Research Publications

2022

Remote Sensing | Free Full-Text | An Unsupervised Canopy-to-Root Pathing (UCRP) Tree Segmentation Algorithm for Automatic Forest Mapping (mdpi.com) Carpenter, J. et al. 2022. An Unsupervised Canopy-to-Root Pathing (UCRP) Tree Segmentation Algorithm for Automatic Forest Mapping. Remote Sensing. 14(17), 4274.
Remote Sensing | Free Full-Text | Automated Inventory of Broadleaf Tree Plantations with UAS Imagery (mdpi.com) Chandrasekaran, A. et al. 2022. Automated inventory of broadleaf tree plantations with UAS imagery. Remote Sensing 14(8), 1931.
Remote Sensing | Free Full-Text | Comparative Analysis of Multi-Platform, Multi-Resolution, Multi-Temporal LiDAR Data for Forest Inventory (mdpi.com) Lin, Y.C., Shao, J., Shin, S.-Y., Saka, Z., Joseph, M., Manish, R., Fei, S., Habib, A., 2022. Comparative Analysis of Multi-Platform, Multi-Resolution, Multi-Temporal LiDAR Data for Forest Inventory. Remote Sensing. 14, 649
Precise Quantification of Land Cover before and after Planned Disturbance Events with UAS-Derived Imagery | Semantic Scholar Miller, Z., Hupy, J., Hubbard, S., Shao, G. 2022. Precise Quantification of Land Cover before and after Planned Disturbance Events with UAS-Derived Imagery. Drones. 6, 52.
Preferential allocation of carbohydrate reserves belowground supports disturbance-based management of American chestnut (Castanea dentata) | Semantic Scholar Montague, M.S., Landhäusser, S.M., McNickle, G.G., Jacobs, D.F. 2022. Preferential allocation of carbohydrate reserves belowground supports disturbance- based management of American chestnut (Castanea dentata). Forest Ecology and Management. 509:120078
Remote Sensing | Free Full-Text | High-Resolution Canopy Height Model Generation and Validation Using USGS 3DEP LiDAR Data in Indiana, USA (mdpi.com) Oh, S. et al. 2022.Canopy height model generation and validation using USGS 3DEP LiDAR data in Indiana, USA. Remote Sensing. 14 (4), 935.
Remote Sensing | Free Full-Text | Comparative Evaluation of a Newly Developed Trunk-Based Tree Detection/Localization Strategy on Leaf-Off LiDAR Point Clouds with Varying Characteristics (mdpi.com) Zhou, T., dos Santos, R. C., Liu, J., Lin, Y.C., Fei, W.C., Fei, S., and Habib, A., 2022. Comparative Evaluation of a Newly Developed Trunk-Based Tree Detection/Localization Strategy on Leaf-O£ LiDAR Point Clouds with Varying Characteristics. Remote Sensing. 14, no. 15: 3738.
7138d2b834f1393a032be394a2dee88c68b9.pdf (semanticscholar.org) Zhou, T., Fei, S., and Habib., A. 2022. Forest Feature-based LiDAR SLAM (F2-SLAM) for Backpack Systems. Manuscript is finalized for submission to Remote Sensing of Environment.

