Peer-Reviewed Journal Articles (48 articles, 3854 citations, h-index: 26, 14 corresponding author*, co-first authors †)

48. Fusi, R., Milner, S. G., Rosignoli, S., Bovina, R., Vieira Teixeira, C. J., Lou, H., Brian S. Atkinson1, B. S., Borkar, A. N., York, L. M., Jones, D. H., Sturrock, C. J., Stein, N., Mascher, M., Tuberosa, R., O’Connor, D., 12, Bennett, M. J., 1,2, Bishopp, A., Salvi, S., and Bhosale, R. (In Press). The auxin efflux carrier PIN1a regulates vascular patterning in cereal roots. New Phytologist.

47. Weihs, B. J., Heuschele, D., Tang, Z., York, L. M., Zhang, Z., Xu, Z., (In Press) The State of the Art in Root System Architecture Image Analysis Using Artificial Intelligence: A Review. Plant Phenomics.

46. Lynch, J. P., Galindo-Castañeda, T., Schneider, H. M., Sidhu, J. S., Rangarajan, H., York, L. M. (2023). Root phenotypes for improved nitrogen capture. Plant and Soil. DOI: 10.1007/s11104-023-06301-2

45. Lagergren, J., Pavicic, M., Chhetri, H. B., York, L. M., Hyatt, P. D., Kainer, D., Rutter, E. M., Flores, K., Bailey-Bale, J., Klein, M., Taylor, G., Jacobson, D., Streich, J. (2023). Few-shot learning enables population-scale analysis of leaf traits in Populus trichocarpa. Plant Phenomics 5. 0072. DOI: 10.34133/plantphenomics.0072

44. Yao, T., Zhan, J., Yates, T. B., Shrestha, H. K., Engle, N. L., Ployet, R., John, C., Feng, K., Bewg, W. P., Chen, M., Lu, H., Harding, S. A., Qiao, Z., Jawdy, S. S., Shu, M., Harman-Ware, A. E., Happs, R. M., York, L. M., Binder, B. M., Yoshinaga, Y., Daum, C., Tschaplinski, T. J., Abraham, P. E., Tsai, C. J., Barry, K., Lipzen, A., Schmutz, J., Tuskan,G. A., Chen, J. G., and Muchero, W. (2023). eQTL mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus. New Phytologist 239, 2248–2264. DOI: 10.1111/nph.19126


43. Weigelt, A., Mommer, L., Andraczek, K., Iversen, C. M., Bergmann, J., Bruelheide, H., Fan, Y., Freschet, G. T, Guerrero-Ramírez, N. R., Kattge, J., Kuyper, T. W., Laughlin, D. C., Meier, I. C., van der Plas, F., Poorter, H., Roumet, C., van Ruijven, J., Sabatini, F. M., Semchenko, M., Sweeney, C. J., Valverde-Barrantes, O. J., York, L. M., and McCormack, M. L. (2023). The importance of trait selection in ecology: Roots redefine the global spectrum of plant form and function. Nature 618, E29-E30. DOI: 10.1038/s41586-023-06148-8


42. O’Leary, B. M., Scafaro, A. P., and York, L. M. (2023). High-throughput, dynamic, multi-dimensional: an expanding repertoire of plant respiration measurements. Plant Physiology 191, 2070–2083. DOI: 10.1093/plphys/kiac580


41. Fusi, R., Rosignoli, S., Lou, H.,  Giuseppe Sangiorgi, G.,  Bovina, R., Pattem, J. K., Borkar, A. N., Lombardi, M., Forestan, C., Milner, S. G., Davis, J. L., Lale, A., Kirschner, G. K., Swarup, R., Tassinari, A., Pandey, B. K.,  York, L. M., Atkinson, B. S., Sturrock, C. J., Mooney, S. J., Hochholdinger, F., Tucker, M. R., Himmelbach, A., Stein, N., Mascher, M., Nagel, K. A., De Gara, L., Simmonds, J., Uauy, C.,  Tuberosa, R., Lynch, J. P., Yakubov, G. E., Bennett, M. J., Bhosale, R., and Salvi, S. (2022). Root angle is controlled by EGT1 in cereal crops employing a novel anti-gravitropic mechanism. Proceedings of the National Academy of Sciences. 119: e2201350119. DOI: 10.1073/pnas.2201350119

