Faculty Publications

• Bal, Myers, Panella, Dickinson, Storer. Refinement of a Grafting Program for the Propagation of BBD-Resistant American Beech. Science Report NPS/SR—2025/276. National Park Service, Fort Collins, Colorado. 
• Rekola, Taber, Sharik, Dockry, Babalola, Bal, et al., 2024. Social and knowledge diversity in forest education: vital for the world's forests. Ambio
• Gauthier, Djoumad, Bal, Bilodeau, Digirolomo, Ony, Hadziabdic, McLaughlin, Miles, Munck, Snover-Clift, Tanguay. 2024. Interlaboratory evaluation of Bretziella fagacearum molecular detection assays to guide the eDNA monitoring of the oak wilt disease. Environmental DNA
• Stump, Bershing, Bal, Külheim. 2024. Current and Potential Insect Threats to Oaks in the Great Lakes Region. Forests. 
• Higdon, Brzeski, Ottino, Bal. 2024. Establishing Silphids in the invertebrate DNA toolbox: A proof of concept. PeerJ. 
• Dolinski, Bal, Webster, Resh. 2024. Assessing the utility of a native pathogenic fungus as a biocontrol alternative to herbicide on invasive buckthorns in forests of Upper Michigan. Natural Areas Journal.
• Lane-Clark, Gagnon, Bal. 2024. Shifting the language of ‘invasion’ ecology: Two-eyed seeing as a framework for discourse regarding introduced species. Socio-Ecological Practice Research.
• Bal, Beaudoin, Carter. 2024. Berries without Bugs: Recreational Foraging and a Fruit Fly Threat in Rural Michigan. Journal of Gastronomy and Tourism.
• Bal. 2023. Promoting culturally conscious students: a course model in maple syrup management and culture. Natural Sciences Education.
• Myers, Dickinson, Storer, Bal. 2023. A review of propagation and restoration techniques for American Beech and their current and future application in mitigation of beech bark disease. Sustainability.
• Bal. 2023. Draw a bee: a simple drawing activity can highlight our misperceptions and diversity of bees. The American Biology Teacher.
• Camp & Bal. 2022. The Turkey Tail Mushroom and its Many Look-alikes. Digital Commons Open Access Books. 
• Myers, Dickinson, Storer, Bal. 2022. A pilot study of transplanting methods for wildling American Beech (Fagus grandifolia).  Horticulturae.
• Bal, Dickinson, Storer. 2023. Exotic earthworms impact forests: increase awareness and integrate impacts into forest management decisions. In: Proceedings of the Northern Hardwood Conference 2021. General Technical Report. 
• Schneider, Bal, Brzeski. Novel applications of iDNA tool for measuring small mammal community biodiversity via Silphid beetles. 2023. In: Proceedings of the Northern Hardwood Conference 2021. General Technical Report. 
• Burmann, Kelly, Schelly, and Bal. 2022. Formative interests and pathways to natural resources careers among historically underrepresented people.  Society & Natural Resources.
• 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 
• Owuor, Giessen, Prior, Cilio, Bal, et al., 2021. Trends in forest-related employment and tertiary education: Insights from selected key countries around the globe. European Forest Institute. 
• 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.
• 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.
• 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.
• 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
• 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.
• 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.
• Bal, T.L., 2014. Forest Health Detectives. The American Biology Teacher. 76 (8): 532-537
• 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.
• 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.

• Fine-Scale Mapping of Natural Ecological Communities Using Machine Learning Approaches
• Comparison of high-resolution NAIP and unmanned aerial vehicle (UAV) imagery for natural vegetation communities classification using machine learning approaches
• A spectral three-dimensional color space model of tree crown health
• A theoretical framework for the ecological role of three‐dimensional structural diversity
• Image Processing in Dense Forest Areas using Unmanned Aerial System (UAS)
• Mapping Coastal Wetland and Phragmites on the Hiawatha National Forest Using Unmanned Aerial System (UAS) Imagery: Proof of Concepts

• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.

Bartlick, C. I. *, Burton, J. I., Webster, C. R., Froese, R. E., & Y. L. Dickinson. 2023. An experimental approach to identify drivers of tree regeneration diversity, composition, and heterogeneity in northern hardwood forests. Forest Ecology and Management, 546, 121320. Link

Webster, C. R., Burton, J. I., & Y. L. Dickinson. 2023. Influence of silvicultural practices in northern hardwood forests on a long-lived perennial herb, Trillium cernuum L. Forest Ecology and Management, 545, 121282. Link

Evans, G. R.^*, Burton, J. I., Powell, W. A., & J. E. Drake 2023. Comparative growth and physiological performance of American chestnuts, oaks, hickories, and sugar maple across a silvicultural gradient in overstory retention. Forest Ecology and Management, 536, 120908. Link

Bartlick, C. I. ^*, Burton, J. I., Webster, C. R., Froese, R. E., Hupperts, S. F., & Y. L. Dickinson. 2023. Artificial tip-up mounds influence tree seedling composition in a managed northern hardwood forest. Canadian Journal of Forest Research. Link

Patton, R.M.^*, Kiernan, D.H., Burton, J.I. & J.E. Drake, 2022. Management trade-offs between forest carbon stocks, sequestration rates and structural complexity in the central Adirondacks. Forest Ecology and Management, 525, 120539. Link

