PUBLICATIONS

Most mammals do not wander: little taxonomic overlap among continents

Balk, M.A., Pardi, M.I., Tomé, C.P., Pedersen, R.Ø., Grady, J.M., Lyons, S.K., Harding, L.E., Westover, M.L., Schroeder, K., Brown, J.H., and Smith, F.A. 2025 Ecography, e07966 🔗

The Unified Phenotype Ontology : a framework for cross-species integrative phenomics Open Access

Matentzoglu, N., Bello, S.M., Stefancsik, R., Alghamdi, S.M., Anagnostopoulus, A.V., Balhoff, J.P., Balk, M.A., Bradford, Y.M., Bridges, Y., Callahan, T.J., Caufield, H., Cuzick, A., Carmody, L.C., Caron, A.R., de Souza, V., Engel, S.R., Fey, P., Fisher, M., Gehrke, S., Grove, C., Hansen, P., Harris, N.L., Harris, M.A., Harris, L., Ibrahim, A., Jacobsen, J.O.B., Köhler, S., McMurry, J.A., Munoz-Fuentes, V., Munoz-Torres, M.C., Parkinson, H., Pendlington, S.M., Pilgrim, C., Robb, S.M.C., Robinson, P.N., Seager, J., Segerdell,E., Smedley, D., Sollis, E., Toro, S., Vasilevsky, N., Wood, V., Haendel, M.A., Mungall, C.J., McLaughlin, J.A., Osumi-Sutherland, D. 2025. Genetics, 229(3): iyaf027. 🔗

Diving deeper: Leveraging the chondrichthyan fossil record to investigate environmental, ecological, and biological change

Kim, S.L., Balk, M.A., Sibert, E.C., and Whitenack, L. 2024. Annual Review of Earth and Planetary Sciences, 53: 223–250. 🔗

The paradox of predictability provides a bridge between micro-and macroevolution

Tsuboi, M., Liow, L.H., De Lisle, S., Grabowski, M., Hopkins, M., Hunt, G., Porto, A., Sztepanacz, J., Voje, K.L., Balk, M.A., Hildesheim, L., Horta-Lacueva, Q., Hohmann, A.H., Lürig, M., Milocco, L., Nilen, S., Passarotto, A., Pontarp, M., Rossani, D., Svennson, E., Villegas, C., Winslott, E., Love, A., and Houle, D. 2024. Journal of Experimental Biology, 37(12): 1413–1432. 🔗

A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics

Balk, M.A., Bradley, J., Maruf, M., Altintas, B., Bakis, Y., Bart, H.L. Jr., Breen, D., Florian, C.R., Greenberg, J., Karpatne, A., Karnani, K., Mabee, P., Pepper, J., Jebbia, D., Tabarin, T., Wang, X., Lapp, H. 2024. Methods in Ecology and Evolution, 15(6): 1129–1145. 🔗

Meeting report for the Phenoscape TraitFest 2023 with comments on organising interdisciplinary meetings

Girón Duque, J.C., Mikó, I., Balk, M.A., Dahdul, W., Lapp, H., Alhajjar, E., Wynd, B., Tarasov, S., Lawrence, C. Khakurel, B., Porto, A., Yan, L., Fluck, I.E., Porto, D.S., Keating, J.N., Borokini, I.T., Seltmann, K.C., and Montanaro, G.2024. Biodiversity Information Science and Standards, 8: 31152332. 🔗

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

Stefancsik, R., Balhoff, J.P., Balk, M.A., Ball, R.L, Bello, S.M., Caron, A.R., Chesler, E.J., de Souza, V., Gehrke, S., Haendel, M., Harris, L.W., Harris, N.L., Ibrahim, A., Koehler, S., Matentzoglu, N., McMurry, J.A., Mungall, C.J., Munoz-Torres, M.C., Putman, T., Robinson, P., Smedley, D., Sollis, E., Thessen, A.E., Vasilevsky, N., Walton, D.O., Osumi-Sutherland, D. 2023. Mammalian Genome, 34(3): 1–15. 🔗