40. Prince, S., Anower, M. R., Motes, C. M., Hernandez, T. D., Liao, F., Putman, L., Mattson, R., Seethepalli, A., Shah, K., Komp, M., Mehta, P., York, L. M., Young, C., and Monteros, M. J. (2022). Intraspecific variation for leaf physiological and root morphological adaptation to drought stress in Alfalfa (Medicago sativa L.). Frontiers in Plant Science. 13:795011. DOI: 10.3389/fpls.2022.795011

39. Xu, Z, York, L. M.*, Seethepalli, A., Bucciarelli, B., Cheng, H., and Samac, D. A. (2022). Objective phenotyping of root system architecture using image augmentation and machine learning in alfalfa (Medicago sativa L.). Plant Phenomics. 9879610. DOI: 10.34133/2022/9879610

38. Maqbool, S., Hassan, M., Xia, X., York, L. M., Rasheed, A., and He, Z. (2022). Root system architecture in cereals: progress, challenges, and perspective. The Plant Journal 110, 23–42. DOI: 10.1111/tpj.15669

37. Griffiths, M., Mellor, N., Sturrock, C. J., Atkinson, B. S., Johnson, J., Mairhofer, S., York, L. M., Atkinson, J. A., Soltaninejad, M., Foulkes, J. F., Pound, M. P., Mooney, S. J., Pridmore, T. P., Bennett, M. J., and Wells, D. M. (2022). X-ray CT reveals 4D root system development and lateral root responses to nitrate in soil. The Plant Phenome Journal. 5: e20036. DOI: 10.1002/ppj2.20036

36. York, L. M.*, Griffiths, M., and Maaz, T. M. (2022). Whole-plant phenotypic engineering: Moving beyond ratios for multi-objective optimization of nutrient use efficiency. Current Opinion in Biotechnology. 75:102682. DOI: 10.1016/j.copbio.2022.102682

35. Roy, S., Griffiths, M., Torres-Jerez, I., Sanchez, B., Antonelli, E., Jain, D., Krom, N., Zhang, S., York, L. M., Scheible, W., and Udvardi, M. K. (2022). Application of synthetic peptide CEP1 increases nutrient uptake rates along plant roots. Frontiers in Plant Science. 12:793145. DOI: 10.3389/fpls.2021.793145

34. York, L. M.*, Cumming, J. R., Trusiak, A., Bonito, G., von Haden, A. C., Kalluri, U. C.,  Tiemann, L. K., Andeer, P. F., Blanc-Betes, E., Diab, J. H., Favela, A., Germon, A., Gomez-Casanovas, N., Hyde, C. A., Kent, A. D., Ko, D. K., Lamb, A., Missaoui, A., Northern, T. R., Pu, Y., Ragauskas, A. J., Raglin, S., Scheller, H. V., Ware, A., Washington, L., and Yang, W. H. (2022). Bioenergy Underground: challenges and opportunities for phenotyping roots and the microbiome for sustainable bioenergy crop production. The Plant Phenome Journal. 5: e20028. DOI: 10.1002/ppj2.20028

33. Griffiths, M., Wang, X., Dhakal, K., Guo, H., Seethepalli, A., Kang, Y., and York, L. M.* (2022). Interactions among rooting traits for deep water and nitrogen uptake in upland and lowland ecotypes of switchgrass (Panicum virgatum L.). Journal of Experimental Botany 73, 967–979.

32. Seethepalli, A., Dhakal, K., Griffiths, M., Guo, H., Freschet, G. T., and York, L. M.* (2021). RhizoVision Explorer: Open-source software for root image analysis and measurement standardization. AoB Plants 13, plab056. DOI: 10.1093/aobpla/plab056

31. Fonseca, J. P., Griffiths, M., York, L.M.* and Mysore, K. S. (2021). Dark respiration measurement from shoots in Arabidopsis. Bio-protocol 111(19), e4181 DOI: 10.21769/BioProtoc.4181

30. Weigelt, A., Mommer, L., Andraczek, K., Iversen, C. M., Bergmann, J., Bruelheide, H., Freschet, G. T., Guerrero-Ramirez, N. R., Kattge, J., Kuyper, T. W., Laughlin, D.C., Meier, I. C., van der Plas, F., Poorter, H., Fan, Y., Roumet, C., van Ruijven, J., Sabatini, F. M., Semchenko, M., Sweeney, C. J., Valverde-Barrantes, O. J., York, L. M., and McCormack, M. L. (2021). An integrated framework of plant form and function: The belowground perspective. New Phytologist 232, 42-59.

