Faculty Publications

Leitão P.J.,   Andrew, C.J., Engelhardt, E.K., Graham, C.H., Martinez‐Almoyna, C., Mimet, A., Pinkert, S., Schröder, B., Voskamp, A., Hof, C., Fritz, S.A. 2019. Macroecology as a hub between research disciplines: Opportunities, challenges and possible ways forward. Journal of Biogeography.   47: 13-5

Aas, A.B.,   Andrew, C.J., Blaalid, R., Vik, U., Kauserud, H., Davey, M.L. 2019. Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms. FEMS Microbial Ecology, 95,   doi.org/10.1093/femsec/fiz058 .

Gange, A.C., Allen, L.P., Nussbaumer, A., Gange, E.G.,   Andrew, C., Egli, S., Senn-Irelet, B., Boddy, L. 2019. Multiscale patterns of rarity in fungi, inferred from fruiting records. Global Ecology and Biogeography, 28: 1106-1117,   doi.org/10.1111/geb.12918

Andrew, C., Büntgen, U., Egli, S., Senn-Irlet, B., Grytnes, J., Heilmann-Clausen, J., Boddy, L., Bässler, C., Gange, A.C., Heegaard, E., Høiland, K., Kirk, P.M., Krisai-Greilhüber, I., Kuyper, T., W., Kauserud, H. 2019. Open-source data reveal how collections-based fungal diversity is sensitive to global change. Applications of Plant Science.   7: e1227 .

Dawson, S.K., Boddy, L., Halbwachs, H., Bässler, C.,  Andrew, C. , Crowther, T.W., Heilmann-Clausen, J., Nordén J., Ovaskainen O., Jönsson, M. Handbook for standardised measurement of macrofungal traits; a start with basidiomycete wood fungi. 2019. Functional Ecology.   33: 372-387 .

Andrew, C., Diez, J., James, T.Y., Kauserud, H. Fungarium specimens – a largely untapped source in global change biology and beyond. 2018. Philosophical Transactions Royal Society B. 374: 20170392.   http://dx.doi.org/10.1098/rstb.2017.0392

Bidartondo, M.I., Ellis, C., Kauserud, H., Kennedy, P.G., Lilleskov, E.A., Suz, L.M.,   Andrew, C.  2018. The state of the world's fungi report - 2018. Chapter 9. Climate Change: Fungal responses and effects. Royal Botanic Gardens, Kew.

Khomich, M, Cox, F,   Andrew, C.J., Andersen, T., Kauserud, H., Davey, M.L. 2018. Coming up short: Identifying substrate and geographic biases in fungal sequence databases. Fungal Ecology.   36: 75-80 .

Andrew, C., Halvorsen, R., Heegaard, E., Kuyper, T.W., Heilmann-Clausen, J., Krisai-Greilhuber, I., Bässler, C., Egli, S., Gange, A.C., Høiland, K., Kirk, P.M., Senn-Irlet, B., Boddy, L., Büntgen, U., Kauserud, H. 2018. Continental‐scale macrofungal assemblage patterns correlate with climate, soil carbon and nitrogen deposition. Journal of Biogeography.   45: 1942-1953 .

Andrew, C., Heegaard, E., Høiland, K., Senn-Irlet, B., Kuyper, T.W., Krisai-Greilhuber, I., Kirk, P.M., Heilmann-Clausen, J., Gange, A.C., Egli, S., Bässler, C., Büntgen, U., Boddy, L., Kauserud, H. 2018. Explaining European fungal phenology with climate variability. Ecology.   99: 1306-1315 .

Andrew, C., Heegaard, E., Gange, A.C., Senn-Irlet, B., Egli, S., Kirk, P.M., Büntgen, U., Kauserud, H., Boddy, L. 2018.  Congruency in fungal phenology patterns across dataset sources and scales. Fungal Ecology.   32: 9-17 .