Hecking, M.J.^*, Zukswert J.M.^*, Drake, J.E., Dovciak, M. and J.I. Burton. 2022. Montane temperate-boreal forests retain the leaf economics spectrum despite intraspecific variability. Frontiers in Forests and Global Change, 4. Link

Burton, J.I., D.J. Mladenoff, J.A. Forrester and M.K. Clayton. 2021. Effect of forest gap dynamics on community heterogeneity in the ground-layer depends on deer – evidence from a controlled experiment. Journal of Vegetation Science 32(1) e12969. Link

Pettit, J.M.^*, Voelker, S.L., DeRose, R.J. & J.I. Burton. 2020. Spruce beetle outbreak was not driven by drought stress: Evidence from a tree-ring iso-demographic approach indicates temperatures were more important. Global Change Biology, 26, 5829-5843. Link

Burton, J.I., Perakis, S.S., Brooks, J.R. & K.J. Puettmann, K.J. 2020. Trait integration and functional differentiation among co-existing plant species. American Journal of Botany, 107, 628-638. Link  
Featured in issue highlights: https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/ajb2.1464

Pettit, J.M.^*, J.I. Burton, R.J. DeRose, J.N. Long and S.L. Voelker. 2019. Epidemic spruce beetle outbreak changes drivers of Engelmann spruce regeneration. Ecosphere 10: e02912. Link.

^*Graduate student author

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

• Line Rochefort, Maria Strack, Rodney Chimner. Regional Assessment for North America. UNEP Global Peatlands Assessment – The State of the World’s Peatlands: Evidence for action toward the conservation, restoration, and sustainable management of peatlands. Main Report. 2022. Global Peatlands Initiative. United Nations Environment Programme, Nairobi.
• Chimner, R.A.Sidebar 7.2: Cedar Swamp Restoration in Storm, L., and L.S. Kenefic. Northern White-Cedar: The Tree of Life. Michigan State University Press, 2022. https://doi.org/10.14321/j.ctv2m2fv73.
• Chimner, R. S. Resh, J. A. Hribljan, M. Battaglia, L. Bourgeau-Chavez, G. Bowser, E. A. Lilleskov. Mountain Wetland Soil Carbon Stocks of Huascarán National Park, Peru. Submitted to Frontiers in Plant Science.
• Rahay, S. Tata H.L., H.S. Nuroniah, D.A. Ahsania, H. Anggunira, S.N. Hidayati, M. Pratama, Istomo, A. Chimner, M. van Noordwijk, R. Kolka. Tree species distribution in naturally regenerated peatland canal blocking sites of the Sebangau River, Sebangau National Park, Central Kalimantan. In revision at Mires and Peat.
• Uhelshiki D. *, E. Kane, R.A. Chimner, K. Heckman, J. Miesel, L. Xie. 2022. Infrared Spectroscopy Estimates Pyrogenic Carbon Content of Peat Soils. Mires and Peat. 28, Article 30, 22 pp
• Stuart, J.E.M, C.L. Tucker, E.A. Lilleskov, R. K. Kolka, A. Chimner, K. A. Heckman, and E. S. Kane. 2022. Evidence for older carbon loss and changing decomposition regimes with low water tables in peatlands. Global Change Biology.

• Jachowski, D.S., Bergeson, S.M., Cotey, S.R., Croose, E., Hofmeester, T.R., MacPherson, J., Wright, P., Calderón‐Acevedo, C.A., Carter, S.P., Dürst, A.C. and Egloff, G.B., 2024. Non‐invasive methods for monitoring weasels: emerging technologies and priorities for future research. Mammal Review.
• Weerarathne, P., Sanders, T.L., Kao, Y.F., Cotey, S.R., Place, J.D., Fairbanks, W.S., Miller, C.A. and Reichard, M.V., 2023. High Prevalence of Cytauxzoon felis in bobcats (Lynx rufus) across Oklahoma and occurrence in west Texas, USA. Journal of Wildlife Diseases.
• Cotey, S.R., Scimeca, R., Chang, L., Carpenter, A.L., Will, E.E., Ott-Conn, C., Mayer, A.L. and Reichard, M.V., 2022. Toxoplasma gondii prevalence, partial genotypes, and spatial variation in north american river otters (Lontra canadensis) in the Upper Peninsula of Michigan, USA. The Journal of Wildlife Diseases, 58(4), pp.869-881.
• Reichard, M.V., Sanders, T.L., Prentiss, N.L., Cotey, S.R., Koch, R.W., Fairbanks, W.S., Interisano, M., La Rosa, G. and Pozio, E., 2021. Detection of Trichinella murrelli and Trichinella pseudospiralis in bobcats (Lynx rufus) from Oklahoma. Veterinary Parasitology: Regional Studies and Reports, 25, p.100609.

• 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. 