29. Udvardi, M., Below, F. E., Castellano, M. J., Eagle, A., Giller, K. E., Ladha, J. K.,Liu, X., Maaz, T. M., Nova-Franco, B., Raghuram, N., Robertson, G. P., Saha, M., Roy, S., Schmidt, S., Tegeder, M., York, L. M., and Peters J. W. (2021). A research road map for responsible use of agricultural nitrogen. Frontiers in Sustainable Food Systems. 5:660155 DOI: 10.3389/fsufs.2021.660155

28. Laughlin, D.C., Mommer, L., Sabatini, F. M., Bruelheide, H., Kuyper, T. W., McCormack, M. L., Bergmann, J., Freschet, G. T., Guerrero-Ramirez, N. R., Iversen, C. M., Kattge, J., Meier, I. C., Poorter, H., Roumet, C., Semchenko, M., Sweeney, C. J., Valverde-Barrantes, O. J., van der Plas, F., van Ruijven, J., York, L. M., Aubin, I., Burge, O. R., Byun, C., Ćušterevska, R. Dengler, J., Forey, E., Guerin, G. R., Hérault, B., Jackson, R., Karger, D. N., Lenoir, J., Lysenko, T., Meier, P., Niinemets, U., Ozinga, W. A., Penuelas, J., Reich, P. B., Schmidt, M., Schrodt, F., Velázquez, E., and Weigelt, A. (2021). Root traits explain plant species distributions along climatic gradients yet challenge the nature of ecological trade-offs. Nature Ecology and Evolution 5, 1123-1134.

27. Freschet, G. T., Pagès, L., Iversen, C. M., Comas, L. H., Rewald, B., Roumet, C., Klimešová, J., Zadworny, M., Poorter, H., Postma, J. A., Adams, T. S., Bagniewska-Zadworna, A., Bengough, A. G., Blancaflor, E. B., Brunner, I., Cornelissen, J. H. C., Garnier, E., Gessler, A., Hobbie, S. E., Meier,  I. C., Mommer, L., Picon-Cochard, C., Rose, L., Ryser, P., Scherer-Lorenzen, M., Soudzilovskaia, N. A., Stokes, A., Sun, T., Valverde-Barrantes, O. J., Weemstra, M., Weigelt, A., Wurzburger, N., York, L. M., Batterman, S. A., Gomes de Moraes, M., Janeček, Š., Lambers, H., Salmon, V., Tharayil, N., and McCormack, M. L. (2021). A starting guide to root ecology: strengthening ecological concepts and standardizing root classification, sampling, processing and trait measurements. New Phytologist 232, 973-1122.

26. Nehe, A. S., Foulkes, M. J., Ozturk, I., Rasheed, A., York, L. M., Kefauver, S. C., Ozdemir, F., and Morgounov, A. (2021). Root and canopy traits and adaptability genes explain drought tolerance mechanism in winter wheat. PLOS One. DOI: 10.1371/journal.pone.0242472

25. Guo, H., Ayalew, H., Seethepalli, A., Dhakal, K., Griffiths, M., Ma, X., and York, L. M.* (2021). Functional phenomics and genetics of the root economics space in winter wheat using high-throughput phenotyping of respiration and architecture. New Phytologist 232, 91-112.

24. Bardhan, K., York, L. M., Hasanuzzaman, M., Parekh, V., Jena, S., and Pandya, M. N.  (2021). Can smart nutrient applications optimize the plant's hidden half to improve drought resistance? Physiologia Plantarum 172, 1007-1015.