Gange, A.C., Heegaard, E., Boddy, L.,   Andrew, C., Kirk, P., Halvorsen, R., Kuyper, T.W., Bässler, C., Diez, J., Heilman-Clausen, J. and Høiland, K., Büntgen, U., Kauserud, H. 2017. Trait-dependent distributional shifts in fruiting of common British fungi. Ecography. 40,   doi: 10.1111/ecog.03233

Andrew, C., Heegaard, E., Kirk P.M., Bässler, C., Heilmann-Clausen, J., Krisai-Greilhuber, I., Kuyper, T., Senn, B., Büntgen, U., Diez, J., Egli, S., Gange, A., Halvorsen, R., Høiland, K., Nordén, J., Rustøen, F., Boddy, L., Kauserud, H. 2017. Big data integration: Pan-European fungal species observations assembly that addresses contemporary questions in ecology and global change biology.  Fungal Biology Reviews.   31: 88-98 .

Andrew, C., Heegaard, E., Halvorsen, R., Martinez-Peña, F., Egli, S., Kirk, P.M., Bässler, C. Büntgen, U., Aldea, J., Høiland, K., Boddy, L., Kauserud, H. 2016.  Climate change impacts on fungal community and trait dynamics. Fungal Ecology.   22: 17-25 .

• Ela, Chipkar, Bal, Xie, and Ong. 2021. Lignin-Propiconazole nanocapsules are an effective bio-based wood preservative. ACS Sustainable Chemistry & Engineering, https://dx.doi.org/10.1021/acssuschemeng.0c07742 
• Bal, Schneider, and Richter. 2020. Decay of birdseye sugar maple ( Acer saccharum ) and curly red maple ( Acer rubrum ) figured woods.  Wood and Fiber Science , 52(3): 292-297  https://doi.org/10.22382/wfs-2020-027
• 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

• Heppenheimer,E., K. Brzeski, J. Hinton, M. Chamberlain, J. Robinson, R. Wayne, B. vonHoldt. 2020 . A Genome-wide perspective on the persistence of red wolf ancestry in southeastern canids. Journal of Heredity. 111(3), 277-286.
• 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. 9(4), 2046-2060.
• 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.
• 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., B. Bartel, W. Waddell, K. Wolf, D. Rabon, S. Taylor. 2015.Infectious disease and red wolf conservation: assessment of disease occurrence and associated risks. Journal of Mammalogy, 96:751-761.
• Brzeski, K., D. Rabon, M. Chamberlain, L. Waits, S. Taylor. 2014. Inbreeding and inbreeding depression in endangered red wolves ( Canis rufus). Molecular Ecology, 23:4241–4255.

• 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

Azeez A, Zhao YC, Singh RK, Yordanov YS, Dash M, Miskolczi P, Stojkovic K, Strauss SH, Bhalerao RP, Busov VB (2021) EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy. Nat Communications 12 (1):1123. doi:10.1038/s41467-021-21449-0

Azeez A, Busov V (2020) CRISPR/Cas9-mediated single and biallelic knockout of poplar STERILE APETALA (PopSAP) leads to complete reproductive sterility. Plant biotechnology journal. doi:10.1111/pbi.13451

Rauschendorfer J, Yordanov Y, Dobrev P, Vankova R, Sykes R, Kulheim C, Busov V (2020) Overexpression of a developing xylem cDNA library in transgenic poplar generates high mutation rate specific to wood formation. Plant biotechnology journal 18 (6):1434-1443

Busov VB (2019) Plant Development: Dual Roles of Poplar SVL in Vegetative Bud Dormancy. Current Biology 29 (2):R68-R70. doi:10.1016/j.cub.2018.11.061

Singh RK, Maurya JP, Azeez A, Miskolczi P, Tylewicz S, Stojkovic K, Delhomme N, Busov V, Bhalerao RP (2018) A genetic network mediating the control of bud break in hybrid aspen. Nature Communications 9:4173

