Yellowstone elk by gray wolves and hunters. Journal of Wildlife Management, in press.
• Weise, JW, C Nagaswami, RO Peterson. 2005. River otter hair structure facilitates interlocking to impede penetration of water and allow trapping of air. Canadian Journal of Zoology 83:649-655.
• Jost, C, G Devulder, JA Vucetich, RO Peterson, R Arditi. 2005. The wolves of Isle Royale display scale-invariant satiation and density dependent predation on moose. J. Anim. Ecol., in press.
• Potvin, MJ, D Beyer, TD Drummer, RO Peterson, JA Vucetich, & J Hammill. 2005 Monitoring and habitat analysis for wolves in Upper Michigan. J. Wildlife Management, in press
• Vucetich, JA, & RO Peterson. 2004. The influence of top-down, bottom-up, and abiotic factors on the moose (Alces alces) population of Isle Royale. Proceeding Royal Soc Lond, B 271:183-189.
• Potvin, M.J., R.O. Peterson, and J.A. Vucetich. 2004. Wolf homesite attendance patterns. Canadian Journal of Zoology 82:1512-1518. 

• Mosier, SL, ES Kane, D Richter, E Lilleskov, MF Jurgensen, AJ Burton, SC Resh. 2017. Interactive effects of climate change and fungal communities on wood-derived carbon in forest soils. Soil Biology and Biochemist 117: 297-309.
• Gollany, H.T., Titus, B.D.,Scott, D., Asbjornsen, H., Resh, S.C., Chimner, R.A., Kaczmarek, D., Leite, L.F.C., Ferreira, A.C.C., Rod, K.,Hilbert, J., Galdos, M.V., Cisz, M., 2015.  Biogeochemical research priorities for sustainable biofuel and bioenergy feedstock production in Pan-America. Environmental Management.
• Schrank, AJ, SC Resh, WJ Previant, and RA Chimner. 2015. Characterization and Classification of Vernal Pool Vegetation, Soil, and Amphibians of Pictured Rocks National Lakeshore. American Midland Naturalist 174(1): 161-179.
• Chimner, RA and SC Resh. 2014. Water Sources of Riparian Bur Oak Using Stable Water Isotopes in Homestead National Monument, Nebraska. Natural Areas Journal 34(1):56-64.
• Resh, S.C., L. Joyce, M.G. Ryan. 2008. Fuel Treatments by Mulching—A Synthesis of the Ecological Impacts. In review with USDA-Forest Service, Rocky Mountain Research Station GTR.
• Resh, S.C., M. Battaglia, D. Worledge, and S. Ladiges. 2003. Coarse root biomass for eucalypt plantations in Tasmania, Australia: sources of variation and methods for assessment. Trees: Structure and Function 17:389-399.
• Rothe, A., Cromack, K. Jr., Resh, S., Makineci, E., and Son, Y. 2002. Soil carbon and nitrogen changes under Douglas-fir with and without red alder. Soil Science Society of America Journal 66:1988-1995.
• Resh, S.C., D. Binkley, and J.A. Parrotta. 2002. Greater soil carbon sequestration under nitrogen-fixing tree species compared with Eucalyptus species. Ecosystems 5:217-231.
• Kaye, J., S.C. Resh, M.W. Kaye, and R.A. Chimner. 2000. Nutrient and carbon dynamics in a replacement series of Eucalyptus and Albizia trees. Ecology 81:3267-3273. 
• Smith, F.W. and S.C. Resh. 1999. Age-related changes in production and below-ground carbon allocation in Pinus contorta forests. Forest Science 45:1-9.
• Binkley, D. and S.C. Resh. 1999. Rapid changes in soils following Eucalyptus afforestation in Hawaii. Soil Science Society of America Journal 63:222-225. 

• Webster, Charels E., David D. Reed, Blair D. Orr, James M. Schmierer, and James B. Pickens. 2009. Expected rates of value growth for individual sugar maple crop trees in the Great lakes Region. Northern journal of Applied Forestry, 26(4): 133-140.

•  Ebanyenle, E, A.J. Burton and A.J. Storer. 2016. Elevated tropospheric CO2 and O-3 may not alter

  initial wood decomposition rate or wood-decaying fungal community composition of Northern

  Hardwoods. International Biodeterioration & Biodegradation: 111: 74-77

•  Mercader, RJ, DG McCullough, AJ Storer, JM Bedford, R Heyd, TM Poland and S. Katovich. 2016.