2021

Chemically-mediated colonization of black cherry by the peach bark beetle, Phloeotribus liminaris - PubMed (nih.gov) Ethington, M.W., G.P. Hughes, N.R. VanDerLaan, M.D. Ginzel. 2021. Chemically-mediated colonization of black cherry by the peach bark beetle, Phloeotribus liminaris. Journal of Chemical Ecology. 47 (3): 303-312
[PDF] A commentary review on the use of normalized difference vegetation index (NDVI) in the era of popular remote sensing | Semantic Scholar Huang, S., L.N. Tang, J.P. Hupy, Y. Wang, and G.F. Shao. 2021. Commentary review on the use of normalized difference vegetation index (NDVI) in the era of popular remote sensing. Journal of Forestry Research. 32: 1–6.
[PDF] Vacuum Steam Treatment Effectiveness for Eradication of the Thousand Cankers Disease Vector and Pathogen in Logs From Diseased Walnut Trees | Semantic Scholar Juzwik, J., A. Yang, S. Heller, M. Moore, Z Chen, M. White, H. Wantuch, M.D. Ginzel, R. Mack. 2021. Vacuum steam treatment effectiveness for eradication of the Thousand cankers disease vector and pathogen in logs from diseased walnut trees. Journal of Economic Entomology. 114 (1): 100 - 111.
Drones | Free Full-Text | Leaf-Off and Leaf-On UAV LiDAR Surveys for Single-Tree Inventory in Forest Plantations (mdpi.com) Lin, Y., J. Liu, S. Fei, and A. Habib. 2021. Leaf-off and Leaf-on UAV LiDAR Surveys for Single Tree Inventory in Forest Plantations. Drones. 5(4): 115
Remote Sensing | Free Full-Text | Comparative Analysis of Multi-Platform, Multi-Resolution, Multi-Temporal LiDAR Data for Forest Inventory (mdpi.com) Lin, Y., Shao, J., Shin, Y., Saka, Z., Joseph, M., Manish, R., Fei, S., and Habib, A. 2021. Comparative Analysis of Multi-platform, Multi-resolution, and Multi-temporal LiDAR Data for Forest Inventory. (Submitted to Remote Sensing Journal.)
Application of Postprocessing Kinematic Methods with UAS Remote Sensing in Forest Ecosystems | Semantic Scholar Miller, Z., J. Hupy, A. Chandrasekaran, G. Shao, and S. Fei. 2021. Application of Post-Processing Kinematic Methods with UAS Remote Sensing in Forest Ecosystems. Journal of Forestry. 119: 454–466.
Quantification of Land Cover Surrounding Planned Disturbances Using UAS Imagery (purdue.edu) Miller, Zachary. 2021. Quantification of Land Cover Surrounding Planned Disturbances using UAS Imagery. M.S. Thesis, School of Aviation and Transportation Technology, Purdue University
(PDF) In Situ Calibration and Trajectory Enhancement of UAV and Backpack LiDAR Systems for Fine-Resolution Forest Inventory (researchgate.net) Ravi, R., Y. Lin, R. Manish, S. Fei, and A. Habib. 2021. Backpack and UAV LiDAR Data Fusion for Trajectory Enhancement and Derivation of Accurate Forest Inventory Metrics. (Submitted to ISPRS Journal for Photogrammetry and Remote Sensing.)
[PDF] Introducing Image Classification Efficacies | Semantic Scholar Shao, G.F., L.N. Tang, and H. Zhang. 2021. Introducing Image Classification Efficacies. IEEE Access 9:134809-134816.
Frontiers | Competitive Advantage of Geosmithia morbida in Low-Moisture Wood May Explain Historical Outbreaks of Thousand Cankers Disease and Predict the Future Fate of Juglans nigra Within Its Native Range (frontiersin.org) Williams, G.W., M.D. Ginzel. Competitive advantage of Geosmithia morbida in low-moisture wood may explain historical outbreaks of Thousand cankers disease and predict the future fate of Juglans nigra. Frontiers in Forests and Global Change. 4.

2020

Consequences of Discount Rate Selection for Financial and Ecological Expectation and Risk in Forest Management 2020. Buongiomo, J., and Zhou, M. Journal of Forest Economics 35(1):1-17.
Estimating Dynamics of Central Hardwood Forests Using Random Forests 2020. Ma, W., Lin, G., and Liang, J. Ecological Modeling 419:108947.
A Machine Learning-Based Classification System for Urban Built-Up Areas Using Multiple Classifiers and Data Sources 2020. Sun,L., Tang, L, Shao, G., and Qiu, Q. Remote Sensing 12(1): DOI:10.3390/rs12010091.
Forest Genomics and Biotechnology 2020. Eds. Meilan, R., Kirst, M published CABI, Boston, MA
Hardwood Species Show Wide Variability in Response to Silviculture during Reclamation of Coal Mine Sites 2020. Schempf, W.M. and Jacobs, D.F. Forest 11(1) DOI:10.3390/f11010072.
The complete chloroplast genome sequence of American elm (Ulmus americana) and comparative genomics of related species 2020. Ebrahimi, A., Antonides, J.D., Pinchot, C.C., Slavicek, J.M., Flower, C.E., and Woeste, K.E. bioRxiv The preprint server for Biology.
Remotely Sensed Mid-Channel Bar Dynamics in Downstream of the Three Gorges Dam, China 2020. Wen, Z., Yang, W., Zhang, C., Shao, G., and Wu, S. Remote Sensing 12(3):409.

