2025

Biswas S, Boothby TC. Diversity in the protective role(s) of the conserved motif 1 from tardigrade cytoplasmic-abundant heat-soluble proteins during drying. Protein Science. 2025; 34(3):e70059. https://doi.org/10.1002/pro.70059

Ginell, G. M., Emenecker, R. J., Lotthammer, J. M., Keeley, A. T., Plassmeyer, S. P., Razo, N., Usher, E. T., Pelham, J. F., & Holehouse, A. S. (2025). Sequence-based prediction of intermolecular interactions driven by disordered regions. Science, 388(6749). https://doi.org/10.1126/science.adq8381

Holehouse, A. S. & Alberti, S. Molecular determinants of condensate composition. Mol. Cell 85, 290–308 (2025). https://doi.org/10.1016/j.molcel.2024.12.021

Leventhal, L., Ruffley, M., & Exposito-Alonso, M. (2025). Planting Genomes in the Wild: Arabidopsis From Genetics History to the Ecology and Evolutionary Genomics Era. Annual Review of Plant Biology, 76. https://doi.org/10.1146/annurev-arplant-071123-095146

Marks, R. A., J T B Ekwealor, M A S Artur, Bondi, L., Boothby, T. C., Carmo, O. M. S., Centeno, D. C., Coe, K. K., Dace, H. J. W., Field, S., Hutt, A., Porembski, S., Thalhammer, A., van, Wood, A. J., Alpert, P., Bartels, D., S Boeynaems, Datar, M. N., Giese, T., & Rhee, S. Y. (2025). Life on the dry side: a roadmap to understanding desiccation tolerance and accelerating translational applications. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-58656-y 

Nicholson V, Nguyen K, Gollub E, McCoy M, Yu F, Holehouse AS, et al. LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation. Protein Science. 2025; 34(2):e70028. https://doi.org/10.1002/pro.70028

Romero-Pérez, P. S., Moran, H. M., Cordone, D. P., Horani, A., Truong, A., Manriquez-Sandoval, E., Ramirez, J. F., Martinez, A., Gollub, E., Hunter, K., Kolamunna, K. C., Lotthammer, J. M., Emenecker, R. J., Liu, H., Iwasa, J. H., Boothby, T. C.,Holehouse, A. S., Fried, S. D., & Sukenik, S. (2025). Protein surface chemistry encodes an adaptive tolerance to desiccation. Cell Systems, 101407. https://doi.org/10.1016/j.cels.2025.101407

2024

Alston, J. J., Soranno, A., Holehouse, A. S. (2024) Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation. Biophysical Journal. 123(3). https://doi.org/10.1016/j.bpj.2023.11.260

Biswas, S., Gollub, E., Yu, F., Ginell, G., Holehouse, A., Sukenik, S., Boothby, T.C. (2024) Helicity of a tardigrade disordered protein contributes to its protective function during desiccation. Protein Science. 33, 2. DOI: https://doi.org/10.1002/pro.4872 

Czech, L., Spence, J. P., & Expósito-Alonso, M. (2024). grenedalf: population genetic statistics for the next generation of pool sequencing. Bioinformatics, 40(8), btae508. https://doi.org/10.1093/bioinformatics/btae508

Gillespie, L. E., Ruffley, M., & Expósito-Alonso, M. (2024). Deep learning models map rapid plant species changes from citizen science and remote sensing data. Proceedings of the National Academy of Sciences of the United States of America, 121(37), e2318296121. https://doi.org/10.1073/pnas.2318296121

Ginzburg, D. N., Cox, J. A., Rhee, S. Y. (2024) Non‐destructive, whole‐plant phenotyping reveals dynamic changes in water use efficiency, photosynthesis, and rhizosphere acidification of sorghum accessions under osmotic stress. Plant Direct. 8(3). https://doi.org/10.1002/pld3.571

Huynh, A. V., Gillespie, L. E., Lopez-Saucedo, J., Tang, C., Sikand, R., & Expósito-Alonso, M. (2024). Contrastive ground-level image and remote sensing pre-training improves representation learning for natural world imagery. In European Conference on Computer Vision (pp. 173-190). Cham: Springer Nature Switzerland. 
https://doi.org/10.48550/arXiv.2409.19439

KC, S., Nguyen, K., Nicholson, V.,Walgren, A., Trent, T., Gollub, E., Romero, S., Holehouse, A.S., Sukenik, S., Boothby, T.C. (2024) Disordered proteins interact with the chemical environment to tune their protective function during drying. bioRxiv.  DOI: https://doi.org/10.1101/2024.02.28.582506 