  Estimating local spread of recently established emerald ash borer, Agrilus planipennis ,

  infestations and the potential to influence it with a systemic insecticide and girdled ash trees.

  Forest Ecology and Management 366:87-97.

•  Brockerhoff, EG, M.Dick, R. Ganley, A Roques and AJ Storer. 2016. Role of insect vectors in

  epidemiology and invasion risk of Fusarium circinatum , and risk assessment of biological control

  of invasive Pinus contorta . Biological Invasions 18: 1177-1190.

•  Shartell, LM, GR Corace III, AJ Storer,and DM Kashian. 2015. Broad and local-scale patterns of

  exotic earthworm functional groups in forests of National Wildlife Refuges of the Upper Midwest,

  USA. Biological Invasions 17: 3591-3607.

•  Clark, RE, KN Boyes, LE Morgan, AJ Storer and JM Marshall. 2015. Development and assessment of

  ash mortality models in relation to emerald ash borer infestation. Arboriculture and Urban

  Forestry 41(5): 270-278.

• Virto, I., C. Moni, C. Swanston, and C. Chenu. 2010. Turnover of intra- and extra-aggregate organic matter at the silt-size scale. Geoderma 156:1-10.
• Nave, L.E., E.D. Vance, C.W. Swanston, and P.S. Curtis. 2010. Harvest impacts on soil carbon storage in temperate forests. Forest Ecology and Management 259:857-866.
• Torn, M.S., C.W. Swanston, C. Castanha, and S. Trumbore. 2009. Storage and Turnover of Organic Matter in Soil, p. 219-272, In P. M. Huang and N. Senesi, eds. Biophysico-Chemical Processes Involving Natural Nonliving Organic Matter in Environmental Systems. Wiley, Hoboken.
• Sollins, P., M.G. Kramer, C. Swanston, K. Lajtha, T. Filley, A.K. Aufdenkampe, R. Wagai, and R.D. Bowden. 2009. Sequential density fractionation across soils of contrasting mineralogy: Evidence for both microbial- and mineral-controlled soil organic matter stabilization. Biogeochemistry 96:209-231.
• Nave, L.E., E.D. Vance, C.W. Swanston, and P.S. Curtis. 2009. Impacts of elevated N inputs on north temperate forest soil C storage, C/N, and net N-mineralization. Geoderma 153:231-240.
• Marin-Spiotta, E., W.L. Silver, C.W. Swanston, and R. Ostertag. 2009. Soil organic matter dynamics during 80 years of reforestation of tropical pastures. Global Change Biology 15:1584-1597.
• Gaudinski, J.B., M.S. Torn, W.J. Riley, C. Swanston, S.E. Trumbore, J.D. Joslin, H. Majdi, T.E. Dawson, and P.J. Hanson. 2009. Use of stored carbon reserves in growth of temperate tree roots and leaf buds: Analyses using radiocarbon measurements and modeling. Global Change Biology 15:992-1014. 