2019

Optimal forest management under financial risk aversion with discounted Markov decision process models 2019. Zhou, M. and Buongiomo, J. Canadian Journal of Forest Research 49(7):802-809.
Accelerating upward treeline shift in the Altai Mountains under last-century climate change 2019. Cazzolla Gatti, R., Callaghan, T., Velichevskaya, A., Dudko, A.. Fabbio, L., Battipaglia, G., and Liang, J. Scientific Reports 9:7678.
Parameterization of biodiversity-productivity relationship and its scale dependency using georeferenced tree-level data 2019. Luo, W., Liang, J., Cazzolla Gatti, R., Zhao, X., and Zhang, C. Journal of Ecology 107(3):1106-1119.
Climatic controls of decomposition drive the global biogeography of forest-tree symbioses 2019. Steidinger, B.S., Crowther, T.W., Liang, J., Van Nuland, M.E., Werner, G.D.A., Reich, P.B., Nabuurs, G.J., de-Miguel, S., Zhou, M., Picard, N., Herault, B., Zhao, X., Zhang, C., Routh, D., Peay, K.G., and GFBI consortium Nature 569:404-408.
Coastal Alaska forests under climate change: What to expect? 2019. Ma, W., Zhou, X., Liang, J. and Zhou, M. Forest Ecology and Management 448:432-444.
Predicting invasiveness of exotic woody species using a traits-based framework 2019. Nunez-Mir, G.C., Guo, Q., and Fei, S. Ecology Ecological Society of America 100(10):e02797 DOI:https://doi.org/10.1002/ecy.2797.
Using a tree seedling mortality budget as an indicator of landscape-scale forest regeneration security 2019. Vickers, L,A., McWilliams, W.H. ,Knapp, B.O., D'Amato, A.W., Saunders, M.R., Shifley, S.R., Kabrick, J.M., Dey, D.C., Larsen, D.R., and Westfall, J.A. Ecological Indicators 96(1):718-727.
Short-term, spatial regeneration patterns following expanding group shelterwood harvests and prescribed fire in the Central Hardwood Region 2019. Greenler, S.M. and Saunders, M.R. Forest Ecology and Management 432:1053-1063.
Shifts in forest composition in the eastern United States 2019. Knott, J.A., Desprez, J.M., Oswalt, C.M., and Fei, S. Forest Ecology and Management 433:176-183.
Microbial mechanisms and ecosystem flux estimation for aerobic NOy emissions from deciduous forest soils 2019. Mushinski, R.M., Phillips, R.P., Payne, Z.C., Abney, R.B., Jo, I., Fei, S., Pusede,S.E., White, J.R.. Rusch, D.B. and Raff, J.D. PNAS 116(6):2138-2145.
Influence of mulching and tree shelters on 4-year survival and growth of zeen oak (Quercus canariensis) seedlings 2019. Mechergui.T, Pardos, M., and Jacobs, D.F. Journal of Forestry Research 30:129-141.
Natural regeneration of Pinus pinaster facilitates Quercus ilex survival and growth under severe deer browsing pressure 2019. Maltoni, Al., Mariotti, B. Tani, A., Martini, S., Jacobs, D.F., and Tognetti, R. Forest Ecology and Management 432:356-364.
Microsatellite Borders and Micro-sequence Conservation in Juglans 2019. Ebrahimi, A., Mathur, S., Lawson, S.S., LaBonte, N.R., Lorch, A., Coggeshall,M.V., and Woeste, K.E. Scientific Reports 9:2748 DOI: https://doi.org/10.1038/s41598-019-39793-z.
Delineation of individual deciduous trees in plantations with low-density LiDAR data 2019. Shao, G., Shao, G., and Fei, S. International Journal of Remote Sensing 40(1):346-363.
Trends in ecology: shifts in ecological research themes over the past four decades 2019. McCallen, E., Knott, J., Nunez-Mir, G., Taylor, B., Insu, J., Fei, S. Frontiers in Ecology and the Environment 17(2):109-116.
An integrated assessment of the potential impacts of climate change on Indiana forests 2019. Phillips, R.P., Brandt, L., Polly, P.D., Zollner, P., Saunders, M.R., Clay, K, Iverson, L., and Fei, S. Climatic Change DOI: https://doi.org/10.1007/s10584-018-2326-8.
Shifts in dominant tree mycorrhizal associations in response to anthropogenic impacts 2019. Jo, I., Fei, S., Oswalt, C.M., Domke, G.M., and Phillips, R.P. Science Advances 5(4):eaav6358.
Tree diversity regulates forest pest invasion 2019. Guo, Q., Fei, S., Potter, K.M., Liebhold, A.M., and Wen, J. PNAS 116(15):7382-7386.
Mapping global forest biomass and its changes over the first decade of the 21st century 2019. Chen, A., Peng, S., and Fei, S. Science China Earth Sciences 62:585-594.
Using a tree seedling mortality budget as an indicator of landscape-scale forest regeneration security 2019. Vickers, L.A., McWilliams, W.H., Knapp, B.O., D’Amato, A.W., Saunders, M.R., Shifley, S.R., Kabrick, J.M., Dey, D.D., Larsen, D.R., and Westfall, J.A. Ecological Indicators 96(1):718-727.
Restoring forests: regeneration and ecosystem function for the future 2019. Lof, M., Madsen, P., Metslaid, M., Witzell, J., and Jacobs, D.F. New Forests 50:139-151.
Regeneration niches in Nothofagus-dominated old-growth forest after partial disturbance: Insights to overcome arrested succession 2019. Soto, D.P, Puettmann, K.J., Fuentes, C., and Jacobs, D.F. Forest Ecology and Management 445:26-36.
Photosynthetic parameters of Juglans nigra trees are linked to cumulative water stress 2019. Gauthier, M.M. and Jacobs, D.F. Canadian Journal of Forest Research 49:752-758.
