Publications
37. CyVerse: Cyberinfrastruture for Open Science Preprint BioArxiv, in review PLOS Computational Biology as Software Paper
Recommended Citation: Swetnam T.L, P.B. Antin, R. Bartelme, A. Bucksch, D. Camhy, G. Chism, I. Choi, A.M. Cooksey, M. Cosi, C.Cowen, M. Culshaw-Maurer, R. Davey, S. Davey, U.Devisetty, T. Edgin, A. Edmonds, D. Fedorov, J. Frady, J. Fonner, J.K. Gillan, I. Hossain, B.L. Joyce, K. Lang, T. Lee, S. Littin, I. Mcewen, N. Merchant, D. Micklos, A. Nelson, A. Ramsey, S. Roberts, P. Sarando, E. Skidmore, J. Song, M.M. Sprinkle, S. Srinivasan, J.D. Strootman, S. Stryeck, R. Tuteja, M. Vaughn, M. Wali, M. Wall, R. Walls, L. Wang, T. Wickizer, J. Williams, J.Wregglesworth, & E. Lyons (2023) CyVerse: Cyberinfrastructure for Open Science. BioArxiv https://doi.org/10.1101/2023.06.16.545223
36. Using knowledge graphs to infer gene expression in plants. Published in Frontiers in Artificial Intelligence
Thessen, A., L. Cooper, T.L. Swetnam, et al. (2023) Using knowledge graphs to infer gene expression in plants. Frontiers in Artificial Intelligence, 6, 92 10.3389/frai.2023.1201002
35. PhytoOracle Published in Frontiers in Plant Sciences
Gonzalez, E.M., A. Zarei, N. Hendler, et al. (2023). PhytoOracle: Scalable, modular phenomics data processing pipelines. Frontiers in Plant Science, 14, 1112973-1112973 10.1002/essoar.10508789.1
34. Reimagine fire science for the anthropocene Published in PNAS Nexus
Recommended Citation: Jacquelyn K Shuman, Jennifer K Balch, Rebecca T Barnes, Philip E Higuera, Christopher I Roos, Dylan W Schwilk, E Natasha Stavros, Tirtha Banerjee, Megan M Bela, Jacob Bendix, Sandro Bertolino, Solomon Bililign, Kevin D Bladon, Paulo Brando, Robert E Breidenthal, Brian Buma, Donna Calhoun, Leila M V Carvalho, Megan E Cattau, Kaelin M Cawley, Sudeep Chandra, Melissa L Chipman, Jeanette Cobian-Iñiguez, Erin Conlisk, Jonathan D Coop, Alison Cullen, Kimberley T Davis, Archana Dayalu, Fernando De Sales, Megan Dolman, Lisa M Ellsworth, Scott Franklin, Christopher H Guiterman, Matthew Hamilton, Erin J Hanan, Winslow D Hansen, Stijn Hantson, Brian J Harvey, Andrés Holz, Tao Huang, Matthew D Hurteau, Nayani T Ilangakoon, Megan Jennings, Charles Jones, Anna Klimaszewski-Patterson, Leda N Kobziar, John Kominoski, Branko Kosovic, Meg A Krawchuk, Paul Laris, Jackson Leonard, S Marcela Loria-Salazar, Melissa Lucash, Hussam Mahmoud, Ellis Margolis, Toby Maxwell, Jessica L McCarty, David B McWethy, Rachel S Meyer, Jessica R Miesel, W Keith Moser, R Chelsea Nagy, Dev Niyogi, Hannah M Palmer, Adam Pellegrini, Benjamin Poulter, Kevin Robertson, Adrian V Rocha, Mojtaba Sadegh, Fernanda Santos, Facundo Scordo, Joseph O Sexton, A Surjalal Sharma, Alistair M S Smith, Amber J Soja, Christopher Still, Tyson Swetnam, Alexandra D Syphard, Morgan W Tingley, Ali Tohidi, Anna T Trugman, Merritt Turetsky, J Morgan Varner, Yuhang Wang, Thea Whitman, Stephanie Yelenik, Xuan Zhang, Reimagine fire science for the anthropocene, PNAS Nexus, Volume 1, Issue 3, July 2022, pgac115, https://doi.org/10.1093/pnasnexus/pgac115
33. Remote sensing from unoccupied aerial systems: Opportunities to enhance Arctic plant ecology in a changing climate Published in Journal of Ecology