1. Vucetich JA, DW Macdonald. 2017. Some essentials on coexisting with carnivores. Open Access Government. August Issue: 216-217. Read more…
2. Vucetich JA. 2016. Should humans intervene when climate threatens an island’s ecology. Natural History. July Issue 124(7):20-23. Read more…
3. Vucetich JA, MP Nelson, JT Bruskotter. 2017. Conservation triage falls short because conservation is not like emergency medicine. Frontiers in Ecology and Evolution 5:45. Read more…
4. Vucetich JA, JT Bruskotter, MP Nelson (2015). Evaluating whether nature's intrinsic value is an axiom of or anathema to conservation. Conservation Biology 29, 321-332. Read more…
5. Nelson MP, JA Vucetich 2009. On Advocacy by Environmental Scientists: What, Whether, Why and How. Conservation Biology 23, 1090–1101. Read more…
6. Vucetich, J.A. 2017. Testimony presented before the U.S. Senate Committee on Environment and Public Works, pertaining to wolf management and the Endangered Species Act. 17 July 2017. Read more…
7. Bruskotter JT, JA Vucetich et al. 2017. Modernization, Risk, and Conservation of the World's Largest Carnivores. BioScience 67:646-55. Read more…
8. Bruskotter JT, JA Vucetich, MP Nelson. 2017. Animal Rights and Conservation: Conflicting or Compatible? The Wildlife Professional July/August 2017 40-42.  Read more
9. Vucetich, J.A. 2017. Are humans and nature fundamentally one and the same? Center for Humans and Nature, 18 Aug. Read more…
10. Vucetich JA, MP Nelson. 2010. Sustainability: virtuous or vulgar? Bioscience 60, 539-544. Read more…
11. Vucetich, JA, MP Nelson, MK Phillips. 2006.  The normative dimension & legal meaning of ‘endangered’ & ‘recovery’ within the United States’ Endangered Species Act.  Conservation Biology 20, 1383-1390. Read more…
12. Hedrick P, J Adams, JA Vucetich. 2011. Genetic Rescue: Re-evaluating and Broadening the Definition. Conservation Biology 25, 1069-1070. Read more…
13. 13.  Peterson RO, JA Vucetich, JK Bump, DW Smith. 2014. Trophic cascades in a multi-causal world: Isle Royale and Yellowstone. Annual Review of Ecology and Systematics. DOI: 10.1146/annurev-ecolsys-120213-091634 . Read more…
14. Uboni A, JA Vucetich, DR Stahler, DW Smith. 2015. Interannual variability: a crucial component of space use at the territory level. Ecology 96, 62-70. Read more…
15. Montgomery RA, JA Vucetich, RO Peterson, GJ Roloff, KF Millenbach 2013. The influence of winter severity, predation and senescence on moose habitat use. Journal of Animal Ecology 82, 301-309. Read more…
16. MacNulty D, D Smith, D Mech, JA Vucetich, C Packer. 2011. Nonlinear effects of group size on the success of wolves hunting elk.   Behavioral Ecology Read more…
17. Parikh GL, Forbey JS, Robb B, Peterson RO, Vucetich LM, Vucetich JA (2016). The influence of plant defensive chemicals, diet composition, and winter severity on the nutritional condition of a free‐ranging, generalist herbivore. Oikos doi:10.1111/oik.03359. Read more…

• Oelfke, J, RO Peterson, JA Vucetich, & LM Vucetich. 2003. Wolf handling at Isle Royale: Can we find another approach? George Wright Soc. 20(3):50-58.
• Vucetich, LM; JA Vucetich, CP Joshi, TA Waite, RO Peterson. 2001. Genetic (RAPD) diversity in Peromyscus maniculatus in a naturally fragmentation landscape. Mol. Ecol. 10(1): 35-40.
• Vucetich, LM, Vucetich, JA, Cleckner, LB, Gorski, PR, & RO Peterson. 2001. Mercury concentrations in deer mouse (Peromyscus maniculatus) tissues from Isle Royale National Park. Environmental Pollution 14(1):113-118.
• Paquet, P, JA Vucetich, MK Phillips, LM Vucetich. 2001. Mexican wolf recovery: three-year program review and assessment. Prepared by the Conservation Breeding Specialist Group for the United States Fish and Wildlife Service.
• Oelfke, J, RO Peterson, JA Vucetich, and LM Vucetich. 2000. Wolf research in the Isle Royale wilderness: Do the ends justify the means? In Cole, D. and S. McCool (eds.). Proceedings: Wilderness Science in a time of change. Proc. RMRS-P-000, UT: U.S. Dept of Agriculture, Forest Service, Rocky Mountain Research Station.
• Nelson, MP, JA Vucetich, RO Peterson, LM Vucetich. 2011. The Isle Royale Wolf-Moose Project (1958-present) and the Wonder of Long-Term Ecological Research. Endeavour 35(1):30-38.
• Adams JR, LM Vucetich, PW Hedrick, RO Peterson, JA Vucetich. in 2011. Genomic sweep and potential genetic rescue during limiting environmental conditions in an isolated wolf population. Proceedings Royal Soc B 278:3336-3344 (doi:10.1098/rspb.2011.0261)
• Vucetich JA, Vucetich LM, Peterson, RO. 2012. The causes and consequences of partial prey consumption by wolves preying on moose. Behavioral Ecology and Sociobiology 66: 295-303, DOI: 10.1007/s00265-011-1277-0.  
• Vucetich JA, Huntzinger BA, Peterson RO, Vucetich LM, Hammill JH, Beyer DE. 2012. Intra-seasonal variation in wolf Canis lupus kill rates. Wildlife Biology 18:1-12.
• Marucco F, Vucetich LM, Peterson RO, Adams JR, Vucetich JA. 2012. Evaluating the efficacy of non-invasive genetic methods and estimating wolf survival during a ten-year period. Conservation Genetics (DOI 10.1007/s10592-012-0412-4) (Sept 2012) 13(6):1611-1622.
• Peterson RO, JA Vucetich and LM Vucetich. 2013. Osteoarthritis in nature: osteoarthritis phenotypes are sexually dimorphic in moose (Alces alces). Osteoarthritis and Cartilage 21:S69.
• Räikkönen J, Vucetich JA, Peterson RO, Nelson MP, Vucetich LM. 2013. What the inbred Scandinavian wolf population tells us about the nature of conservation. PLOS ONE 8(6): e67218. doi:10.1371/journal.pone.0067218.  