• Nookaraju, A., Pandey, S. K., Ahlawat, Y. K., & Joshi, C. P. (2022). Understanding the Modus Operandi of Class II KNOX Transcription Factors in Secondary Cell Wall Biosynthesis. Plants, 11(4), 493.
• Ahlawat YK, Nookaraju A, Harman-Ware AE, Doeppke C, Biswal AK and Joshi CP (2021) Genetic Modification of KNAT7 Transcription Factor Expression Enhances Saccharification and Reduces Recalcitrance of Woody Biomass in Poplars. Front. Plant Sci. 12:762067. doi: 10.3389/fpls.2021.762067
• AHLAWAT, Y.; Joshi, C.P. Overexpression of Arabidopsis Laccase2, Laccase4 and Peroxidase52 in hybrid poplar under developing xylem specific DX15 promoter improves saccharification efficiency in a woody biofuel feedstock, in Proceedings of the 1st International Electronic Conference on Plant Science, 1–15 December 2020.
• AHLAWAT, Y.; Joshi, C.P. Genetic manipulation of KNAT7 transcription factor enhances saccharification by reducing recalcitrance in the bioenergy crop Populus, in Proceedings of the 1st International Electronic Conference on Plant Science, 1–15 December 2020.
• Huang, J., Hao, X., Jin, Y. et al. Temporal transcriptome profiling of developing seeds reveals a concerted gene regulation in relation to oil accumulation in Pongamia (Millettia pinnata). BMC Plant Biol 18, 140 (2018).
• Joshi, C. P. (2018, June). Cell Wall Biotechnology of Bioenergy Plants for Improved Biofuel Production. In IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL (Vol. 54, pp. S14-S14). 233 SPRING ST, NEW YORK, NY 10013 USA: SPRINGER.
• 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.

(* asterisk denotes student mentee) 

Wyatt KH, Cielik J, Dieleman CM, Kane ES, Rober AR, Sullivan B, Turetsky MR. 2024. Legacy Effects of Plant Community Structure Are Manifested in Microbial Biofilm Development With Consequences for Ecosystem CO2 Emissions. Global Change Biology, https://doi.org/10.1111/gcb.17603.

Thayamkottu S, Smallman TL, Parn J, Mander U, Euskirchen ES, Kane ES. 2024. Greening of a boreal rich fen driven by CO₂ fertilisation. Agricultural and Forest Meteorology, https://doi.org/10.1016/j.agrformet.2024.110261.

*Russell MD, Heckman K, Pan L, Ye X, Zalesny R, Kane ES. 2024. Mine waste rock as a soil amendment for enhanced weathering, ecosystem services, and bioenergy production. Frontiers in Earth Science, doi: 10.3389/feart.2024.1414437.

Kuhn MA, Varner RK, McCalley CK, Perryman CR, Aurela M, Burke SA, Chanton JP, Crill PM, DelGreco J, Deng J, Heffernan L, Herrick C, Hodgkins SB, Jones CP, Juutinen S, Kane ES, Lamit LJ, Larmola T, Lilleskov E,….Waldrop MP. 2024. Controls on Stable Methane Isotope Values in Northern Peatlands and Potential Shifts in Values Under Permafrost Thaw Scenarios.  Journal of Geophysical Research- Biogeosciences, https://doi.org/10.1029/2023JG007837.

Su P, Dai Q, Kane ES. 2024. Predicting chloride ingression in concrete containing different SCMs based on chloride binding and electrical resistivity. Construction and Building Materials, https://doi.org/10.1016/j.conbuildmat.2024.134928.

*Boyle G, Kane ES, Nave L, Heckman K, Jurgensen M. 2024. Refinement of the Carbon to Loss on Ignition Relationship in Forest Soils. Canadian Journal of Soil Science, https://doi.org/10.1139/CJSS-2023-0089.

Euskirchen ES, Edgar CW, Kane ES, Waldrop MP, Neumann RB, Manies KL, Douglas TA, Dieleman C, Jones MC, Turetsky MR. 2024. Persistent net release of carbon dioxide and methane from an Alaskan lowland boreal peatland complex. Global Change Biology, https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.17139.