Recommended Citation: Yang, D., Morrison, B. D., Davidson, K. J., Lamour, J., Li, Q., Nelson, P. R., Hantson, W., Hayes, D. J., Swetnam, T. L., McMahon, A., Anderson, J., Ely, K. S., Rogers, A., & Serbin, S. P. (2022). Remote sensing from unoccupied aerial systems: Opportunities to enhance Arctic plant ecology in a changing climate. Journal of Ecology, 00, 1– 24. https://doi.org/10.1111/1365-2745.13976
32. Harnessing the NEON data revolution to advance open environmental science with a diverse and data‐capable community Published in Ecosphere
Recommended citation: Nagy, R. C., Balch, J. K., Bissell, E. K., Cattau, M. E., Glenn, N. F., Halpern, B. S., Ilangakoon, N., Johnson, B., Joseph, M. B., Marconi, S., O’Riordan, C., Sanovia, J., Swetnam, T. L., Travis, W. R., Wasser, L. A., Woolner, E., Zarnetske, P., Abdulrahim, M., Adler, J., Barnes, G., Bartowitz, K. J., Blake, R. E., Bombaci, S. P., Brun, J., Buchanan, J. D., Chadwick, K. D., Chapman, M. S., Chong, S. S., Chung, Y. A., Corman, J. R., Couret, J., Crispo, E., Doak, T. G., Donnelly, A., Duffy, K. A., Dunning, K. H., Duran, S. M., Edmonds, J. W., Fairbanks, D. E., Felton, A. J., Florian, C. R., Gann, D., Gebhardt, M., Gill, N. S., Gram, W. K., Guo, J. S., Harvey, B. J., Hayes, K. R., Helmus, M. R., Hensley, R. T., Hondula, K. L., Huang, T., Hundertmark, W. J., Iglesias, V., Jacinthe, P.-A., Jansen, L. S., Jarzyna, M. A., Johnson, T. M., Jones, K. D., Jones, M. A., Just, M. G., Kaddoura, Y. O., Kagawa-Vivani, A. K., Kaushik, A., Keller, A. B., King, K. B. S., Kitzes, J., Koontz, M. J., Kouba, P. V., Kwan, W.-Y., LaMontagne, J. M., LaRue, E. A., Li, D., Li, B., Lin, Y., Liptzin, D., Long, W. A., Mahood, A. L., Malloy, S. S., Malone, S. L., McGlinchy, J. M., Meier, C. L., Melbourne, B. A., Mietkiewicz, N., Morisette, J. T., Moustapha, M., Muscarella, C., Musinsky, J., Muthukrishnan, R., Naithani, K., Neely, M., Norman, K., Parker, S. M., Perez Rocha, M., Petri, L., Ramey, C. A., Record, S., Rossi, M. W., SanClements, M., Scholl, V. M., Schweiger, A. K., Seyednasrollah, B., Sihi, D., Smith, K. R., Sokol, E. R., Spaulding, S. A., Spiers, A. I., St. Denis, L. A., Staccone, A. P., Stack Whitney, K., Stanitski, D. M., Stricker, E., Surasinghe, T. D., Thomsen, S. K., Vasek, P. M., Xiaolu, L., Yang, D., Yu, R., Yule, K. M., and Zhu, K.. 2021. Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community. Ecosphere 12( 12):e03833. 10.1002/ecs2.3833
31. Movement of sediment through a burned landscape: Sediment volume observations and model comparisons in the San Gabriel Mountains, California, USA Published in Journal of Geophysical Research: Earth Surface
Recommended citation: Rengers FK, LA McGuire, JW Kean, DM Staley, et.al. Movement of sediment through a burned landscape: Sediment volume observations and model comparisons in the San Gabriel Mountains, California, USA - Journal of Geophysical Research: Earth Surface, 2021 https://doi.org/10.1029/2020JF006053
30. UAS-Based Plant Phenotyping for Research and Breeding Applications, 2021 Published in Plant Phenomics