23. Griffiths, M., Roy, S., Guo, H., Seethepalli, A., Huhman, D., Ge, Y., Sharp, R. E., Fritschi, F. B., and York, L. M.* (2021). A multiple ion-uptake phenotyping platform reveals shared mechanisms affecting nutrient uptake by roots. Plant Physiology 185, 781-795.

22. Dhanapal, A. P., York, L. M., Hames, K. A., and Fritschi, F. B. (2021). Genome-wide association study of topsoil root system architecture in field-grown soybean [Glycine max (L.) Merr.]. Frontiers in Plant Science. 11:590179. DOI: 10.3389/fpls.2020.590179

21. Freschet, G. T., Roumet, C., Comas, L. H., Weemstra, M., Bengough, A. G., Rewald, B., Bardgett, R. D., De Deyn, G. B., Johnson, D., Klimešová, J., Lukac, M., McCormack, M. L., Meier, I. C., Pagès, L., Poorter, H., Prieto, I., Wurzburger, N., Zadworny, M., Bagniewska-Zadworna, A., Blancaflor, E. B., Brunner, I., Gessler, A., Hobbie, S. E., Iversen, C. M., Mommer, L., Picon-Cochard, C., Postma, J. A., Rose, L., Ryser, P., Scherer-Lorenzen, M., Soudzilovskaia, N. A., Sun, T., Valverde-Barrantes, O. J., Weigelt, A., York, L. M., and Stokes, A. (2021). Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs. New Phytologist 232, 1123-1158.

20. Burridge, J. D., Black, C. K., Nord, E. A., Postma, J. A., Sidhu, J. S., York, L. M., and Lynch, J. P. (2020). An analysis of soil coring strategies to estimate root depth in maize (Zea mays) and common bean (Phaseolus vulgaris). Plant Phenomics 2020. 3252703 DOI: 10.34133/2020/3252703

19. Fonseca, J. P., Lee, H-K., Boschiero, C., Griffiths, M., Lee, S., Zhao, P. X., York, L. M., and Mysore, K. S. (2020). Iron-sulfur cluster protein NITROGEN FIXATION S-LIKE 1 and its interactor FRATAXIN function in plant immunity. Plant Physiology 184, 1532-1548. DOI: 10.1104/pp.20.00950

18. Guerrero-Ramírez, N. R., Mommer, L., Freschet, G. T., Iversen, C. M., McCormack, M. L., Kattge, J., Poorter, H., van der Plas, F., Bergmann, J., Kuyper, T. W., York, L. M., Bruelheide, H., Laughlin, D.C., Meier, I.C., Roumet, C., Semchenko, M., Sweeney, C. J., van Ruijven, J., Valverde-Barrantes, O. J., Aubin, I., Catford, J. A., Manning, P., Martin, A., Milla, R., Minden, V., Pausas, J. G., Smith, S. W., Soudzilovskaia, N. A., Ammer, C., Butterfield, B., Craine, J., Cornelissen, J. H. C., de Vries, F. T., Isaac, M. E., Kramer, K., König, C., Lamb, E. G., Onipchenko, V. G., Peñuelas, J., Reich, P. B., Rillig, M. C., Sack, L., Shipley, B., Tedersoo, L., Valladares, F., van Bodegom, P., Weigelt, P., Wright, J. P., and Weigelt, A. (2020). Global root traits (GRooT) database. Global Ecology and Biogeography 30, 25-37. DOI: 10.1111/geb.13179

17. Bergmann, J., Weigelt, A., van der Plas, F., Laughlin, D. C., Kuyper,  T. W., Guerrero-Ramirez, N., Valverde-Barrantes, O. J., Bruelheide, H., Freschet, G. T., Iversen, C.M., Kattge, J., McCormack, M.L., Meier, I.C., Rillig, M.C., Roumet, C., Semchenko, M., Sweeney, C.J., van Ruijven,  J., York, L. M., and Mommer, L. (2020). The fungal collaboration gradient dominates the root economics space in plants. Science Advances 6. DOI: 10.1126/sciadv.aba37

16. Griffiths, M. G. and York, L. M.* (2020). Targeting root ion uptake kinetics for increasing plant productivity and nutrient use efficiency. Plant Physiology 182, 1854-1868.