• Rauschendorfer J, Rooney R, Külheim C (2022) Strategies to mitigate shifts in red oak (Quercus sect. Lobatae) distribution under a climate change. Tree Physiology (in print)
• Rauschendorfer J, Lindback E, Rooney R, Frantti S, Peck V, Cavaleri M, Külheim C (2022) Seed source climatic variables determine Quercus rubra provenance growth and environmental responses. In review: Northern Hardwood Conference (in print)
• Ghirado A, Blande J, Ruehr NK, Balestrini RM, Külheim C (2022) Adaptation of Trees to Climate Change: Mechanisms Behind Physiological and Ecological Resilience and Vulnerability Frontiers in Forests and Global Change 4: 831701
• Mhoswa L, Slipper B, Myburg AA, Külheim C, Naidoo S (2022) Genome-wide association study identifies SNP markers and putative candidate genes for terpene profiles in Eucalyptus grandis. Resubmission in preparation after major revision requested by G3: Genes Genome Genetics 12: jkac004
• Hsieh S, Krause S, Kainer D, Degenhardt J, Foley WJ, Külheim C (2021) Terpene profiling and functional characterization of terpene synthases responsive to myrtle rust in Melaleuca quinquenervia. Plant Environment Interactions 2: 177-193
• Li T, Kainer D*, Foley WJ, Rodrigo AG, Külheim C (2021) The draft genome sequence of Eucalyptus polybractea based on hybrid assembly with Oxford Nanopore and Illumina reads. bioRxiv: https://doi.org/10.1101/2021.05.18.444652
• Orr AJ, Padovan A, Kainer D, Külheim C, Bromham L, Bustos-Segura C, Foley WJ, Haff T, Hsieh J-F, Morales-Suarez A, Cartwright RA, Lanfear R (2020) A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant. Proceeding of the Royal Society B 287: 20192364
• Rauschendorfer J, Yordanov Y, Dobrev P, Vankova R, Sykes R, Külheim 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: 1434-1443 https://doi.org/10.1111/pbi.13309 
• Marsh KJ, Wallis IR, Külheim C, Clark R, Nicolle D, Foley WJ, Salminen J-P (2020) New approaches to tannin analysis of leaves explain biological activity associated with herbivore defence. New Phytologist 225: 488-498 https://doi.org/10.1111/nph.16117 
• Naidoo S, Oates C, Mhoswa L, O’ Neil M, Acosta J, Christie N, Mphahlele M, Payn K, Myburg A, Slippers B, Külheim C (2020) Factors underpinning resistance against the galling pest, Leptocybe invasa in Eucalyptus grandis. Proceedings of the Sixth International Workshop on the Genetics of Host-Parasite Interactions in Forestry
• Choi B, Crisp MD, Cook LG, Edwards BD, Toon A, Külheim C (2019) Identifying genetic markers for a range of phylogenetic utility – from species to family level. PLoS One 14: e0218995 
• Kainer D, Padovan A, Degenhardt J, Krause S, Mondal P, Foley WJ, Külheim C (2019) High marker density GWAS provides novel insights into the genomic architecture of terpene oil yield in Eucalyptus. New Phytologist 223: 1489-1504 
• Thornhill AH, Crisp MD, Külheim C, Lam KE, Nelson LA, Yeates DK, Miller JT (2019) A dated molecular perspective of eucalypt taxonomy, evolution, and diversification. Australian Systematic Botany 32: 29-48 
• Kanagendran A, Pazouki L, Bichele R, Külheim C, Niinemets Ü (2018) Temporal regulation of terpene synthase gene expression in Eucalyptus globulus leaves upon ozone and wounding stresses: relationships with stomatal ozone uptake and emission responses. Environmental and Experimental Botany 155: 552-565 
• Kainer D, Stone E, Padovan A, Foley WJ, Külheim C (2018) High accuracy genomic prediction for foliar terpene traits in Eucalyptus polybractea. G3 – Genes, Genomes, Genetics 8: 2573-2583 doi.org/10.1534/g3.118.200443 

• Langston, N. 2021. Climate Ghosts: Restoring Migratory Species in the Anthropocene. Brandeis University Press. 
• Langston, N. and K. Brosemer. 2022 (27: 2). Loons and the risk of extinction in a warming world." Environmental History 340-348.
• SV Nguyen, N Langston, A Wellstead, M Howlett. 2020. Mining the evidence: Public comments and evidence-based policymaking in the controversial Minnesota PolyMet mining project, Resources Policy 69, 101842
• Langston, N. 2019. “Environment and sustainability in mining.” Chapter for Environment and Sustainability in a Globalizing World, Ed. A. Nightingale and T Bohler, Routledge.
• Baeten, J. P., Langston, N., Lafreniere, D. J. 2018. “A Spatial Evaluation of Historic Iron Mining Impacts on Current Impaired Waters in Lake Superior's Mesabi Range.” Ambio 47 (2): 231-244.
• Langston, N. and K. Christen. 2019. Conservation policies threaten Indigenous reindeer herders in Mongolia. The Conversation, Oct. 10, 2019.
• Langston, N. 2019. “Closing nuclear plants will increase climate risks.” NICHE: The Otther, Jan. 30, 2019. http://niche-canada.org/2019/01/30/closing-nuclear-plants-will-increase-climate-risks/ Co-published with Activehistory.ca and Historicalclimatology.org
• Langston, N. 2019. “Will woodland caribou survive in the Lake Superior basin?” Agate Magazine Jan. 14, 2019. http://www.agatemag.com/2019/01/will-woodland-caribou-survive-in-the-lake-superior-basin/
• Langston, N. 2018. “Are woodland caribou doomed by climate change?” Historical Climatology July 26, 2018. https://www.historicalclimatology.com/blog/are-woodland-caribou-doomed-by-climate-change
• Langston, N. 2018 “The Syllabus Project: Diversifying the Environmental History Syllabus.” NICHE: The Otter. July 5, 2018. http://niche-canada.org/2018/07/05/the-syllabus-project/
• Langston. N. 2017 Sustaining Lake Superior: An Extraordinary Lake in a Changing World. Yale U. Press. Paperback March 2019.
• Langston, N. 2017 “Iron Mines, Toxicity, and Indigenous Communities in the Lake Superior Basin,” pp. 313-338 in Mining North America, eds. G. Vrtis and J. McNeil, U of CA Press.
• Langston, N. 2017. “Resiliency and Collapse: Lake Trout, Sea Lamprey, and Fisheries Management in Lake Superior.” Pp. 239-262 in Lynne Heasley and Daniel Macfarlane, eds Border Flows: A Century of Canadian-American Water Relations, U. Calgary Press.
• John Baeten, Nancy Langston, and Don Lafreniere. 2016. “A geospatial approach to uncovering the hidden waste footprint of Lake Superior’s Mesabi Iron Range.” The Extractive Industries and Society 3(4): 1031-1045.
• Thistle, J. and N. Langston. 2016. “Entangled histories: Iron ore mining in Canada and the United States.” TheExtractive Industries and Society 3(2): 269-277. 10.1016/j.exis.2015.06.00
• 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.
• 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).
• 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.
• Langston, N. 2015. “Thinking Like A Microbe: Borders and Environmental History.” Canadian Historical Review. 95(4): 592-603
• 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.
• 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.

• 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. 