• Kennard D, Matlaga D, Joanne S, Clay K, Alonso-Rodriguez Aura, Reed SC, Cavaleri MA, and Wood TE. In press. Tropical understory herbaceous community responds more strongly to hurricane disturbance than to experimental warming. Ecology and Evolution.
• Reed SC, Reibold R, Cavaleri MA, Alonso-Rodríguez AM, Berberich ME, Wood TE. (2020). Soil biogeochemical responses of a tropical forest to warming and hurricane disturbance. Advances in Ecological Research. https://doi.org/10.1016/bs.aecr.2020.01.007
• Kramer R*, Ishii, HR, Carter KR, Miyazaki Y, Cavaleri MA, Araki M, Azuma W, Inoue Y, and Hara C. (2020). Predicting effects of climate change on productivity and persistence of forest trees. Ecological Reviews. https://doi.org/10.1111/1440-1703.12127
• Benedicte B, Alonso-Rodríguez AM, Aldrich-Wolfe L, Cavaleri MA, Reed SC, Wood TE. (2020). Altered climate leads to positive density-dependent feedbacks in a tropical rainforest. Global Change Biology. https://doi.org/10.1111/gcb.15087
• Kumarathunge DP*, Medlyn BE, Drake JE, Tjoelker MG, Aspinwall MJ, Battaglia M, Cano FJ, Carter KR*, Cavaleri MA, Cernusak LA, Chambers JQ, Crous KY, De Kauwe MG, Dillaway DN, Dreyer E, Ellsworth DS, Ghannoum O, Han Q, Hikosaka K, Jensen AM, Kelly JWG, Kruger EL, Mercado LM, Onoda Y, Reich PB, Rogers A, Slot M, Smith N, Tarvainen L, Tissue DT, Togashi HF, Tribuzy ES, Uddling J, Vårhammar A, Wallin G, Warren JM and Way DA (2019) Acclimation and adaptation components of the temperature dependence of plant photosynthesis at the global scale. New Phytologist, 222: 768-784. https://doi.org/10.1111/nph.15668
• Wood TE, González G, Silver WL, Reed SC, and Cavaleri MA (2019) On the Shoulders of Giants: Continuing the Legacy of Large-Scale Ecosystem Manipulation Experiments in Puerto Rico. Forests, 10: 210. https://doi.org/10.3390/f10030210
• Wood TE, Cavaleri MA, Giardina G, Khan S, Mohan JE, Nottingham A, Reed SC and Slot M. (2019) Soil warming effects on low-latitude forests with highly-weathered soils. In JE Mohan (Ed.), Ecosystem Consequences of Soil Warming: Microbes, Vegetation, Fauna, and Soil Biogeochemistry (pp. 385-439). London, UK: Academic Press, Elsevier. https://doi.org/10.1016/B978-0-12-813493-1.00015-6