Recommended citation: Wei Guo, Matthew E. Carroll, Arti Singh, Tyson L. Swetnam, Nirav Merchant, Soumik Sarkar, Asheesh K. Singh, Baskar Ganapathysubramanian, "UAS-Based Plant Phenotyping for Research and Breeding Applications", Plant Phenomics, vol. 2021, Article ID 9840192, 21 pages, 2021. https://doi.org/10.34133/2021/9840192
29. Ten simple rules to cultivate transdisciplinary collaboration in data science Published in PLoS Computational Biology
Recommended citation: Sahneh F, Balk MA, Kisley M, Chan C-k, Fox M, Nord B, et al. (2021) Ten simple rules to cultivate transdisciplinary collaboration in data science. PLoS Comput Biol 17(5): e1008879. https://doi.org/10.1371/journal.pcbi.1008879
28. On the Use of Standardized Multi-Temporal Indices for Monitoring Disturbance and Ecosystem Moisture Stress across Multiple Earth Observation Systems in the Google Earth Engine Published in Remote Sensing
Recommended citation: Swetnam, T.L.; Yool, S.R.; Roy, S.; Falk, D.A. On the Use of Standardized Multi-Temporal Indices for Monitoring Disturbance and Ecosystem Moisture Stress across Multiple Earth Observation Systems in the Google Earth Engine. Remote Sens. 2021, 13, 1448. https://doi.org/10.3390/rs13081448
27. Innovations to expand drone data collection and analysis for rangeland monitoring, 2021 Published in Ecosphere
Recommended citation: Gillan, J. K., Ponce-Campos, G. E., Swetnam, T. L., Gorlier, A., Heilman, P., & McClaran, M. P. (2021). Innovations to expand drone data collection and analysis for rangeland monitoring. Ecosphere, 12(7). https://esajournals.onlinelibrary.wiley.com/doi/10.1002/ecs2.3649
26. Rangewide habitat suitability analysis for the Mexican wolf (Canis lupus baileyi) to identify recovery areas in its historical distribution, 2020 Published in Diversity and Distributions
Recommended citation: Martínez-Meyer, E, González-Bernal, A, Velasco, JA, et al. Rangewide habitat suitability analysis for the Mexican wolf (Canis lupus baileyi) to identify recovery areas in its historical distribution. Divers Distrib. 2021; 27: 642– 654. https://doi.org/10.1111/ddi.13222
25. Ten simple rules for organizing a data science workshop, 2020 Published in PLoS Computational Biology
Recommended citation: Ponsero A, Bartelme R, de Oliveira Almeida G, Bigelow A, Tuteja R, Ellingson H, et al. (2020) Ten simple rules for organizing a data science workshop. PLoS Comput Biol 16(10): e1008226. https://doi.org/10.1371/journal.pcbi.1008226
24. Extreme drought and adaptive resource selection by a desert mammal, 2020 Published in Ecosphere
Recommended citation: Gedir, J. V., Cain III, J. W., Swetnam, T. L., Krausman, P. R., & Morgart, J. R. (2020). Extreme drought and adaptive resource selection by a desert mammal. Ecosphere, 11(7), e03175. https://doi.org/10.1002/ecs2.3175
23. The Rockerverse: Packages and Applications for Containerisation with R, 2020 Published in The R Journal
Recommended citation: Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daróczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Péter Sólymos, Tyson Lee Swetnam, Nitesh Turaga, Charlotte Van Petegem, Jason Williams, Craig Willis and Nan Xiao , The R Journal (2020) 12:1, pages 437-461.