​Kumara, U.G.V.S.S, Ramirez, J.F., Boothby, T.C. (2024) The effect of sucrose polymer-size on glass transition temperature, glass former fragility, and water retention during drying. Frontiers in Materials. 11. DOI: https://doi.org/10.3389/fmats.2024.1351671

Lotthammer, J. M., Ginell, G. M., Griffith, D., Emenecker, R. J., & Holehouse, A. S. (2024). Direct prediction of intrinsically disordered protein conformational properties from sequence. Nature Methods, 21(3), 465–476. doi:10.1038/s41592-023-02159-5 
​
Marks, R. A. (2024) Resurrection plants revisited: Bridging the gap between bryophytes and angiosperms to decode desiccation tolerance. New Phytologist. https://doi.org/10.1111/nph.19719

Marks, R. A., Delgado, P., Makonya, G. M., Cooper, K., VanBuren, R., Farrant, J. M., (2024) Higher order polyploids exhibit enhanced desiccation tolerance in the grass Microchloa caffra, Journal of Experimental Botany. https://doi.org/10.1093/jxb/erae126

Marks, R.A., Van Der Pas, L., Schuster, J. Gilman, I.S., VanBuren, R., (2024) Convergent evolution of desiccation tolerance in grasses. Nat. Plants. 10, 1112–1125. https://doi.org/10.1038/s41477-024-01729-5

Nicholson, V., Meese, E., Boothby, T. C. “Osmolyte-IDP interactions during desiccation.” Progress in Molecular Biology and Translational Science. Academic Press. August 31, 2024. ISSN 1877-1173. https://doi.org/10.1016/bs.pmbts.2024.08.007 

Ramirez, J.F., Kumara, U.G.V.S.S, Arulsamy, N., Boothby, T.C. (2024) Water content, transition temperature and fragility influence protection and anhydrobiotic capacity. BBA Advances. DOI: https://doi.org/10.1016/j.bbadva.2024.100115 ​

Sanchez‐Martinez, S., Nguyen, K., Biswas, S., Nicholson, V., Romanyuk, A. V., Ramirez, J., Kc, S., Akter, A., Childs, C., Meese, E. K., Usher, E. T., Ginell, G. M., Yu, F., Gollub, E., Malferrari, M., Francia, F., Venturoli, G., Martin, E. W., Caporaletti, F., Giubertoni, G., Woutersen, S., Sukenik, S., Woolfson, D. N., Holehouse, A. S., Boothby, T. C. (2024) Labile Assembly of a tardigrade protein induces biostasis. Protein Science. 33(4). https://doi.org/10.1002/pro.4941

Shorinola, O., Marks, R., Emmrich, P., Jones, C., Odeny, D., Chapman, M.A., (2024) Integrative and inclusive genomics to promote the use of underutilised crops. Nat Commun. 15, 320. https://doi.org/10.1038/s41467-023-44535-x

VanBuren, R.,Nguyen, A., Marks, R.A., Mercado, C., Pardo, A., Pardo, J., Schuster,J., St Aubin, B., Lipham Wilson, M., Rhee, S.Y. (2024) Variability in drought gene expression datasets highlight the need for community standardization. bioRxiv. DOI: 10.1101/2024.02.04.578814 

2023

Alston, J. J., Ginell, G. M., Soranno, A., & Holehouse, A. S.  (2023). The Analytical Flory Random Coil Is a Simple-to-Use Reference Model for Unfolded and Disordered Proteins. https://doi:10.1101/2023.03.12.531990 

Boeynaems, S., Chong, S., Gsponer, J., Holt, L., Milovanovic, D., Mitrea, D. M., … Kriwacki, R. (2023). Phase separation in biology and disease; current perspectives and open questions. Journal of Molecular Biology, 435(5), 167971. doi:10.1016/j.jmb.2023.167971 

Boeynaems, S., Dorone, Y., Zhuang, Y., Shabardina, V., Huang, G., Marian, A., … Gitler, A. D. (2023). Poly(A)-binding protein is an ataxin-2 chaperone that regulates biomolecular condensates. Molecular Cell, 83(12). doi:10.1016/j.molcel.2023.05.025 

Field, S., Jang, G.-J., Dean, C., Strader, L. C., Rhee, S. Y. (2023) Plants use molecular mechanisms mediated by biomolecular condensates to integrate environmental cues with development. The Plant Cell. 35(9), 3173–3186. https://doi.org/10.1093/plcell/koad062

Lalmansingh, J. M., Keeley, A. T., Ruff, K. M., Pappu, R. V., & Holehouse, A. S. (2023). Soursop: A python package for the analysis of simulations of intrinsically disordered proteins. Journal of Chemical Theory and Computation, 19(16), 5609–5620. https://doi:10.1021/acs.jctc.3c00190 