• Janowiak, M.K., and C.R. Webster. 2010. Promoting ecological sustainability in woody biomass harvesting. Journal of Forestry 108(1):16-23. (featured on cover)
• Stehn, S.E., C.R. Webster, J.M. Glime, and M.A. Jenkins. 2010. Elevational gradients of bryophyte diversity, life forms, and community assemblage in the southern Appalachians. Canadian Journal of Forest Research 40:2164-2174.
• Stehn, S.E., C.R. Webster, J.M. Glime, and M.A. Jenkins. 2010. Ground-layer bryophyte communities of post-adelgid Picea-Abies forests. Southeastern Naturalist 9:435-452.
• Powers, M.D, B.J. Palik, J.B. Bradford, S. Fraver, C.R. Webster. 2010. Thinning method and intensity influence long-term mortality trends in a red pine forest: implications for climate change mitigation. Forest Ecology and Management 260:1138-1148
• Witt, J.C., and C.R. Webster. 2010. Regeneration dynamics in remnant Tsuga canadensis stands in the northern Lake States: potential direct and indirect effects of herbivory. Forest Ecology and Management 269:519-525
• Holmes, S.A, and C.R. Webster. 2010. Acer saccharum response to concurrent disturbances: the importance of stem layering as an adaptive trait. Canadian Journal of Forest Research 40:1627-1635
• Webster, C.R., D.J. Flaspohler, R.D. Jackson, T. Meehan, C. Gratton. 2010. Diversity, productivity and landscape-level effects of grasslands managed for biomass production. Biofuels 1(3):251-461.(invited) 

• 1) Fang, Y, L. Chen, K. Lin, Y. Feng, P. Zhang, J. Sanders, X. Pan, Y. Wu, X. Wang, Z. Su, C. Chen, H. Wei*, W. Zhang*. 2019. Characterization of functional relationships of R-loops with gene transcription and epigenetic modifications in rice . Genome Research ( In press) ( IF =10.1 ) 

• Zheng, J., C. He, Y. Qin, G. Lin, D. Park, M. Sun, J. Li, X. Lu, C. Zhang, C. Zhang, D. D Bade, CT “Eddy” Yeh, E. Zeng, H. Wei, P. S. Schnable, G. Wang, S. Liu. 2018. Co-expression analysis aids in the identification of new genes in the epicuticular wax pathway. Plant Journal  ( In press)

• Deng, W., K. Zhang, S. Liu, P. Zhao and S. Xu and  H. Wei*.  2018. JRmGRN: Joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions.   Bioinformatics .  https://doi.org/10.1093/bioinformatics/bty354.

• Peng, T., M. Qiao, H. Liu, S. Teotia, Y. Zhao, D. Zhao, L. Shi, B. Le, K. Rogers, C. Gunasekara, H. Duan, Y. Gu, L. Tian, Z. Zhang, F. Meng, L. Huang, Q. Chen, Z. Wang, J. Tang, X. Tang, H. Wei*, X. Chen*, Q. Zhao* and G. Tang*.  2018. A resource for inactivation of microRNAs using short tandem target mimic technology in model and crop plants. Molecular Plant ( In press )

• Gunasekara, C, K. Zhang, W. Deng, L. Brown and H. Wei*. 2018. TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction. Nucleic Acids Res. 46(11):e67.

• Wei, H.  2017. Construction of a hierarchical gene regulatory network centered around a transcription factor (Review). Briefing in Bioinformatics . DOI: 10.1093/bib/bbx152. ( IF =6.7 ).