Effect of Prescribed Fire on Timber Volume and Grade in the Hoosier National Forest 2019. Stanis, S., Wiedenback, J., and Saunders, M.R. Forest Science 65(6):714-724 https://doi.org/10.1093/forsci/fxz039.
Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut 2019. Zhang, B.W., Xu, L.L., Li, N., Yan, P.C., Jiang, X.H., Woeste, K.E., Lin, K., Renner, S.S., Zhang, D.Y. and Bai, W.N. Molecular Biology and Evolution 36(11):2451-2461 DOI:10.1093/molbev/msz112.
Detection of Geosmithia morbida on Numerous Insect Species in Four Eastern States 2019. Moore, M., Juzwik, J., Miller, F., Roberts, L., and Ginzel, M.D. Plant Health Progress 20(3):133-139.
Overcoming cellulose recalcitrance in woody biomass for the lignin-first biorefinery 2019. Yang, H., Zhang, X., Luo, H., Liu, B., Shiga,T.M., Li, X., Kim, J.I., Rubinelli, P., Overton, J.C., Subramanyam, V., Cooper, B.R., Mo, H., Abu-Omar, M.M., Chapple, C., Donohoe, B.S., Makowski, L., Mosier, N.S., McCann, M.C., Carpita, N.C., and Meilan, R. Biotechnology for Biofuels 12:171-188.
High rates of primary production production in structurally complex forests 2019. Gough, C.M., Atkins, J.W., Fahey, R.T., and Hardiman, B.S. Ecology:100(10):e2864 https://doi.org/10.1002/ecy.2864.
An enhanced strategy for molecular detection of thousand cankers disease 2019. Stackhouse, T., Oren, E., Boggess, S., Ginzel, M., Hadziabdic, D., Trigiano R., and Klingeman, W. Mid-Atlantic States Mycological Conference (MASMC) University of Tennessee-Knoxville April 12-14, 2019.
Urban sprawl scenario simulations based on cellular automata and ordered weighted averaging ecological constraints 2019. Liao, J., Shao, G., Wang, C., Tang, L., Huang, Q., and Qiu, Q. Ecological Indicators Volume 107:105572.
Ecologically distinct pine species show differential root development after outplanting in response to nursery nutrient cultivation 2019. Toca, A., Oliet, J.A., Villar-Salvador, P., Catalan, R.A.M., and Jacobs, D.F. Forest Ecology and Management Vol: 451:117562.
Defining a spectrum of integrative trait-based vegetation canopy structural types 2019. Fahey, R.T., Atkins, J.W., Gough, C.M., Hardiman, B.S., Nave, L.E., Tallant, J.M., Nadehoffer, K.J., Vogel, C., Scheuermann, C.M., Stuart-Haentjens, E., Haber, L.T., Fotis, A.T., Ricart, R., and Curtis, P.S. Ecology Letters 22(12):2049-2059 DOI: 10.1111/ele.13388.
Structural diversity as a predictor of ecosystem function 2019. LaRue, E.A., Hardiman, B.S., Elliott, J.M., and Fei, S. Environmental Research Letters 14(11)114011.
Overselling overall map accuracy misinforms about research reliability 2019. Shao, G., Tang, L. and Liao, J. Landscape Ecology 34:2487-2492.
Rhamnogalacturonan-I is a determinant of cell-cell adhesion in poplar wood 2019. Yang, H., Benatti, M.R., Karve, R.A., Fox, A., Meilan, R., Carpita, N.C., and McCann, M.C. Plant Biotechnology Journal (https://doi.org/10.1111/pbi.13271)
Age structure and recruitment of Trillium luteum (Trilliaceae) populations in secondary forests of the southern Appalachian Mountains 2019. Jenkins, M.A. and Webster, C.R. The Journal of the Torrey Botanical Society 146(4): 239-251.
Herbivory and Competing Vegetation Interact as Site Limiting Factors in Maritime Forest Restoration 2019. Thyroff, E.C., Burney, O.T., and Jacobs, D.F. Forest 10, 950; doi:10.3390/f10110950.
Unraveling Shade Tolerance and Plasticity of Semi-Evergreen Oaks: Insights From Maritime Forest Live Oak Restoration 2019. Thyroff, E.C., Burney, O.T., Mickelbart, M.V. and Jacobs, D.F. Frontiers in Plant Science DOI: 10.3389/fpls.2019.01526.
Spatial and Climatic Factors Influence Ambrosia Beetle (Coleoptera: Curculionidae) Abundance in Intensively Managed Plantations of Eastern Black Walnut 2019. Williams, G.M. and Ginzel, M.D. Environmental Entomology DOI: 10.1093/ee/nvz125.
Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China 2019. Sun, Y.W., Hou, N., Woeste, K., Zhang, C., Yue, M., Yuan, X.Y., and Zhao, P. Ecology and Evolution DOI: 10.1002/ece3.5850.
Water stress rather than N addition mitigates impacts of elevated O3 on foliar chemical profiles in popular saplings 2019. Li, Z., Yang, J., Shang, B., Xu, Y., Couture, J.J., Yuan, X., Kobayashi, K., and Feng, Z. Science of The Total Environment.
Implications of climate change for managing urban green infrastructure: an Indiana, US case study 2019. Reynolds, H.L., Brandt, L., Fischer, B.C., Hardiman, B.S., Moxley, D.J., Sandweiss, E., Speer, J.H., and Fei, S. Climate Change DOI: https://doi.org/10.1007/s10584-019-02617-0.
Surface and subsurface material selections influence the early outcomes of boreal upland forest restoration 2020. Stack, S., Jones, C., Bockstette, J., and Jacobs, D.F. Ecological Engineering 144:1057052.
Implications of climate change for managing urban green infrastructure: an Indiana, US case study 2019. Reynolds, H.L., Brandt, L., Fischer, B.C., Hardiman, B.S., Moxley, D.J., Sandweiss, E., Speer, J.H., and Fei, S. Climate Change DOI: https://doi.org/10.1007/s10584-019-02617-0.