Shannon*, J. P., R. Kolka, M. Van Grinsven, and F. Liu (2022). Joint Impacts of Future Climate Conditions and Invasive Species on Black Ash Forested Wetlands. Frontiers in Forests and Global Change, 5:957526. doi: 10.3389/ffgc.2022.957526.

Porter*, V. M., J. B. Shanley, S. D. Sebestyen, and F. Liu^† (2022). Controls on decadal, annual, and seasonal solute concentration-discharge relationships in the Sleepers River Research Watershed, Vermont, northeastern United States. Hydrological Processes, 36(3), e14559. https://doi.org/10.1002/hyp.14559.

Hofmeister**, K., R. Lerch, C. Baffaut, J. Yang, and F. Liu (2022). Characterizing Groundwater Chemistry and Recharge in the Critical Zone of an Agricultural Claypan Watershed. Water Resources Research, 58(10), e2021WR031797. https://doi.org/10.1029/ 2021WR031797.

Liu, F., R. N. Lerch, J. Yang, and G. Peters* (2020). Determining Streamflow Pathways Using Geochemical Tracers in a Claypan Watershed. Hydrological Processes, 34 (11): 2494-2509. DOI: 10.1002/HYP.13743. 

Ackerer**, J., C. Steefel, F. Liu, R. Bart, S. Khan, A. O'geen, C. Hunsaker, R. C. Bales (2020). Determining how Critical Zone structure constrains hydrogeochemical behavior of watersheds: learning from an elevation gradient in California’s Sierra Nevada. Frontiers in Water, doi: 10.3389/frwa.2020.00023.

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. 

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. 

Wang* Y., Y. Ding, B. Ye, F. Liu, J. Wang, and J. Wang (2013). Contributions of climate and human activities to changes in runoff of the Yellow and Yangtze Rivers from 1950 to 2008. Science China Earth Sciences, doi: 10.1007/s11430-012—4505-1.

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., 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. 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.
• 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. 

• 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. 

• Dolinski, L, T Bal, C Webster, SC Resh. 2024. Assessing the Utility of a Native Pathogenic Fungus as a Biocontrol Alternative to Herbicide on Invasive Buckthorns in Forests of Upper Michigan. Natural Areas Journal 44(2):57-64; https://doi10.3375/2162-4399-44.2.57
• Young KR, E Alata, RA Chimner, RB Boone, G Bowser, L Bourgeau-Chavez, B Fuentealba, J Gilbert, JA Ñaupari, MH Polk, SC Resh, C Turin, and M Zarria-Samanamud. 2023. Ecological Dynamism and Livestock Governance in a Peruvian National Park. Land 12(11): 2051;
  https://doi.org/10.3390/land12112051
• 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 Biochemistry 117: 297-309.

• 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
• Ross R.J. Wang X.; Rudnicki, M. 2017. New technologies aid in assessing trees. The Forestry Source 22:2:22-23. Society of American Foresters.
• Rudnicki M. Wang X. Ross R. Xiping W. and Prezinski K. (2016) Measuring Wood Quality in Standing Trees. Gen. Tech. Rep. FPL-GTR-248. Madison, WI: US Department of Agriculture, Forest Service, Forest Products Laboratory. 248:13 p.
• 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

• Tiwari, S., Schelly, C., Sidortsov, R. (2023). Legacies matter: Exploring social acceptance of pumped storage hydro in Michigan’s Upper Peninsula. Case Studies in the Environment. 7 (1): 2004414. https://doi.org/10.1525/cse.2023.2004414

• Ahamed, S., Schelly, C., Floress, K., Lytle, W., Caggiano, H., Cuite, C., Wallace, C., Cook, R., Jarvis, R., Shwom, R., Watkins, D. (2023) Being Able to Work Has Kept Our Life Fairly Constant:” Reconciling Social Practice Models to Assess the Impact of (Infra)Structural Inequities on Household Wellbeing During the COVID-19 Pandemic. Environmental Research: Infrastructure and Sustainability 3(1): 015012

• Lee, D., Schelly, C., Tiwari, S., Smith, S., Gagnon, V. (2023) Preferences and Perceived Barriers to Pursuing Energy Sovereignty and Renewable Energy: A Tribal Nations Perspective. Energy Research & Social Science 97 https://doi.org/10.1016/j.erss.2023.102967

• Tiwari, S., Schelly, C., Ou, G., Ardakani, M.S., Chen, J. (2022). Conceptualizing Resilience: An Energy Services Approach. Energy Research and Social Science 94: https://doi.org/10.1016/j.erss.2022.102878

• Pascaris, A., Schelly, C., Pearce, J. (2022). Advancing Agrivoltaics within the U.S. Legal Framework:  A Multidimensional Assessment of Barriers & Opportunities. Agrivoltaics 2021 AIP Conference Proceedings. 2635, 050002 https://doi.org/10.1063/5.0103386

• Pascaris, A., Schelly, C., Rouleau, M., Pearce, J. (2022). Do Agrivoltaics Improve Public Support for Solar? A Survey on Perceptions, Preferences, and Priorities. Green Technology, Resilience, and Sustainability 2(8) https://doi.org/10.1007/s44173-022-00007-x 

• Gagnon, V., Schelly, C., Lytle, W., Kliskey, A., Dale, V., Marshall, A-M, Rodriguez, L., Williams, P., Price, M.W., Redd, E., Noodin, M.A. (2022). Enacting Boundaries or Building Bridges? Language and Engagement in Food-Energy-Water Systems Science. Socio-Ecological Practice Research https://doi.org/10.1007/s42532-022-00110-0

• Schelly, C., Gagnon, V., Arola, K., Fiss, A., Schaefer, M., Halvorsen, K.E. (2021). Cultural Imaginaries or Incommensurable Ontologies? Recognizing relationality and sovereignty as worldviews in socio-technological system transitions. Energy Research and Social Science 80 https://doi.org/10.1016/j.erss.2021.102242

• 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.