• Gunasekara, C. A. Subramanian, Avvari, R. K., B. Li, Chen, S. and H. Wei. 2016. ExactSearch: A web-based plant motif search tool (http://sys.bio.mtu.edu/motif/index.php). Plant Methods 12:26 Read More
• Kumari, S., W. Deng, C. Gunasekara, V. Chiang, H.S. Chen, H. Ma, X. Davis, and H. Wei. 2016. Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes. BMC Bioinformatics 2016, 17:132 Read More
• Dash, M, Y. Yordan, S. Kumari, T. Georgieva, H. Wei and V. Busov. 2015. A system biology approach identifies new regulators of poplar root development under low nitrogen. Plant Journal, 84(2):335-346 Read More
• Yang, C and H. Wei. 2014, Designing microarray and RNA-seq experiments for greater systems biology discovery in modern plant genomics. Molecular Plant 8, 196–206. Read More
• Lin, Y.C.*, Li, W., Sun, Y.H., Kumari, S., Wei, H., Li, Q.Z., Tunlaya-Anukit, S., Sederoff, R.R., and Chiang, V.L. (2013). SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell. 25(11):4324-41. Read More
• Wei, H. Y. Yordan, T. Georgieva, X. Li, V. Busov. 2013. Nitrogen deprivation promotes Populus root growth via global transcriptomic reprogramming and activation of hierarchical genetic networks. New Phytologist 200 (2), 483-97 Read More
• Lu, S., Li, Q., Wei, H., Chang, M.J., Anukit, S.T., Kim, H., Liu, J., Song, J., Sun, Y.H., Yuan, L., Yeh, T.F., Peszlen, I., Ralph, J. Sederoff, R.R., Chiang, V.L. 2013. Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa. Proc Natl Acad Sci USA 110 (26) 10848-10853 Read More
• Li, J. H. Wei, T. Liu and P. Zhao. 2013. GPLEXUS: Enable genome-scale gene regulatory network analysis for plants through ultrafast mutual information computing and filtering. Nucleic Acids Research. (online now: 10.1093/nar/gkt983) Read More
• Kumari, S., J. Nie,, H.S. Chen, R. Stewart, H. Ma, X. Li, M. Lu, W.M. Taylor, and H. Wei. 2012. Evaluation of gene association methods for coexpression network construction and biological knowledge discovery. PLos ONE 7(11): e50411 Read More
• Nie, J., R. Stewart, F. Ruan, J. Thomson, H. Zhang, X. Cui and H. Wei. 2011. TF-cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). BMC Systems Biology, 5:53 Read More
• Cui, X, T. Wang, H.S. Chen, V. Busov and H. Wei. 2010. TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base. BMC Bioinformatics, 11:425 Read More
• Ming, R., S. Hou, Y. Feng, Q. Yu, A. Dionne-Laporte, J. Saw, P. Senin, W. Wang, S. Salzberg, X. Wang, E. Lyons, D. Rice, M. Riley, R. Skelton, J. Murray, C. Chen, M. Eustice, E. Tong, H. Albert, R. E. Paull, M.-L. Wang, Y. Zhu, M. Schatz, N. Nagarajan, R. Agbayani, P. Guan, A. Blas, J. Wang, J.-K. Na, T. Michael, E. V. Shakirov, B. Haas, J. Thimmapuram, D. Nelson, H. Tang, J. E. Bowers, J. Suzuki, S. Tripathi, K. Neupane, H. Wei, R. Singh, B. Irikura, N. Jiang, W. Zhang, K. Wall, G. Presting, A. Gschwend, Y. Li, A. Windsor, R. N. Pérez, M. J. Torres, F. A. Feltus, B. Porter, M. Paidi, M.-C. Luo, L. Liu, D. Christopher, P. H. Moore, T. Sugimura, C. dePamphilis, J. Jiang, M. Schuler, T. Mitchell-Olds, D. Shippen, J. Palmer, M. R. Freeling, A. H. Paterson, D. Gonsalves, L. Wang and M. Alam. 2008. The genome sequence of transgenic papaya, Carica papaya. Nature, Vol. 452, No. 7190:991-996 Read More
• Wei, H., P. F. Kuan, S. Tian, C. Yang, J. Nie, S. Sengupta, V. Ruotti, G. Jonsdottir, S. Keles, J. Thomson and R. Stewart. 2008. A study of the relationships between oligonucleotide properties and hybridization intensities in NimbleGen platform. Nucleic Acids Research, Vol. 36, No. 9:2926-2938 Read More
• Pan, P., S. Tian, J. Nie, C. Yang, V. Ruotti, H. Wei, G. Jonsdottir, R. Stewart, and J. Thomson. 2007. Whole genome analysis of Histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell, Vol. 1, No 3:299~312. Read More
• Wei, H , S. Persson, T. Mehta, V. Srinivasasainagendra, L. Chen, G. Page, C. Somerville, A. Loraine. 2006. Transcriptional coordination of the metabolic network in Arabidopsis thaliana. Plant Physiology. 142(2):762-74. Read More
• Persson, S., H. Wei, J. Milne, G. Page, C. Somerville. 2005. Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proc Natl Acad Sci USA, 102: 8633-8638. (Faculty 1000 evaluation) Read More
• Wei, H., Y. Kaznessis. 2005. Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination. Biotechnology and Bioengineering. Vol. 89, No1: 53-77 Read More
• Albert, H and H. Wei. Sugarcane Ubi9 gene promoter and methods of use thereof. 2004, U.S. Patent No. 6706948 