15. Seethepalli, A., Guo, H., Liu, X., Griffiths. M. G., Almtarfi, H., Li, Z., Liu, S., Zare, A., Fritschi, F., Blancaflor, E., Ma, X., and York, L. M.* (2020). RhizoVision Crown: An integrated hardware and software platform for root crown phenotyping. Plant Phenomics 2020.  DOI:10.34133/2020/3074916

14. Le Marié, C. A., York, L. M., Strigens, A., Malosetti, M., Camp, K. H., Giuliani, S, Lynch, J. P., and Hund, A. (2019). Shovelomics root traits assessed on the EURoot maize panel are highly heritable across environments but show low genotype-by-nitrogen interaction. Euphytica. 215 (173). DOI: 10.1007/s10681-019-2472-8

13. Guo, H., and York, L. M.* (2019). Maize with fewer nodal roots allocates mass to more lateral and deep roots that improve nitrogen uptake and shoot growth. Journal of Experimental Botany 70, 5299-5309.

12. Mattupalli, C., Seethepalli, A., York, L. M.*, and Young, C. A. (2019). Digital imaging to evaluate root system architectural changes associated with soil biotic factors. Phytobiomes Journal. DOI: 10.1094/pbiomes-12-18-0062-r.

11. York, L. M.* (2019). Functional phenomics: an emerging field integrating high-throughput phenotyping, physiology, and bioinformatics. Journal of Experimental Botany 70, 379-386.

10. Huang, H., Liang, L., Sturrock, C. J., Pandey, B. K., Giri, J., Mairhofer, S., Wang, D., Muller, L., Tan, H., York, L. M., Yang, J., Song, Y., Kim, Y-J, Qiao, Y., Xu, J., Kepinski, S., Bennett, M. J., and Zhang, D. (2018). Rice actin binding protein RMD controls crown root angle in response to external phosphate. Nature Communications, 9, 2346. DOI: 10.1038/s41467-018-04710-x.

 9. York, L. M. and Lobet, G. (2017). Phenomics of root system architecture: Measuring and analyzing root phenes. Teaching Tools in Plant Biology: Lecture Notes.  The Plant Cell (online). DOI: 10.1105/tpc.117.tt0917.

 8. York, L. M., Silberbush, M., and Lynch, J. P. (2016). Spatiotemporal variation of nitrate uptake kinetics within the maize (Zea mays L.) root system is associated with greater nitrate uptake and interactions with architectural phenes. Journal of Experimental Botany 67, 3763-3775.

 7. York, L. M.*, Carminati, A., Mooney, S. J., Ritz, K., and Bennett, M. J. (2016). The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots. Journal of Experimental Botany 67, 3629-3643.

 6. York, L. M. and Lynch, J. P. (2015). Intensive field phenotyping of maize (Zea mays L.) root crowns identifies phenes and phene integration associated with plant growth and nitrogen acquisition. Journal of Experimental Botany 66, 5493-5505.

 5. York, L. M., Galindo-Castañeda, T., Schussler, J., and Lynch, J. P. (2015). Evolution of US maize (Zea mays L.) root system architectural and anatomical phenes over the past 100 years corresponds to increased tolerance of nitrogen stress. Journal of Experimental Botany 66, 2347-2358.

 4. Colombi, T., Kirchgessner, N., Le Marie, C., York, L. M., Lynch, J. P., and Hund, A. (2015). Next generation shovelomics: set up a tent and REST. Plant and Soil 388, 1-20.

 3. Zhang, C., Postma, J. A., York, L. M., and Lynch, J. P. (2014). Root foraging elicits niche complementarity-dependent overyielding in the ancient “three sisters” (maize, bean, squash) polycultures. Annals of Botany 114, 1719-1733.

 2. Bucksch, A., Burridge, J., York, L. M., Das, A., Nord, E. A., Weitz, J. S., and Lynch, J. P. (2014). Image-based high-throughput field phenotyping of crop roots. Plant Physiology 166, 470-486.

 1. York, L. M., Nord, E. A., and Lynch, J. P. (2013). Integration of root phenes for soil resource acquisition. Frontiers in Plant Science 4:355. DOI: 10.3389/fpls.2013.00355