2018

Pooled whole-genome sequencing of interspecific chestnut (Castanea) hybrids reveals loci associated with differences in caching behavior of fox squirrels (Sciurus niger L.) 2018. LaBonte, N.R. and Woeste, K.E. Ecology and Evolution 8(22):10638-10654.
Simulated predation of of Quercus variabills acorns impairs nutrient remobilzation and seedlings performance irrespective of soil fertility 2018. Shi, W., Villar-Salvador, P., Jacobs, D.F., Li, G., and Jiang, X. Plant and Soil 423:295-306.
Alleviation of heavy metal phytotoxicity in sewage sludge by vermlcoposting with additive urban plant litter 2018. Wu, D., Yu, X., Chu,S, Jacobs, D.F., Wei, X., Wang, C., Long, F., Chen, X., and Zeng, S. Science of the Total Environment 633:71-80.
Trends in Production of Hardwood Tree Seedlings Across the Northeast United States From 2008 to 2016 2018. Pike, C., Warren, J., and Coggeshall, M. Tree Planter's Notes 61(1):18-25.
Reproduction and potential range expansion of walnut twig beetle across the Juglandaceae 2018. Hefty, A.R., Aukema, B.H., Venette, R.C., Coggeshall, M.V., McKenna, J.R., and Seybold, S.J. Biological Invasions 20(8):2141-2155.
A novel molecular toolkit for rapid detection of the pathogen and primary vector of thousand cankers disease 2018. Oren, E., Klingeman, W., Gazis, R., Moulton, J., Lambdin, P., Coggeshall, M., Hulcr, J., Seybold, S.J., and Hadziabdic, D. PLoS ONE 13(1):e018587,
Discrimination and assessment of black walnut (Juglans nigra L.) cultivars using phenology and microsatellite markers (SSRs) 2018. Zhao, P., Zhou, H., Coggeshall, M.V., and Chung-Ho, L. Canadian Journal of Plant Science 98(3):616-627.
Identification and Characterization of Phenolic Compounds in Black Walnut Kernels 2018. Vu, D.C., Vo, P.H., Coggeshall, M.V., and Lin, C.H. Journal of Agriculture and Food Chemistry 66(17):4503-4511.
Genomic Variation Among and Within Six Juglans Species 2018. Stevens, K.A., Woeste, K., Chakraborty, S., Crepeau, M.W., Leslie, C.A., Martinez-Garcia, P.J., Puiu, D., Romero-Sevenson, J., Coggeshall, M., Dandekar, A.M., Kluepfel, D., Neale, D.B., Salzberg, S.L., and Langley, C.H. Genes Genomes Genetics 8(7):2153-2165.
Pollen flow and paternity in an isolated and non-isolated black walnut (Juglans nigra L.) timber seed orchard 2018. Ebrahimi, A., Lawson, S.S., Frank, G.S., Coggeshall, M.V., Woeste, K.E., McKenna, J.R. PLoS ONE 13(12):e0207861.
Growth traits of juvenile American chestnut and red oak as adaptations to disturbance 2018. Belair, E.P., Saunders, M.R., and Landhausser, S.M. Restoration Ecology 26(4):712-719.
Ten-Year Responses of Underplanted Northern Red Oak to Silvicultural Treatments, Herbivore Exclusion, and Fertilization 2018. Frank, G.S., Rathfon, R.A., and Saunders, M.R. Forests 9(9):571.