• Hupperts, S. F.*, Webster, C. R., Froese, R. E., Lilleskov, E., Marcarelli, A. and Dickinson, Y.L. (2020) Increasing ground-layer plant taxonomic diversity masks declining phylogenetic diversity along a silvicultural disturbance gradient. Canadian Journal of Forest Research.
• Hupperts, S. F.*, Webster, C. R., Froese, R. E., and Dickinson, Y.L. (2020). Seedling and sapling recruitment following novel silvicultural treatments in Great Lakes northern hardwoods.  Forest Ecology and Management 462: 117983.
• Vickers, L.A., McWilliams, W.H., Knapp, B.O., D’Amato, A.W., Dey, D.C., Dickinson, Y.L., Kabrick, J.M., Kenefic, L.S., Royo, A.A., Saunders, M.R., Shifley, S.R. and Westfall, M.R., (2019) Are current seedling demographics poised to regenerate northern US forests? Journal of Forestry fvz046: 1–21
• Dickinson, Y.L., Battaglia, M.A. and Asherin, L. (2019) Evaluation of the GENGYM diameter growth model and potential modifications in structurally-complex ponderosa pine ( Pinus ponderosa Douglas ex C. Lawson) forests. Journal of Forest Ecology 448: 1–10
• Dickinson, Y.L., Wang, X., Wiedenbeck, J. and Ross, R.J. (2019) Effects of silvicultural practices on engineering properties of northern hardwood species of the Great Lakes region — A Literature Review. General Technical Report FPL-GTR-269. Madison, WI: U.S. Department of Agriculture, Forest Service, Forest Products Laboratory. 17p.
• 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. (2018) Principles and practices for the restoration of ponderosa pine and dry mixed-conifer forests of the Colorado Front Range .Gen. Tech. Rep. RMRS-GTR-372. Ft Collins, CO. US Department of Agriculture, Forest Service, Rocky Mountain Research Station. 121p.
• Fahey, R.T., Alveshere, B., Burton, J.I., D’Amato, A., Dickinson, Y.L., Keeton, W.S., Kern, C.C., Larson, A.J., Palik, B.J., Puettmann, K.J., Saunders, M.R., Webster, C.R., Atkins, J.W., Gough. C.M., Hardiman, B.S. (2018) Shifting conceptions of complexity in forest management and silviculture. Forest Ecology and Management. 421:59–71

• 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. 

• Halvorsen, K.E., C. Schelly, R. Handler, E.C. Pischke, and J.L. Knowlton (eds). 2019.  A Research Agenda for Environmental Management. Edward Elgar Publishing: Cheltenham, UK.
• Halvorsen, K.E., Jessie L. Knowlton, Robert M. Handler, Chelsea Schelly and Erin C. Pischke. ‘Integrating across sectors and disciplines: transdisciplinary teamwork challenges and strategies.’ 2019. In  K.E. Halvorsen, C. Schelly, R. Handler, E.C. Pischke, and J.L. Knowlton (eds). A Research Agenda for Environmental Management. Edward Elgar Publishing: Cheltenham, UK.
• Dunn, J.L, Jessie L. Knowlton, Robert M. Handler, Erin C. Pischke, K. E. Halvorsen, M. Azahara Mesa-Jurado, Theresa L. Selfa, David J. Flaspohler, Julian Licata, Ena E. Mata-Zayas, Rodrigo Medeiros, Cassandra Moseley, Erik A. Nielsen, Valentin D Picasso Risso, Julio C. Sacramento-Rivero, Tatiana de Souza, Cesar J. Vazquez Navarrete and Nathan Basiliko. 2019. ‘Lessons from the transdisciplinary, international BIOPIRE project.’ In  K.E. Halvorsen, C. Schelly, R. Handler, E.C. Pischke, and J.L. Knowlton (eds). A Research Agenda for Environmental Management. Edward Elgar Publishing: Cheltenham, UK.
• Pischke, E.C., M. A. Mesa-Jurado, A. Eastmond, J. Abrams, K. E. Halvorsen. Community Perceptions of Climate Change and Adaptation Strategies in Tabasco, Mexico. 2018.  Journal of Environmental Studies and Sciences 8(4)441-451. DOI: 10.1007/s13412-018-0493-6.
• Kozich, A.T., K.E. Halvorsen, and A.S. Mayer. 2018. Perspectives on Water Resources among Anishinaabe and Non-Native Residents of the Great Lakes Region.  Journal of Contemporary Water Research and Education 163(April)94-108.

• 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.