• Wolfe, J. D., P. C. Stouffer, R. O. Bierregaard, Jr., D. Luther and T. E. Lovejoy. 2019. Effects of a regenerating matrix on the survival of birds in tropical forest fragments. In review 

• Wolfe, J. D. and P. Elizondo. 2019. Integrating bird conservation into ecosystem service payments and carbon offsets: a case study from Costa Rica. In review 

•  Long, L. and J. D. Wolfe. 2019. A Review the Science Directly Related to the Effects of Barred Owls ( Strix varia) on Spotted Owls ( Strix occidentalis). In review 

• Wolfe, J. D., J. D. Alexander, J. L. Stephens, and C. J. Ralph. 2019. A novel approach to understanding bird communities using informed diversity estimates at local and regional scales in northern California and southern Oregon. In press Ecology and Evolution. 

•  Rutt, C., S. Midway, V. Jirinec, J. D. Wolfe, P. C. and Stouffer. 2018. Examining the microclimate hypothesis in Amazonian birds: Indirect tests of the ‘visual constraints’ mechanism. Oikos. https://doi.org/10.1111/oik.05781

• Ralph, C. J. and J. D. Wolfe. 2018. Factors affecting the distribution and abundance of autumn vagrant warblers in northwestern California and southern Oregon. PeerJ. 6: e5881

•  
   
   

• Yuan Y, Chung J-D, Fu X, Johnson VE, Ranjan P, Booth SL, Harding SA, Tsai C-J (2009) Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis. Proceedings of the National Academy of Sciences USA 106: 22020-22025
• Tsai C-J, Harding SA, Tschaplinski TJ, Lindroth RL, Yuan Y (2006) Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus. New Phytologist 172: 47-62.
• Chan AP, Pertea G, Cheung F, Lee D, Zheng L, Whitelaw C, Pontaroli AC, SanMiguel P, Yuan Y, Bennetzen J, Barbazuk WB, Quackenbush J, Rabinowicz PD (2006) The TIGR Maize Database. Nucleic Acids Research. 34 (Database issue): D771-6.
• Emberton J, Ma J, Yuan Y, SanMiguel P, Bennetzen JL (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Research. 15(10): 1441-6.
• Lin, J-Y., B. Hass-Jacobus, P. SanMiguel, J.G. Walling, Y. Yuan, J. Doyle, R.C. Shoemaker, N.D. Young and S.A. Jackson. (2005) Molecular and cytogenetic characterization of gene-poor, heterochromatic regions of Glycine max L. Merr. Genetics 170: 1221-1230.
• Whitelaw,C.A.; Barbazuk,W.B.; Pertea,G.; Chan,A.P.; Cheung,F.; Lee,Y.; Zheng,L.; van Heeringen,S.; Karamycheva,S.; Bennetzen, J.L.; SanMiguel,P.; Lakey,N.; Bedell,J.; Yuan,Y.; Budiman,M.A.; Resnick,A.; Van Aken,S.; Utterback,T.; Riedmuller,S.; Williams,M.; Feldblyum,T.; Schubert,K.; Beachy,R.; Fraser,C.M.; Quackenbush,J. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science 302: 2118-2120.
• Yuan, Y., SanMiguel, P. and Bennetzen, J. (2003) High Cot sequence analysis of the maize genome. Plant Journal. 34 (2): 249-255.