2017

Characterization of Juglans nigra (L.), Juglans regia (L.) and Juglans x intermedia (Carr.) by SSR markers: a case study in Italy 2017. Pollegioni, P., Woeste, K., Major, A., Mugnozza, G.S., and Malvolti, M.E. Silvae Genetica 58(1-6):68-78.
Characterization of the complete chloroplast genome of Platycarya strobilacea (Juglandaceae) 2017. Yan, J., Han, K., Zeng, S., Zhao, P., Woeste, K., Li, J., and Liu, Z. Conservation Genetics Resources 9(1):7981
Response of spring flora to nearly two decades of deer exclusion and resurgent woody understories within exclosures 2017. Webster, C.R., Rock, J.H., and Jenkins, M.A. Journal of the Torrey Botanical Society 144(1):1-14.
Combining Biodiversity Resurveys across Regions to Advance Global Change Research 2017. Verheyen, K., De Frenne, P., Baeten, L., Waller, D.M., Hedl, R., Perring, M.P., Blondeel, H., Brunet, J., Chudomelova, M., Decocq, G., De Lombaerde, E., DePauw, L., Dirnbock, T., Durak, T., Eriksson, O., Guilliam, F.S., Heinken, T., Heinrichs, S., Hermy, M., Jaroszewicz, B., Jenkins, M.A., Johnson, S.E., Kirby, K.J., Kopecky, M., Landuyt, D., Lenoir, J., Li, D., Macek, M., Maes, S.L., Malis, F., Mitchell, F.J.G., Naaf, T., Peterken, G., Petrik, P., Reczynska, K., Rogers, D.A., Schei, F.H., Schmidt, W., Standovar, T., Swierkosz, K., Ujhazy, K., Van Calster, H., Vellend, M., Vild, O., Woods, K., Wulf, M., and Bernhardt-Romermann, M. BioScience 67(1):73-83.
Pollen gene flow, male reproductive success, and genetic correlations among offspring in a northern red oak (Quercus rubra L.) seed orchard 2017. Alexander, L. and Woeste, K. PLOS ONE 12(2): e0171598. DOI:10.1371/journal.pone.0171598.
Isolation and characterization of a floral homeotic gene in Fraxinus nigra causing earlier flowering and homeotic alterations in transgenic Arabidopsis 2017. Lee, J.H. and Pijut, P.M. Plant Gene 10:17-25.
Genetic diversity of Persian walnut (Juglans regia) in the cold-temperate zone of the United States and Europe (PDF 268 KB) 2017. Ebrahimi, A., Zarei, A., McKenna, J.R., Bujdoso, G., and Woeste, K.E. Scientia Horticulturae 220:36-41.
Adventitious Shoot Regeneration from in vitro Leaf Explants of Fraxinus nigra 2017. Lee, J.H. and Pijut, P.M. Plant Cell Tissue and Organ Culture 130(2):335-343.
Origin of adventitious roots in black walnut (Juglans nigra) softwood cuttings rooted under optimized conditions in a fog chamber 2017. Stevens, M.E. and Pijut, P.M. New Forests 48(5):685-697.
Development of Novel Genic Microsatellite Markers from Transcriptome Sequencing in Sugar Maple (Acer saccharum Marsh.) 2017. Harmon, M., Lane, T., Staton, M. Coggeshall, M.V., Best, T., Chien-Chin Chen, Liang, H., Zembower, N., Drautz-Moses, D.I., Yap Zhei Hwee, Schuster, S.C., Schlarbaum, S.E., Carlson, J.E., Gailing, O. BMC Res. Notes 10:369
High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra 2017. Konar, A., Choudhury, O., Bullis, R., Fiedler, L., Kruser, J.M., Stephens, M.T., Gailing, O., Schlarbaum, S., Coggeshall, M.V., Staton, M.E., Carlson, J.E., Emrich, S., and Romero-Severson, J. BMC Genomics 18:417.
Practical Strategies of Black Walnut Genetic Improvement – An Update 2017. Rink, G, Van Sambeek, J.W., O'Connor, P., and Coggeshall, M.V. Walnut Council Bulletin 44(2): 1-3, 10-11.
Costs and returns of producing hops in established tree plantations 2017. Ha. K., Atallah, S., Benjamin, T., Hoagland, L., Farlee, L., and Woeste, K. Purdue Extension FNR-546W.
Demographically Idiosyncratic Responses to Climate Change and Rapid Pleistocene Diversification of the Walnut Genus Juglans (Juglandaceae) Reveals by Whole-genome Sequences (PDF 959 KB) 2017. Bai, W.N., Yan, P.C., Zhang, B.W., Woeste, K.E., Lin, K., and Zhang, D.Y. New Phytologist 27(4):1726-1736.
Completion of the Chloroplast Genomes of Five Chinese Juglans and Their Contribution to Chloroplast Phylogeny 2017. Hu, Y., Woeste, K.E., and Zhao, P. Frontiers in Plant Science 2017 7:1-6 DOI: 10.3389/pls.2016.01955.
Evaluation of genetic variability among “Early Mature” Juglans regia using microsatellite markers and morphological traits 2017. Ebrahimi, A., Zarei, A., Zamani Fardadonbeh, M., and Lawson, S. PeerJ: 5. e3834. 10.7717/peerj.3834.
Using foliar spectral properties to assess the effects of drought on plant water potential 2017. Cotrozzi, L., Couture, J.J., Cavender-Bares, J., Kingdon, C.C., Fallon, B., Pilz, G., Pellegrini, El, Nali, C., and Townsend, P.A. Tree Physiology 37(11):1582-1591.
Vernal freeze damage and genetic variability alter tree growth, chemistry, and insect interactions 2017. Rubert-Nason, K.F., Couture, J.J., Gryzmala, E. A., Townsend, P.A., and Lindroth, R.L. Plant, Cell, and Environment 40(11):2743-2753.
Effects of elevated carbon dioxide and ozone on foliar quality of trembling aspen (Populus tremuloides) and paper birch (Betula papyrifera) (2017) Couture, J.J., Meehan, T.D., Rubert-Nason, K.F., and Lindroth, R.L. Journal of Chemical Ecology 43(1):26-38.