22. Allometric relationships between primary size measures and sapwood area for six common tree species in snow-dependent ecosystems in the Southwest United States, 2019 Published in Journal of Forest Research
Recommended citation: Mitra, B., Papuga, S.A., Alexander, M.R., Swetnam, T.L., Abramson, N. Allometric relationships between primary size measures and sapwood area for six common tree species in snow-dependent ecosystems in the Southwest United States. J. For. Res. 31, 2171–2180 (2020). https://doi.org/10.1007/s11676-019-01048-y
21. Estimating Forage Utilization with Drone-Based Photogrammetric Point Clouds Published in Rangeland Ecology & Management, 2019
Recommended citation: Gillan, J.K., M.P. McClaran, T.L. Swetnam, P. Heilman, Estimating Forage Utilization with Drone-Based Photogrammetric Point Clouds, Rangeland Ecology & Management,2019, https://doi.org/10.1016/j.rama.2019.02.009.
20. Modeling Riparian Restoration Impacts on the Hydrologic Cycle at the Babacomari Ranch, SE Arizona, USA Published in Water, 2019
Recommended citation: Norman, L.M.; Callegary, J.B.; Lacher, L.; Wilson, N.R.; Fandel, C.; Forbes, B.T.; Swetnam, T. Modeling Riparian Restoration Impacts on the Hydrologic Cycle at the Babacomari Ranch, SE Arizona, USA. Water 2019, 11, 381. https://doi.org/10.3390/w11020381
19. Jetstream—Early operations performance, adoption, and impacts Published in Concurrency and Computation: Practice and Experience, 2018
Recommended citation: Hancock, D, C Stewart, M Vaugh, et al. Concurrency and Computation: Practice and Experience (2018). https://doi.org/10.1002/cpe.4683
18. A net ecosystem carbon budget for snow dominated forested headwater catchments: linking water and carbon fluxes to critical zone carbon storage Published in Biogeochemistry, 2018
Recommended citation: Perdrial, J., Brooks, P.D., Swetnam, T. et al. Biogeochemistry (2018). https://doi.org/10.1007/s10533-018-0440-3
17. Which way do you lean? Using slope aspect variations to understand Critical Zone processes and feedbacks Published in Earth Surface Processes & Landforms, 2018
Recommended citation: Pelletier, J. D., Barron-Gafford, G. A., Guttierez-Jurado, H., Hinckley, E.-L. S., Istanbulluoglu, E., McGuire, L. A., Niu, G.-Y., Poulos, M. J., Rasmussen, C., Richardson, P., Swetnam, T. L., and Tucker, G. E. (2017) Which way do you lean? Using slope aspect variations to understand Critical Zone processes and feedbacks. Earth Surf. Process. Landforms, doi: 10.1002/esp.4306. http://onlinelibrary.wiley.com/doi/10.1002/esp.4306/full
16. Considerations for achieving cross-platform point cloud data fusion across different dryland ecosystem structural states Published in Frontiers in Plant Sciences, 2018
Recommended citation: Swetnam TL, Gillan JK, Sankey TT, McClaran MP, Nichols MH, Heilman P and McVay J (2018) Considerations for Achieving Cross-Platform Point Cloud Data Fusion across Different Dryland Ecosystem Structural States. Front. Plant Sci. 8:2144.doi: 10.3389/fpls.2017.02144 https://www.frontiersin.org/articles/10.3389/fpls.2017.02144/full
15. Fusing tree-ring and forest inventory data to infer influences on tree growth Published in Ecosphere, 2017
Recommended citation: Evans, M. E. K., D. A. Falk, A. Arizpe, T. L. Swetnam, F. Babst, and K. E. Holsinger. 2017. Fusing tree-ring and forest inventory data to infer influences on tree growth. Ecosphere 8(7):e01889. 10.1002/ecs2.1889 http://onlinelibrary.wiley.com/doi/10.1002/ecs2.1889/full
14. Topographically driven differences in energy and water constrain climatic control on forest carbon sequestration Published in Ecosphere, 2017