Discovering novel biological traits from images using phylogeny-guided neural networks

Elhamod, M., Khurana, M., Manogaran, H.B., Uyeda, J., Balk, M.A., Dahdul, W.M., Bakis, Y., Bart, H., Mabee, P., Lapp, H., Balhoff, J., Charpentier, C.P., Carlyn, D.E., Chao, W.-L., Stewart, C., Rubenstein, D., Berger-Wolf, T., Karpatne, A. 2023. Proceedings of the 29th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 3966–3978. 🔗

Unifying the identification of biomedical entities with the Bioregistry

Hoyt, C.T., Balk, M.A., Callahan, T.J., Domingo-Fernández, Haendel, M.A., Hegde, H.B., Himmelstein, D.S., Karis, K., Kunze, J., Lubiana, T., Matentzoglu, N., McMurry, J., Moxon, S., Mungall, C.J., Rutz, A., Unni, D.R., Willighagen, E., Winston, D., and Gyrori, B.M. 2022. Scientific Data, 9: 714. 🔗

A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data

Balk, M.A., Deck, J., Emery, K.F., Walls, R.L., Reuter, D., LaFrance, R., Arroyo-Cabrales, J., Barrett, P., Blois, J., Boileau, A., Brenskelle, L., Cannarozzi, N.R., Cruz, J.A., Davanos, L.M., Hantak, M., Hopkins, S., Kohli, B., King, J.N., Koo, M., Lawing, M., Machado, H., McCrane, S.M., McLean, B., Morgan, M.E., Pilaar-Birch, S., Upham, N.S., Villaseñor, A., Yohe, L., Guralnick, R.P., and Davis, E.B. 2022. iScience, 25(10): 105101. 🔗

Late Quaternary biotic homogenization of North American mammalian faunas

Fraser, D., Villaseñor, A., Tóth, A., Balk, M.A., Eronen, J.T., Barr. W. A., Behrensmeyer, A.K., Davis, M., Du, A., Faith, J.T., Gotelli, N.J., Graves, G.R., Jukar, A.M., Looy, C.V., McGill, B.J., Miller, J.H., Pineda-Munoz, S., Potts, R., Shupinski, A.B., Soul, L.C., and Lyons, S.K. 2022. Nature Communications, 13(3940). 🔗

Decoding the dynamics of dental distributions: insights from shark demography and dispersal

Kim, S., Yeakel, J.D., Balk, M.A., Eberle, J., Zeichner, S., Fieman, D., and Kriwet, J. 2022. Proc. R. Soc. B., 289: 20220808. 🔗

Ten simple rules to cultivate transdisciplinary collaboration in data science

Sahneh, F.†, Balk, M.A.†, Kisley, M., Chan, C.-K., Fox, M., Nord, B., Lyons, E., Swetnam, T., Huppenkothen, D., Sutherland, W., Walls, R.L., Quinn, D., Tarin, T., LeBauer, D., Ribes, D., Birnie, D.P. III, Lushbough, C., Carr, E., Nearing, G., Fischer, J., Tyle, K., Carrasco, L., Lang, M., Rose, P.W., Rushforth, R., Roy, S., Matheson, T., Lee, T., Brown, T., Teal, T., Papes, M., Kobourov, S., and Merchant, N. 2021. PLOS Computational Biology, e1008879. 🔗

Investigating biotic interactions in deep time

Fraser, D., Soul, L.C., Tóth, A.B., Balk, M.A., Eronen, J.T., Pineda-Munoz, S., Shupinski,A.B., Villaseñor, A., Barr, W.A., Behrensmeyer, A.K., Du, A., Faith, J.T., Gotelli, N.J., Graves, G.R., Jukar, A.M., Looy, C.V., Miller, J.H., Potts, R., and Lyons, S.K. 2021. Trends in Ecology & Evolution, 36(10: 61–75. 🔗

Body mass‐related changes in mammal community assembly patterns during the late Quaternary of North America