2016

Genetic diversity and genetic structure of Persian walnut (Juglans regia) accessions from 14 European, African, and Asian countries using SSR markers 2016. Ebrahimi, A., Zarei, A., Lawson, S., Woeste, K.E., and Smulders, M.J.M. Tree Genetics & Genomes 12:114.
Vegetative and Adaptive Traits Predict Different Outcomes for Restoration Using Hybrids 2016. Crystal, P.A., Lichti, N.I., Woeste, K.E., and Jacobs, D.F. Frontiers in Plant Science 7:1711 DOI 10.3389/fpls.2016.01741.
Adventitious root formation in Juglans nigra: a time and place for everything 2016. Stevens, M.E. and Pijut, P.M. Acta Horticulturae 1140:337-339.
Consequences of Shifts in Abundance and Distribution of American Chestnut for Restoration of a Foundation Forest Tree 2016. Dalgleish, H.J., Nelson, C.D., Scrivani, J.A., and Jacobs, D.F. Forests 7(4): 1-9.
Ungulate impacts on herbaceous-layer plant communities in even-ages and uneven-aged managed forests 2016. Murray, B.D., Webster, C.R., Jenkins, M.A., Saunders, M.R., and Haulton, G.S. Ecosphere 7(6):e01378.10.1002/esc2.1378.
Genectic diversity and population structure of common walnut (Juglans regia,) in China based EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (PAL) 2016. Han, H., Woeste, K.E., Hu,Y., Dang, M., Zhang, T., Gao, S., Zhou, H., Feng, X., Zhao, G., and Zhao, P. Tree Genetics & Genomes 12:111-122.
Characterization of the complete chloroplast genome of the endangered species Carya sinensis (Juglandaceae) 2016. Hu, Y., Chen, X., Feng, X., Woeste, K.E., and Zhao, P. Conservation Gent. Resources. 8:467-470.
Two decades of compositional and structural change in deciduous old-growth forests of Indiana, USA 2016. Lowney, C.A., Graham, B.D., Spetich, M.A., Shifley, S.R., Saunders, M.R., and Jenkins, M.A. Journal of Plant Ecology 9(3):236-271.
Predicting the height growth of oak species (Quercus) reproduction over a 23-year period following clearcutting 2016. Swaim, J.T., Dey, D.C., Saunders, M.R., Weigel, D.R., Thornton, C.D., Kabrick, J.M., and Jenkins, M.A. Forest Ecology and Management 364:101-112.
Effectiveness of a detached-leaf assay as a proxy for stem inoculations in backcrossed chestnut (Castanea) blight resistance breeding populations 2016. LaBonte, N.R., McKenna, J.R., and Woeste, K. Forest Pathology 47(2):E12313 DOI: 10.1111/efp.12313.
Improved growth and weed control of glyphosate-tolerant poplars 2016. Ault, K., Viswanath, V., Jayawickrama, C.M., Eaton, J., Meilan, R., Beauchamp, G., Hohenschuh, G.M., and Strauss, S.H. New Forests 47(5):653-667. DOI 10.1007/s11056-016p9536-6.
Protoplast isolation and genetically true-to-type plant regeneration from leaf- and callus-derived protoplasts of Albizia julibrissin 2016. Rahmani, M., Pijut, P.M., and Shabanian, N. Plant Cell Tissue Organ Culture 127(2):475-488.
Germination and early seedling growth of Pinus densata Mast. provenances 2016. Xu, Y, Cai, N., He, B., Zhang, R., Zhao, W., Mao, J., Duan, A., Li, Y., Woeste, K. Journal of Forestry Research 27(2):283-294.
The complete chloroplast genome of common walnut (Juglans regia) 2016. Hu, Y., Woeste, K.E., Dang, M., Zhou, T., Feng, X., Zhao, G., Liu, Z., Li, Z., and Zhao, P. Mitogenome DNA: Resources 1(1):189-190 DOI: 10.108023802359.2015.1137804.
De novo genome assembly of Geosmithia morbida, the casual agent of thousand cankers disease (PDF 159 KB) 2016. Schuelke, T.A., Westbrook, A., Broders, K., Woeste, K., and MacManes, M.D. PeerJ 4:31952: DOI 10.7717/peerj.1952.

2015

Influence of Intensity and Duration of Invasion by Amur Honeysuckle (Lonicera maackii) on Mixed Hardwood Forests of Indiana 2015. Shields, J.M., Jenkins, M.A., Saunders, M.R., Gibson, K.D., Zollner, P.A., and Dunning, Jr., J.B. Invasive Plant Science and Management 8(1):44-56.
Geosmithia morbida Found on Weevil Species Stenomimus pallidus in Indiana 2015. Juzwik, J., Banik, M.T., Reed, S.E., English, J.T., Ginzel, M.D. Plant Health Progress 16(1):7-10.
Restoring forests: What constitutes success in the twenty-first century? 2015. Jacobs, D.F., Oliet, J.A., Aronson, J., Bolte, A., Bullock, J.M., Donoso, P.J., Landhausser, S.M., Madsen, P., Peng, S., Rey-Benayas, J.M., and Weber, J.C. New Forests 46(5-6):601-614.
Propagating figured wood in black walnut 2015. McKenna, J.R., Geyer, W.A., Woeste, K.E., and Cassens, D.L. Open Journal of Forestry 5(5):518-525.
Genetic fidelity assessment of in vitro-regenerated plants of Albizia julibrissin using SCoT and IRAP fingerprinting 2015. Rahmani, M.S., Pijut, P.M., Shabanian, N., and Nasri, M.In Vitro Cellular and Developmental Biology-Plant 51(4):407-419.
Agrobacterium-mediated genetic transformation of Fraxinus americana hypocotyls 2015. Palla, K.J. and Pijut, P.M. Plant Cell Tissue and Organ Culture 120(2):631–641.