Vucetich JA, Burnham D, Macdonald EA, Bruskotter JT, Marchini S,
Zimmermann A, Macdonald DW. (2018). Just conservation: What is it and
should we pursue it?. Biological Conservation, 221, 23-33,
https://doi.org/10.1016/j.biocon.2018.02.022

Vucetich JA, Burnham D, Johnson PJ, Loveridge AJ, Nelson MP,
Bruskotter JT, Macdonald DW. (2019). The value of argument analysis
for understanding ethical considerations pertaining to trophy hunting
and lion conservation. Biological conservation, 235, 260-272,
https://doi.org/10.1016/j.biocon.2019.04.012

Offer-Westort T, Feltz A, Bruskotter JT, Vucetich JA. (2020). What is
an endangered species?: judgments about acceptable risk. Environmental
Research Letters, 15(1), 014010,
https://doi.org/10.1088/1748-9326/ab5cc8

Bruskotter JT, Vucetich JA, Slagle KM, Berardo R, Singh AS, Wilson RS.
(2018). Support for the US Endangered Species Act over time and space:
Controversial species do not weaken public support for protective
legislation. Conservation Letters, 11(6), e12595,
https://doi.org/10.1111/conl.12595

Vucetich JA, Nelson MP, Bruskotter JT. (2020). What Drives Declining
Support for Long-Term Ecological Research?. BioScience. 70:168–173,
https://doi.org/10.1093/biosci/biz151

Hoy SR, MacNulty DR, Smith DW, Stahler DR, Lambin X, Peterson RO,
Ruprecht JS, Vucetich JA. Fluctuations in age structure and their
variable influence on population growth. Functional Ecology. 2020
Jan;34(1):203-16, https://doi.org/10.1111/1365-2435.13431

Hoy SR, Vucetich JA, Liu R, DeAngelis DL, Peterson RO, Vucetich LM,
Henderson JJ. (2019). Negative frequency‐dependent foraging behaviour
in a generalist herbivore (Alces alces) and its stabilizing influence
on food web dynamics. Journal of Animal Ecology, 88(9), 1291-1304,
https://doi.org/10.1111/1365-2656.13031

Hoy SR, Peterson RO, Vucetich JA. (2018). Climate warming is
associated with smaller body size and shorter lifespans in moose near
their southern range limit. Global change biology, 24(6), 2488-2497,
https://doi.org/10.1111/gcb.14015

• Jacqueline A. Robinson, Jannikke RaÃàikkoÃànen, Leah M. Vucetich, John A. Vucetich, Rolf O. Peterson, Kirk E. Lohmueller1, Robert K. Wayne. 2019. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. Science Advances 29 May 2019, Vol. 5, no. 5, eaau0757 DOI: 10.1126/sciadv.aau0757
• Hoy SR, Vucetich JA, Liu R, DeAngelis DL, Peterson RO, Vucetich LM, Henderson JJ. 2019. Negative frequency-dependent foraging behaviour in a generalist herbivore (Alces alces) and its stabilizing influence on food-web dynamics. Journal of Animal Ecology doi.org/10.1111/1365-2656.13031
• Peterson, R. O., Hoy, S. R., Vucetich, L. M., Vucetich, J. A., Kraus, V. B., & Huebner, J. L. (2018). Urinary biomarkers to non-invasively evaluate health in wild moose (Alces alces). Osteoarthritis and Cartilage, 26, S196-S197.
• Long-term trends in prevalence and ecology of Echinococcus in wolves (Canis lupus) in Isle Royale National Park, Michigan, USA. JR Cerda, D Buttke, LR Ballweber, RO Peterson, LM Vucetich, JA Vucetich. 2014. Poster to be presented at the European Scientific Counsel Companion Animal Parasites conference, Lithuania, October, 2014.
• Hedrick, P.W., Peterson, R.O., Vucetich, L.M., Adams, J.R., & Vucetich, J.A. (2014). Genetic rescue in Isle Royale wolves: genetic analysis and the collapse of the population. Conserv. Genet. DOI 10.1007/s10592-014-0604-1

• Bartlick, C.I., J.I. Burton, C.R. Webster, R.E. Froese, Y.L. Dickinson. 2023. An experimental approach to identify drivers of tree regeneration diversity, composition, and heterogeneity in northern hardwood forests. Forest Ecology and Management 546: 121320.
• Bartlick, C.I., J.I. Burton, C.R. Webster, R.E. Froese, S.F. Hupperts, Y.L. Dickinson. 2023. Artificial tip-up mounds influence tree seedling composition in a managed northern hardwood forest. Canadian Journal of Forest Research. 53(11): 893-904.
• Webster, C.R., J.I. Burton, Y.L. Dickinson. 2023. Influence of silvicultural practices in northern hardwood forests on a long-lived perennial herb, Trillium cernuum L. Forest Ecology and Management 545: 121282.
• Webster, C.R., M.S. VanderMolen. 2023. Persistent, transient and emergent influences of deer herbivory on canopy gap ground layers, 18 years post-disturbance. Journal of the Torrey Botanical Society 150:437-454.
• Sample, R.D., Z.J. Delisle, J.M. Pierce, R.K. Swihart, J.N. Caudell, C.R. Webster, M.A. Jenkins. 2023. Predicting and indexing ungulate browse intensity from local to regional scales. Ecological Indicators 154: 110564.