Recommended citation: Swetnam, T. L., P. D. Brooks, H. R. Barnard, A. A. Harpold, and E. L. Gallo. 2017. Topographically driven differences in energy and water constrain climatic control on forest carbon sequestration. Ecosphere 8(4):e01797. 10.1002/ecs2.1797 http://onlinelibrary.wiley.com/doi/10.1002/ecs2.1797/full
13. Mexican wolf habitat suitability analysis in historical range in the Southwestern US and Mexico Published in US Fish and Wildlife Service Draft Report, 2017
Recommended citation: Martínez-Meyer, E., A. González-Bernal, J. A. Velasco, T. L. Swetnam, Z. Y. González-Saucedo, J. Servín, C. A. López González, N. E. Lara Díaz, C. Aguilar Miguel, C. Chávez García, and J. K. Oakleaf. 2017. Mexican wolf habitat suitability analysis in historical range in the Southwestern US and Mexico. U.S. Fish and Wildlife Service, Region 2, Albuquerque, New Mexico, USA. https://www.fws.gov/southwest/es/mexicanwolf/pdf/20170622_DftBioReport_Appendices.pdf
12. Asymmetry of weathering-limited hillslopes: the importance of diurnal covariation in solar insolation and temperature Published in Earth Surface Processes & Landforms, 2017
Recommended citation: Pelletier, J. D., and Swetnam, T. L. (2017) Asymmetry of weathering-limited hillslopes: the importance of diurnal covariation in solar insolation and temperature. Earth Surf. Process. Landforms, 42: 1408–1418. doi: 10.1002/esp.4136. http://onlinelibrary.wiley.com/doi/10.1002/ecs2.1797/full
11. UAV hyperspectral and lidar data and their fusion for arid and semi-arid land vegetation monitoring Published in Remote Sensing in Ecology and Conservation, 2017
Recommended citation: Sankey, T. T., McVay, J., Swetnam, T. L., McClaran, M. P., Heilman, P. and Nichols, M. (2017), UAV hyperspectral and lidar data and their fusion for arid and semi-arid land vegetation monitoring. Remote Sens Ecol Conserv. doi:10.1002/rse2.44 http://onlinelibrary.wiley.com/doi/10.1002/rse2.44/full
10. Scaling GIS analysis tasks from the desktop to the cloud utilizing contemporary distributed computing and data management approaches Published in XSEDE Proceedings, 2016
Recommended citation: Swetnam, T. L., J. D. Pelletier, C. Rasmussen, N. R. Callahan, N. Merchant, E. Lyons, M. Rynge, Yan Liu, Viswanath Nandigam, and C. Crosby. "Scaling GIS analysis tasks from the desktop to the cloud utilizing contemporary distributed computing and data management approaches: A case study of project-based learning and cyberinfrastructure concepts." In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, p. 21. ACM, 2016. http://dl.acm.org/citation.cfm?id=2949573
9. Tree morphologic plasticity explains deviation from metabolic scaling theory in semi-arid conifer forests, southwestern USA Published in PLOS One, 2016
Recommended citation: Swetnam TL, O’Connor CD, Lynch AM (2016) Tree Morphologic Plasticity Explains Deviation from Metabolic Scaling Theory in Semi-Arid Conifer Forests, Southwestern USA. PLoS ONE 11(7): e0157582. https://doi.org/10.1371/journal.pone.0157582
8. Working Paper 35: Carbon Cycling in Southwestern Forests: Reservoirs, Fluxes, and the Effects of Fire and Management Published in Ecological Restoration Institute/Southwest Fire Science Consortium, 2016
Recommended citation: Swetnam, T.L. and Falk, D.A. (2015) Working Paper 35: Carbon Cycling in Southwestern Forests: Reservoirs, Fluxes, and the Effects of Fire and Management. Working Paper. Ecological Restoration Institute/ Southwest Fire Science Consortium, Flagstaff, United States. http://openknowledge.nau.edu/2293/
7. Discriminating disturbance from natural variation with LiDAR in semi-arid forests in the southwestern USA Published in Ecosphere, 2015
Recommended citation: Swetnam, T. L., A. M. Lynch, D. A. Falk, S. R. Yool, and D. P. Guertin. 2015. Discriminating disturbance from natural variation with LiDAR in semi-arid forests in the southwestern USA. Ecosphere 6(6):97. http://dx.doi.org/10.1890/ES14-00384.1 http://onlinelibrary.wiley.com/doi/10.1890/ES14-00384.1/full