• Jurgensen, M.F., Miller, C.A., Trettin, C.T., Page-Dumroese, D.S. 2019.  Bedding of wetland      soil: Effects of bed height and termite activity on wood decomposition. Soil Science     Society America Journal doi:10.2136/sssaj2018.12.0492

• Wang, W., Page-Dumroese, D., Jurgensen,, M.F., Miller, C., Walitalo, J., Chen, X., Liu, Y. 2019. Thinning effects on tree growth and decomposition of standard wood substrates in a pine plantation. Forest Ecology and Management 449:117451 OI:0.1016/j.foreco.2019.117451
• Page-Dumroese, D.S., Jurgensen, M.F., Miller, C.A., Pickens, J., Tirocke, J.M. 2019. Wildfire alters belowground and surface wood decomposition on two national forests in Montana, USA. International Journal of Wildland Fire 28: 456–469. doi.org/10.1071/WF18218
• Wang, W., Page-Dumroese, D., Jurgensen, M., Tirocke, J., and Y. Liu. 2018. Effects of forest thinning and wood quality on the short-term wood decomposition rate in a Pinus tabuliformis plantation. Journal of Plant Research: doi.org/10.1007/s10265-018-1069-y 
• Powers, M., Kolka, R., Bradford, J., Palik, B., Jurgensen, M. 2018. Forest floor and mineral soil respiration rates in a northern Minnesota red pine chronosequence. Forests: 9(1), 16.
• Blanco, J.A., Page-Dumroese, D.S., Jurgensen, M.F., Curran, M., Tirocke, J., Walitalo, J. 2018. Modelling the management of forest ecosystems: importance of wood decomposition. Natural Resource Modeling: DOI: 10.1111/nrm.12173.
• Bal, T.L., Storer, A.J., Jurgensen, M.F. 2018. Evidence of damage from exotic invasive earthworm activity was highly correlated to sugar maple dieback in the Upper Great Lakes region.  Biological Invasions 20:151–164.
• Mosier, S.L., Kane, E.S., Richter, D.L., Lilleskov, E.A., Jurgensen, M.F., Burton, A.J., and S.C. Resh. 2017. Interactive effects of climate change and fungal communities on wood-derived carbon in forest soils. Soil Biol. Biochem. 115: 297- 309.
• Jurgensen, M.F., Page-Dumroese, D.S., Brown, R.E., Tirocke, J.M., Miller, C.A., Pickens, J.B., Wang, M. 2017. Estimating carbon and nitrogen pools in a forest soil: influence of soil bulk density methods and rock content. Soil Science Society America Journal 81:1689 - 1696.
• Acet, M., Jurgensen, M.F., Kane, E., Gailing, O. 2017. Genet diversity, genetic structure, and trait expression of trembling aspen (Populus tremuloides Michx.) after clear-cut harvesting and post-harvest soil treatments. Botany 95: 785 – 798.
• Fissore, C., Jurgensen, M.F., Pickens, J, Miller, C,, Page-Dumroese, D., Giardina, C.P. 2016. Role of soil texture, clay mineralogy, location, and temperature in coarse wood decomposition—a mesocosm experiment. Ecosphere 7(11):e01605. 10.1002/ecs2.1605
• Fresher, K.N., Jurgensen, M.F. Gailing, O. 2016. Comparison of phenotypic and genetic clone delineation in quaking aspen, Populus tremuloides. Trees 30:1657–1667.

Krause L, McCullough KJ, Kane ES, Kolka RK, Chimner RA, Lilleskov EA. 2021. Impacts of historical ditching on peat volume and carbon in northern Minnesota USA peatlands. Journal of Environmental Management, https://doi.org/10.1016/j.jenvman.2021.113090.

Albano LJ, Turetsky MR, Mack MC, Kane ES. 2021. Deep roots of Carex aquatilis have greater ammonium uptake capacity than shallow roots in peatlands following permafrost thaw. Plant and Soil, https://doi.org/10.1007/s11104-021-04978-x.

Rupp DL, Lamit LJ, Techtmann SM, Kane ES, Lilleskov EA, Turetsky MR. 2021. The rhizosphere responds: rich fen peat and root microbial ecology after long-term water table manipulation.  Applied and Environmental Microbiology, DOI: 10.1128/AEM.00241-21.