• Wei, Z. and Wei *. 2023. Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation (Review article). Horticulture Research https://doi.org/10.1093/hr/uhad281.
• Cao, X., L. Zhang, M. Zhao, C. He, K. Zhang, S. Liu, Q. Sha* and Wei*. 2023. TGPred: Efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning, and optimization. NAR Genomics and Bioinformatics 5(3):1-13 https://doi.org/10.1093/nargab/lqad083
• Li, J., F. Han, T. Yuan, W. Li, Y. Li, H. X. Wu, H. Wei and S. Niu. 2023. The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine. Nature Communication 14, 1947. (JIF =17.7). https://doi.org/10.1038/s41467-023-37684-6   
• Niu, S*., J. Li, W. Bo, W. Yang, A. Zuccolo, S. Giacomello, J. Ma, F. Han, X. Chen, J. Yang, Y. Song,Y. Nie, B. Zhou, P. Wang, Q. Zuo, H. Zhang, J. Wang, L. Wang, Z. Liu, X. Zhang, T. Liu, S. Pei, Z. Li, Y. Hu, Y. Yang, W. Li, J. Lin, Y. Zan, L. Zhou, T. Yuan, W. Li, Y. Li, H. Wei* and Harry X. Wu*. 2022. The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 185(1):204-217. (JIF =66.58). https://www.cell.com/cell/pdf/S0092-8674(21)01428-8.pdf 
• Wang, H., S. Pak, J. Yang, Y. Wu, W. Li, H. Feng, J. Yang, H. Wei * and C. Li *. 2022. Two high hierarchical regulators, PuMYB40 and PuWRKY75, control the low phosphorus driven adventitious root formation in Populus ussuriensis. Plant Biotechnology Journal, pp. 1-17 https://doi.org/10.1111/pbi.13833  
• Gao, J., P. Zhang, W. Wu, H. Wei* and W. Zhang*. 2021. Toward an understanding of the detection, and function of R-loops in plants (Review paper).Journal of Experimental Botany 72(18):6110-6122
• Lin, G, C. He, J. Zheng, D.H. Koo, H. Le, H. Zheng, T. M. Tamang, J. Lin, Y. Liu, M. Zhao, Y. Hao, F. McFraland, B. Wang, Y. Qin, H. Tang, D.R. McCarty, H. Wei, M.J. Cho, S. Park, H. Kaeppler, S. Kaeppler, N. Springer, Y/ Liu, P.S. Schnable, G. Wang, F. F. White, S. Liu. Chromosome-level genome assembly of a regenerable maize Inbred line A188. Genome Biology 22, 175 (2021). https://doi.org/1186/s13059-021-02396-x
• Wu, W., K. Du, X. Kang, and Wei*. 2021. The diverse roles of cytokinins in regulating leaf development (Review paper). Horticulture Research 8:118.
• Wu, W., J. Li, Q. Wang, K. Lv, K. Du, W. Zhang, Q. Li, X. Kang* and H. Wei*. 2021. Growth-regulating factor 5 (GRF5)-mediated gene regulatory network promotes leaf growth and expansion in triploid poplar. 230: 612–628. New Phytologist   https://doi.org/10.1111/nph.17179  

• Deng, W., K. Zhang, C. He, S. Liu and H. Wei *. 2021. HB-PLS: A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression. Forestry Research. 1: 6 doi: 10.48130/FR-2021-0006
• Wei, H. 2021. Editorial message, Forestry Research. 1:1 doi:  10.48130/FR-2021-0001 

• 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). 

• 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  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.  https://doi.org/10.1111/nph.16778

• Zhang, P., Y. Feng, Wei* and W. Zhang*. 2019. R-loop identification and profiling in plants. Trends in Plant Science 24(10):971-972.
• Wei, H.  2019. Construction of a hierarchical gene regulatory network centered around a transcription factor (Review). Briefing in Bioinformatics.  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) https://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

• 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. (IF=8.8) https://doi.org/10.1016/j.molp.2014.11.012

• 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 (IF=6.5)  https://doi.org/10.1111/nph.12375

• 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 Res, Vol. 36, No. 9:2926-2938.  https://doi.org/10.1093%2Fnar%2Fgkn133 
• 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 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511551/

• 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 https://doi.org/10.1186/1752-0509-5-53

• 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 https://doi.org/10.1186/1471-2105-11-425
• 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. https://doi.org/10.1104/pp.106.080358 

Long, L. L., F. K. Lake, J. L. Stephens, J. D. Alexander, and J. D. Wolfe. 2023. Using culturally significant birds to guide the timing of prescribed burns in the Klamath-Siskiyou bioregion. Ecosphere https://doi.org/10.1002/ecs2.4541.

DeGroot, T. L., J. D. Wolfe, L. L. Powell, F. Esono, A. Ebana, C. Barrientos, L. Torrent, K. E. Brzeski. 2023. Human impacts on mammal communities in Rio Campo Nature Reserve, Equatorial Guinea. Journal of African Ecology https://doi.org/10.1111/aje.13108.