6. Laser vision lidar as a transformative tool to advance critical zone science Published in Hydrology and Earth Systems Science, 2015
Recommended citation: Harpold, A.A., et al. 2015. Laser vision: lidar as a transformative tool to advance critical zone science, Hydrology and Earth Systems Science https://doi.org/10.5194/hess-19-2881-2015
5. Estimating individual tree mid- and understory rank-size distributions from airborne laser scanning in semi-arid forests Published in Forest Ecology & Management, 2014
Recommended citation: Swetnam T.L., D.A. Falk, A.M. Lynch, S.R. Yool (2014) Estimating individual tree mid- and understory rank-size distributions from airborne laser scanning in semi-arid forests, Forest Ecology and Management 330, 271-282 https://doi.org/10.1016/j.foreco.2014.07.011
4. Application of Metabolic Scaling Theory to reduce error in local maxima tree segmentation from aerial LiDAR Published in Forest Ecology & Management, 2014
Recommended citation: Swetnam T.L., D.A. Falk (2014) Application of metabolic scaling theory to reduce error in local maxima tree segmentation from aerial LiDAR, Forest Ecology and Management 323, 158-167 https://doi.org/10.1016/j.foreco.2014.03.016
3. Coevolution of nonlinear trends in vegetation, soils, and topography with elevation and slope aspect: A case study in the sky islands of southern Arizona Published in Journal of Geophysical Research: Earth Surface, 2013
Recommended citation: Pelletier, J. D., G. A. Barron-Gafford, D. D. Breshears, P. D. Brooks, J. Chorover, M. Durcik, C. J. Harman, T. E. Huxman, K. A. Lohse, R. Lybrand, T. Meixner, J. C. McIntosh, S. A. Papuga, C. Rasmussen, M. Schaap, T. L. Swetnam, and P. A. Troch (2013), Coevolution of nonlinear trends in vegetation, soils, and topography with elevation and slope aspect: A case study in the sky islands of southern Arizona, J. Geophys. Res. Earth Surf., 118, 741–758, doi:10.1002/jgrf.20046.
2. Reconstructing Landscape Pattern of Historical Fires and Fire Regimes Published in Book Chapter: The Landscape Ecology of Fire, 2010
Recommended citation: Swetnam TL, DA Falk, AE Hessl, C Farris (2010) Reconstructing landscape pattern of historical fires and fire regimes, The landscape ecology of fire, 165-192. https://link.springer.com/chapter/10.1007/978-94-007-0301-8_7
1. Comparing selected fire regime condition class (FRCC) and LANDFIRE vegetation model results with tree-ring data Published in International Journal of Wildland Fire, 2010
Recommended citation: Swetnam, T. L., P.M. Brown (2010) Comparing selected fire regime condition class (FRCC) and LANDFIRE vegetation model results with tree-ring data. International Journal of Wildland Fire 19(1) 1-13 https://doi.org/10.1071/WF08001
Emoji Key¶
| Icon | Domain |
|---|---|
| containers | |
| version control | |
| docker | |
| linux | |
| Python | |
| R | |
| Go language | |
| ten rules | |
| collaborative research | |
| open source initiative | |
| temporal | |
| knowledge graphs | |
| ontology | |
| measurement | |
| raster mapping | |
| vector mapping | |
| temporal mapping | |
| habitat mapping | |
| Google Earth Engine | |
| earth observation systems | |
| airborne remote sensing | |
| small uncrewed aerial systems | |
| eddy covariance tower | |
| snow hydrology | |
| semi-arid hydrology | |
| hydrology | |
| atmospheric science | |
| geomorphology | |
| wildland forest fire | |
| genetics | |
| genomics | |
| plant science | |
| forest ecology | |
| desert ecology | |
| grassland ecology | |
| cattle management | |
| range management | |
| entomology |