Richard RP, Kane ES, Bronson DR, MacLean AL, Kolka RK. 2021. Plant communities and landform relationships delineate components of soil complexes subject to whole‐tree harvest restriction.  Soil Science Society of America Journal, https://doi.org/10.1002/saj2.20234.

Kane ES, Dieleman CM, *Rupp D, Wyatt KH, Rober AR, Turetsky MR. 2021. Consequences of Increased Variation in Peatland Hydrology for Carbon Storage: Legacy Effects of Drought and Flood in a Boreal Fen Ecosystem. Frontiers in Earth Science, https://doi.org/10.3389/feart.2020.577746.

Walker XJ, Rogers BM, Veraverbeke S, Johnstone JF, Baltzer JL, Barrett K, Bourgeau-Chavez L, Day NJ, de Groot WJ, Dieleman CM, Goetz S, Hoy E, Jenkins LK, Kane ES, Parisien M-A, Potter S, Schuur EAG, Turetsky M, Whitman E, Mack M. 2020. Fuel availability not fire weather controls boreal wildfire severity and carbon emissions. Nature- Climate Change, https://doi.org/10.1038/s41558-020-00920-8.

Meingast KM, Kane ES, Coble AA, Marcarelli AM, Toczydlowski D. 2020. Climate, snowmelt dynamics and atmospheric deposition interact to control dissolved organic carbon export from a northern forest stream over 26 years. Environmental Research Letters https://iopscience.iop.org/article/10.1088/1748-9326/ab9c4e.

Walker XJ, Baltzer JL, Bourgeau-Chavez L, Day NJ, Dieleman CM, Johnstone JF, Kane ES, Rogers BM, Turetsky MR, Veraverbeke S, Mack MC. 2020. Patterns of Ecosystem Structure and Wildfire Carbon Combustion Across Six Ecoregions of the North American Boreal Forest. Frontiers in Forests and Global Change, https://doi.org/10.3389/ffgc.2020.00087. 

Euskirchen ES, Kane ES, Edgar CW, Turetsky MR. 2020. When the Source of Flooding Matters: Divergent Responses in Carbon Fluxes in an Alaskan Rich Fen to Two Types of Inundation. Ecosystems, https://doi.org/10.1007/s10021-019-00460-z.

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• 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
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• 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.
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• 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.
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• 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. 

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• 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. International 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.
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• Mayer AL. 2021. The Bird and the Bulldozer. Yale University Press.
• Editorial for 2019 special issue on Landscape-scale Dynamics of Family Forest Owners in  Landscape and Urban Planning
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Ploetz, K.*, and B. Orr.  2004.  Wild herb use in Bulgaria.  Economic Botany 58(2):231-241.

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.

Jones, Michael J.*, and B. Orr.  2007.  Resin Tapping and Forest Cooperatives in Honduras.  J. of Sustainable Forestry 22(3/4):135-169.

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.  DOI: 10.1080/10440046.2011.579832

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.  (dated 2012, published 2013)

Kenny, A.L.*, J.B. Pickens, and B. Orr. 2014. Modeling Teak Introduction on Smallholder Farms in Southern Togo.   Journal of Sustainable Forestry.  33(8):776-795.

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

Goltz, S.M., A.L. Mayer, and B. Orr. (2020). Applied behavior analysis as a development tool: Examples from agroforestry. [Graeme Review] Journal of Sustainable Forestry.

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• 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.
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• 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. 