Oliveira, S. L., D. J. Flaspohler, and  J. D. Wolfe. 2022. Winter Territoriality of the American Redstart in Oil Palm Plantations. Diversity 14, 1079. https://doi.org/10.3390/d14121079

Luther, D. A., W. J. Cooper, V. Jirinec, J. D. Wolfe, C. L.  Rutt, R. O. Bierregaard Jr, T. E. Lovejoy,  and P. C. Stouffer. 2022. Long-term changes in avian biomass and functional diversity within disturbed and undisturbed Amazonian rainforest. Proceedings of the Royal Society B, 289(1981), p.20221123.

Tobias, J. A., C. Sheard, [...] J. D. Wolfe, [...], and 104 other authors. 2022. AVONET: morphological, ecological and geographical data for all birds. Ecology Letters 25:581-597.

Oliveira, S. L., D. J. Flaspohler, J. L. Knowlton, and J. D. Wolfe. 2022. Do oil palm plantations provide quality habitat for migratory birds? A case study from Mexico. Ecological Indicators 139: 108964. 

Rodrigues, P., L. L. Powell, C. Rutt, K. Mokross, J. D. Wolfe, E. I. Johnson and P. C. Stouffer. 2022. Sociality and morphology differentiate niches of 13 sympatric Amazonian woodcreepers (Dendrocolaptinae). Ornithology 139, p.ukac002.

Jirinec, V., R. C. Burner, R. O. Bierregaard Jr., A. Hernández-Palma, E. I. Johnson, T. E. Lovejoy, L. L. Powell, C. L. Rutt, J. D. Wolfe, P. C. Stouffer. 2021. Morphological consequences of climate change for birds in “intact” Amazonia. Science Advances https://doi.org/10.1126/sciadv.abk1743.

Pyle, P., M. Gahbauer, E. J. Johnson, T. B. Johnson, and J. D. Wolfe. 2021. Application of a global coding system (“WRP”) to study avian demography based on molt and plumage cycles of birds. Ornithology 139:1-12.

Miller, S. J., J. Wiethase, A. Etingue, E. Franklin, M. F. Mene, J. D. Wolfe, M. K. Gonder and L. Powell. 2021. The impact of new road construction on a pristine Afrotropical mountain: A case study using avian communities on Bioko Island, Equatorial Guinea. Biotropica https://doi.org/10.1111/btp.13014.

Terrill, R. S., Y. Fong, J. D. Wolfe, and A. J. Zellmer. 2021. Threshold models improve estimates of molt parameters in datasets with small sample sizes. Ornithology 138(3), ukab038.

Jarrett, C., T. B. Smith, R. Claire, D. Ferreira, M. Tchoumbou Malange, N. F. Elikwo, J. D. Wolfe, K. Brzeski, J. Cooper, R. Hanna, C. Masso, K. Fiaboe and L. Powell. 2021. Bird communities in African cocoa are diverse but lack specialized forest insectivores. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.13864

Oliveira, S. L., D. J. Flaspohler, J. L. Knowlton, C. R. Webster, and J. D. Wolfe. 2021.  Migratory bird community structure in oil palm (Elaies guineensis) plantations and native forest fragments in southern Mexico. Journal of Field Ornithology 92:1–17.

Stouffer, P. C., V. Jirinec, C. L. Rutt, R. O. Bierregaard, Jr., A. Hernández-Palma, E. I. Johnson, S. R. Midway, L. L. Powell, J. D. Wolfe, and T. E. Lovejoy. 2021. Long-term bird community change in undisturbed Amazonian rainforest: Pervasive abundance declines and a shifting baseline. Ecology Letters 24: 186–195.

• Yuan Y*, Chen C (2018) Widespread Antisense Transcription of Populus Genome under Drought. Molecular Genetics and Genomics 293(4): 1017-1033.
• Fueangfung S, Yuan Y, Fang S (2014) Denaturing Reversed-Phase HPLC Using a Mobile Phase Containing Urea for Oligodeoxynucleotide Analysis. Nucleosides, Nucleotides and Nucleic Acids 33: 481-488.
• Pokharel D, Yuan Y, Fueangfung S, Fang S (2014) Synthetic Oligodeoxynucleotide Purification by Capping Failure Sequences with a Methacrylamide Phosphoramidite Followed by Polymerization. RSC Advances 4: 8746–8757.
• Xue L-J, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, Frost CJ, Chen H-Y, BabstBA,Harding SA, Tsai CJ (2013) Constitutively Elevated Salicylic Acid Levels Alter Photosynthesis and Oxidative State but not Growth in Transgenic Populus. Plant Cell 25: 2714-2730.
• Fang S, Fueangfung S, Yuan Y (2012) Purification of Synthetic Oligonucleotides via Catching by Polymerization. In Current Protocols in Nucleic Acid Chemistry (Martin Egli, Piet Herdewijn, Akira Matusda,Yogesh S. Sanghvi, eds.). John Wiley and Sons, New York, Unit 10.14.1-10.14.21.
• Yuan Y, Fueangfung S, Lin X, Pokharel D, Fang S (2012) Synthetic 5′-Phosphorylated Oligodeoxynucleotide Purification through Catching Full-length Sequences by Polymerization. RSC Advances 2: 2803-2808.