Pineda-Munoz, S., Jukar, A.M., Tóth, A.B., Fraser, D., Du, A., Barr, W.A., Amatangelo, K.L., Balk, M.A., Behrensmeyer, A.K., Blois, J., Davis, M., Eronen, J.T., Gotelli, N.J., Looy, C., Miller, J.H., Shupinski, A.B., Soul, L.C., Villaseñor, A., Wing, S., and Lyons, S.K. 2020. Global Ecology and Biodiversity, 44(1): 56–66. 🔗

Open Science principles for accelerating trait-based science across the Tree of Life

Gallagher, R.V., Falster, D.S., Maitner, B.S., Salguero-Gómez, R., Vandvik, V., Pearse, W.D., Schneider, F.D., Kattge, J., Poelen, J.H., Madin, J.S., Ankenbrand, M.J., Penone, C., Feng, X., Adams, V.M., Alroy, J., Andrew, S.C., Balk, M.A., Bland, L.M., Boyle, B.L., Bravo-Avila, C.H., Brennan, I., Carthey, A.J.R., Catullo, R., Cavazos, B.R., Conde, D.A., Chown, S.L., Fadrique, B., Gibb, H., Halbritter, A.H., Hammock, J., Hogan, J.A., Holewa, H., Hope, M., Iversen, C.M., Jochum, M., Kearney, M., Keller, A., Mabee, P., Manning, P., McCormack, L., Michaletz, S.T., Park, D.S., Perez, T.M., Pineda-Munoz, S., Ray, C.A., Rossetto, M., Sauquet, H., Sparrow, B., Spasojevic, M.J., Telford, R.J., Tobias, J.A., Violle, C., Walls, R., Weiss, K.C.B., Westoby, M., Wright, I.J., Enquist, B.J. 2020. Nature Ecology and Evolution, 4: 294–303. 🔗

A Constraint-based model of Dynamic Island Biogeography: environmental history and species traits predict hysteresis in populations and communities

Burger, J.R., Anderson, R.A., Balk, M.A., and Fristoe, T.S. 2019. Frontiers of Biogeography, 11(3): e44383. 🔗

Investigating (a) symmetry in a small mammal's response to warming and cooling events across western North America over the late Quaternary

Balk, M.A., Betancourt, J.L., and Smith, F.A. 2019. Quaternary Research, 92(2): 408–415. 🔗

Body size evolution across the Geozoic

Smith, F.A., Payne, J.L, Heim, N.A., Balk, M.A., Finnegan, S., Kowalewski, M., Lyons, S.K., McClain, C.R., McShea, D.W., Novak-Gotshall, P.M., Spaeth Anich, P., and Wang, S.C. 2016. Annual Review of Earth & Planetary Science, 44: 523–553. 🔗

Exploring the influence of ancient and historic megaherbivore extirpations on the global methane budget

Smith, F.A., Hammond, J.I., Balk, M.A., Elliot, S.M., Lyons, S.K., Pardi, M.I., Tomé, C.P., Wagner, P.J., and Westover, M.L. 2015. Proceedings of the National Academy of Sciences, 113(4): 874–879. 🔗

Metabolic heat production and thermal conductance are mass-independent adaptations to thermal environment in birds and mammals

Fristoe, T.S., Burger, J.R., Balk, M.A., Khaliq, I., Hof, C., and Brown, J.H. 2015. Proceedings of the National Academy of Sciences, 112(52): 15934–15939. 🔗

Body-size trends of the extinct giant shark Carcharocles megalodon: a deep-time perspective on marine apex predators

Pimiento, C. and Balk, M.A. 2015. Paleobiology, 41(3): 479–490. 🔗

Sizing ocean giants: patterns of intraspecific size variation in marine megafauna

McClain, C.R., Balk, M.A., Benfield, M.C., Branch, T.A., Chen, C., Cosgrove, J., Dove, A.D.M., Helm, R.R., Hochberg, F.G.E., Gaskins, L.C., Lee, F.B., Marshall, A., McMurray, S.E., Schance, C., Stone, S.N., and Thaler, A.D. 2015. Peer J, e715. 🔗

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