• Chimner, RA, R Boone, G Bowser, L Bourgeau-Chavez, B Fuentealba, J Gilbert, JA Ñaupari, M. Polk, S Resh, C Turin, KR Young, M Zarria-Samanamud. 2020. Andes, Bofedales, and the Communities of Huascarán National Park, Peru. Wetland Science and Practice 37: 246-254.
• 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, HT, BD Titus, D Scott, H Asbjornsen, SC Resh, RA Chimner, D Kaczmarek, LFC Leite, ACC Ferreira, K Rod, J Hilbert, MV Galdos, M Cisz. 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, SC, 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, K Cromack Jr., SC Resh, E Makineci, Y Son. 2002. Soil carbon and nitrogen changes under Douglas-fir with and without red alder. Soil Science Society of America Journal 66:1988-1995.
• Resh, SC, D. Binkley, and JA Parrotta. 2002. Greater soil carbon sequestration under nitrogen-fixing tree species compared with Eucalyptus pecies. Ecosystems 5:217-231.
• Kaye, J, SC Resh, MW Kaye, RA Chimner. 2000. Nutrient and carbon dynamics in a replacement series of Eucalyptus and Albizia trees. Ecology 81:3267-3273. 
• Smith, FW and SC Resh. 1999. Age-related changes in production and below-ground carbon allocation in Pinus contorta forests. Forest Science 45:1-9.
• Binkley, D and SC Resh. 1999. Rapid changes in soils following Eucalyptus afforestation in Hawaii. Soil Science Society of America Journal 63:222-225. 

• Bunce A. Volin J. Miller D. Parent J. Rudnicki M. (2019) Determinants of Tree Sway Frequency in Temperate Deciduous Forests of the Northeast United States. 266-267. Agricultural and Forest Meteorology.
• Pringle A.M. Rudnicki M. and Pearce J. (2017) Wood Furniture Waste-Based Recycled 3-D Printing Filament. Forest Products Journal. https://doi.org/10.13073/FPJ-D-17-00042
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• Hiscox A.L. Rudnicki M. and Miller D.R. (2015) Understanding turbulent kinetic energy (TKE) stationarity within a forest canopy. Agricultural and forest meteorology. 214: 124-133

• Lytle, W., Schelly, C., Floress, K., Shwom, R., Halvorsen, K. (2021) Environmental Decision Making Shaped by the Home:  Situating Consumption in the Household Context. Human Ecology Review 26. Read Here.
• Pascaris, A.S., Schelly, C., Burnham, L., Pearce, J. (2021). Integrating Solar Energy with Agriculture: Industry Perspectives on the Market, Community, and Socio-Political Dimensions of Agrivoltaics. Energy Research and Social Sciences 75 https://doi.org/10.1016/j.erss.2021.102023.
• Schaefer, M., Olabisi, L.S., Arola, K., Poitra, C.M. Matz, E., Seigel, M., Schelly, C., Adesanya, A., Bessette, D. (2021). Understanding Socio-Technological Systems Change through an Indigenous Community-Based Participatory Framework. Sustainability 13. https://doi.org/10.3390/su13042257
• Kliskey, A., Williams, P., Griffith, D., Dale, V.H., Schelly, C., Marshall, A.-M., Gagnon, V., Eaton, W., Floress, K. (2021). Thinking big and thinking small: A conceptual framework for best practices in community and stakeholder engagement in food, energy, and water systems. Sustainability 13 https://doi.org/10.3390/su13042160
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• Chen, S., G., Y. Wang, L. Yu, T. Zheng, S. Wang, Z. Yue, J. Jiang, S. Kumari, C. Zheng, H. Tang, J. Li, Y. Li, J. Chen, W. Zhang, H. Kuang, J. Robertson, P. Zhao, H. Li, S. Shu, Y. Yordanov, Ha. Huang, D. Goodstein, Y. Gai, Q. Qi, J. Min, C. Xu, S. Wang, G. Qu, A. Paterson, D. Sankoff, H. Wei, Liu, G,C. Yang,. 2021. Genome sequence and evolution of Betula platyphylla. Horticulture Research 8, 37(2021). ( JIF =5.4 ).