2014

Agrobacterium-mediated transformation of black cherry for flowering control and insect resistance 2014. Wang, Y. and Pijut, P.M. Plant Cell Tissue Organ Culture 119(1):107-116.
Improvement of Agrobacterium-mediated transformation and rooting of black cherry 2014. Wang, Y. and Pijut, P.M. In Vitro Cellular & Developmental Biology - Plant 50(3):307-316.
Agrobacterium-mediated genetic transformation and plant regeneration of the hardwood tree species Fraxinus profunda 2014. Stevens, M.E. and Pijut, P.M. Plant Cell Reports 33(6):861-870.
Biogeomorphic Impacts of Invasive Species 2014. Fei, S., Phillips, J., and Shouse, M. Annual Reviews of Ecology, Evolution, and Systematics 45:69-87.
Spatial analysis facilitates invasive species risk assessment 2014. Liang, L., Clark, J.T., Kong, N., Rieske, L.K., and Fei, S. Forest Ecology and Management 315:22-29.
Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement 2014. Harfouche, A., Meilan, R., and Altman, A. Tree Physiology 34(11):1181-1198
The Cloning and Characterization of a Poplar Stomatal Density Gene 2014. Lawson, Shaneka S., Pijut, Paula M., and Michler, Charles H. Genes & Genomics 36(4):427-441.
Population structure of Geosmithia morbida, the casual agent of Thousand Cankers Disease of walnut trees in the United States 2014. Zerillo, M.M., Caballero, J.I., Woeste, K., Graves, A.D., Hartel, C., Pscheidt, J.W., Tonos, J., Broders, K., Cranshaw, W., Seybold, S.J., and Tisserat, N. Plos One 9(11):1-21.
Overexpression of AtSTO1 leads to improved salt tolerance in Populus tremula x P. alba 2014. Lawson, S.S. and Michler, C.H. Transgenic Research 23(5):817-826.
Landscape genetics of Persian walnut (Juglans regia L.) across its Asian range 2014. Pollegioni, P., Woeste, K.E., Ghiocchini, F., Olimpieri, I., Tortolano, V., Clark, J., Hemery, G.E., Mapelli, S., and Malvolti, M.E. Tree Genetics & Genomes 10(4):1027-1043.
Improvement of Agrobacterium-mediated transformation and rooting of black cherry 2014. Wang, Y. and Pijut, P.M. In Vitro Cellular and Developmental Biology-Plant 50(3):307-316.
How a flower becomes a chestnut: Morphological development of Chinese chestnuts (Castanea mollissima) 2014. Miller, Amy, Miller, Diane D., and Pijut, Paula M. The Journal of American Chestnut Foundation 28 (2):13-18.
Comparison of Arabidopsis Stomatal Density Mutants Indicates Variation in Water Stress Responses and Potential Epistatic Effects (PDF 923 KB) 2014. Lawson, S.S., Pijut, P.M., and Michler, C.H. Journal of Plant Biology. 57(3):162-173.
Can Prunus serotina be Genetically Engineered for Reproductive Sterility and Insect Pest Resistance? 2014. Wang, Y. and Pijut, P.M. Springer Science Reviews 2(1-2):75-93.
Biotic and abiotic factors affecting the genetic structure and diversity of butternut in the southern Appalachian Mountains, USA 2014. Parks, A., Jenkins, M., Ostry, M., Zhao, P., Woeste, K. Tree Genetics & Genomes 10(3):541-554.
Agrobacterium-mediated transformation of black cherry for flowering control and insect resistance 2014. Wang, Y. and Pijut, P.M. Plant Cell Tissue and Organ Culture 119(1):107-116.
Agrobacterium-mediated genetic transformation and plant regeneration of the hardwood tree species Fraxinus profunda (PDF 608 KB) 2014. Stevens, M.E. and Pijut, P.M. Plant Cell Report 33(6):861-870.

2013

In Vitro Culture and Rooting of Diospyros virginiana L. 2013. Palla, K.J., Beasley, R.R., and Pijut, P.M. HortScience 48(6):747-749.
Species selection in hardwoods research: variations in baseline physio-logical responses of select temperate hardwood tree species 2013. Lawson, S.S., Pijut, P.M., and Michler, C.H. Journal of Forestry Research 24(2):285-292.
Bark and Ambrosia Beetles and their Associated Fungi Colonizing Stressed Walnut in Missouri and Indiana 2013. Reed, S., English, J., Juzwik, J., and Ginzel, M. Walnut Bulletin 40(2): 17-19.
Regeneration of plants from Fraxinus nigra Marsh. Hypocotyls 2013. Beasley, R.R. and Pijut, P.M. HortScience 48(7):887-890.
Isolation and characterization of a TERMINAL FLOWER 1 homolog from Prunus serotina Ehrh 2013. Wang, Y. and Pijut, P.M. Tree Physiology 33(8):855-865.
Conservation status of a threatened tree species: Establishing a baseline for restoration of Juglans cinerea L. in the Southern Appalachian Mountains, USA 2013. Parks, A.M., Jenkins, M.A., Woeste, K.E., and Ostry, M.E. Natural Areas Journal 33(4):413-426.

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