• Li, Y.,  H. Wei, J. Yang, L. K. Du, J.Li, Y. Zhang, T. Qiu,Z. Liu, Y. Ren, L. Song, X. Kang. 2020. High quality de novo assembly of the  Eucommia ulmoides haploid genome provides new insights into the evolution and rubber biosynthesis.  Horticulture Research . 7:183 ( JIF =5.4 )  https://doi.org/10.1038/s41438-020-00406-w

• He, C., G. Lin,  H. Wei, H. Tang, F. F. White, B. Valent, and S. Liu. 2020. Factorial estimating assembly base errors using  k-mr abundance difference (KAD) between short reads and genome assembled sequences.  NAR Genomics and Bioinformatics  Vol. 2, No. 3: 1-14.    https://doi.org/10.1093/nargab/lqaa075

• Wei, M., Q. Liu, Z. Wang, J. Yang, W. Li, Y. Chen, H. Lu, J. Nie, B. Liu, K. Lv, X. Mao, S. Chen, J. Sanders,  H. Wei * and Chenghao Li*. 2020. PuHox52-mediated hierarchical multilayered gene regulatory network promotes adventitious root formation in  Populus ussuriensis.  New Phytologist . 228(4): 1369-1385. ( IF =8.5 ) https://doi.org/10.1111/nph.16778

• Wei, H.  2019. Construction of a hierarchical gene regulatory network centered around a transcription factor (Review).  Briefing in Bioinformatics . ( IF =9.3 ). DOI: https://doi.org/10.1093/bib/bbx152. 

• 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  29(8):1287-1297 ( IF =10.1 )  http://www.genome.org/cgi/doi/10.1101/gr.246009.118

• 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 34(20):3470-3478. ( IF=7.3 ) 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  11(11):1400-1417 ( IF=8.8 ) .   https://doi.org/10.1016/j.molp.2018.09.003

• 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 Res.  46(11):e67. ( IF=11.53 )   https://doi.org/10.1093/nar/gky210

• 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  https://doi.org/10.1186/s12859-016-0981-1

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Wolfe, J. D. and P. Elizondo. 2020. Integrating bird conservation into ecosystem service payments and carbon offsets: a case study from Costa Rica. Conservation Science and practice  doi.org/10.1111/csp2.173.

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). Journal of Wildlife Management 83:1281-1296.

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. Ecology and Evolution 9:4431–4442.

Rutt, C., S. Midway, V. Jirinec,  J. D. Wolfe and P. C. Stouffer. 2018. Examining the microclimate hypothesis in Amazonian birds: Indirect tests of the ‘visual constraints’ mechanism. Oikos 128:798-810.

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

Johnson, E. I. and  J. D. Wolfe. 2017. Molt in Neotropical Birds: Life History and Aging Criteria. Studies in Avian Biology, CRC Press, Taylor and Francis Group, Boca Raton, Florida.

Wolfe, J. D., C. J. Ralph and A. K. Wiegardt. 2017. Bottom-up processes influence the demography and life-cycle phenology of Hawaiian bird communities. Ecology 98:2885-2899.

Wiegardt, K. A.,  J. D. Wolfe, C. J. Ralph, J. L. Stephens and J. D. Alexander. 2017. Elevational movements of songbirds after the breeding season. Journal of Ecology and Evolution 7:7750-7764.

West, C.,  J. D. Wolfe, A. K. Wiegardt and T. Williams-Claussen. 2017. Feasibility of California Condor recovery in northern California: assessing spatial and temporal patterns of contaminants using Surrogate species. Condor 119: 720-731. Cooper, J., O. Johnson, T. Davis, R. Terrill, K. Brzeski., J. D. Wolfe, A. Etingüe* and L. Powell. 2017. Notes on the distribution of the avifauna of Bioko Island, Equatorial Guinea, with one new country record. Malimbus 39:1-15.

Wiegardt, K. A., D. C. Barton and  J. D. Wolfe. 2017. Upslope molt migration of the Wilson’s Warbler in the Klamath-Siskiyou Bioregion. Journal of Ornithology 88:47-52.

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