Marks, R.A., Amézquita, E.J., Percival, S., Rougon-Cardoso, A., Chibici-Revneanu, C., Tebele, S.M., Farrant, J.M., Chitwood, D.H., VanBuren, R. (2023) A critical analysis of plant science literature reveals ongoing inequities. PNAS. 120, 10. DOI: https://doi.org/10.1073/pnas.2217564120 

Moses, D., Ginell, G. M., Holehouse, A. S., & Sukenik, S. (2023). Intrinsically disordered regions are poised to act as sensors of cellular chemistry. Trends in Biochemical Sciences, 48(12), 1019–1034. doi:10.1016/j.tibs.2023.08.001 

Packebush, M.H., Sanchez-Martinez, S., Biswas, S., KC, S., Nguyen, K., Ramirez, J.F., Nicholson, V., Boothby, T.C. (2023) Natural and engineered mediators of desiccation tolerance stabilize Human Blood Clotting Factor VIII in a dry state. Scientific Reports. 13, 4542. DOI: https://doi.org/10.1038/s41598-023-31586-9

Romero-Perez, P. S., Dorone, Y., Flores, E., Sukenik, S., Boeynaems, S. (2023) “When Phased without Water: Biophysics of Cellular Desiccation, from Biomolecules to Condensates. Chemical Reviews.123 (14), 9010-9035, DOI: 10.1021/acs.chemrev.2c00659
​
Sanchez-Martinez, S., Ramirez, J.F.,Meese, E.K., Childs, C.A., Boothby, T.C. (2023) The tardigrade protein CAHS D interacts with, but does not retain, water in hydrated and desiccated systems. Scientific Reports. 13, 10449. DOI: 10.1038/s41598-023-37485-3 

Tetreault, H., Fleming, M., Hill, L., Dorr, E., Yeater, K., Richards, C., & Walters, C. (2023). A power analysis for detecting aging of dry‐stored soybean seeds: Germination versus RNA integrity assessments. Crop Science, 63(3), 1481–1493. doi:10.1002/csc2.20821 

VanBuren, R., Wai, C. M., Giarola, V., Župunski, M., Pardo, J., Kalinowski, M., … Bartels, D. (2023). Core cellular and tissue‐specific mechanisms enable desiccation tolerance in craterostigma. The Plant Journal, 114(2), 231–245. doi:10.1111/tpj.16165 

Yu, F., & Sukenik, S. (2023). Structural preferences shape the entropic force of disordered protein ensembles. The Journal of Physical Chemistry B, 127(19), 4235–4244. doi:10.1021/acs.jpcb.3c00698 

2022

Chen, A., Tapia, H., Goddard, J. M., & Gibney, P. A. (2022) Trehalose and its applications in the food industry. Comprehensive Reviews in Food Science and Food Safety, 1–34. DOI: 10.1111/1541-4337.13048

Lasker, K., Boeynaems, S., Lam, V., Scholl, D., Stainton, E., Briner, A., Holehouse, A., … Shapiro, L. (2022). The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems. Nature Communications, 13(1). doi:10.1038/s41467-022-33221-z 

Nguyen, K., KC, S., Gonzalez, T., Tapia, H., Boothby, T. C. (2022) Trehalose and tardigrade CAHS proteins work synergistically to promote desiccation tolerance. Commun. Biol 5, 1046. DOI: 10.1038/s42003-022-04015-2

St. Aubin, B., Wai, C. M., Kenchanmane Raju, S. K., Niederhuth, C. E., & VanBuren, R. (2022). Regulatory Dynamics distinguishing desiccation tolerance strategies within resurrection grasses. Plant Direct, 6(12). doi:10.1002/pld3.457 

2021

Boothby, T. C. (2021) Water content influences the vitrified properties of CAHS proteins. Mol. Cell 81, 411–413. PMID: 33545054

Dorone, Y., Boeynaems, S., Flores, E., Jin, B., Hateley, S., Bossi, F., Lazarus, E., Pennington, J. G., Michiels, E., De Decker, M., Vints, K., Baatsen, P., Bassel, G. W., Otegui, M. S., Holehouse, A. S., Exposito-Alonso, M., Sukenik, S., Gitler, A. D., Rhee, S. Y. (2021) A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation. Cell 184. PMID: 34233164

Hesgrove, C. S., Nguyen, K. H., Biswas, S., Childs, C. A., Shraddha, K. C., Medina, B. X., Alvarado, V., Sukenik, S., Yu, F., Malferrari, M., Francia, F., Venturoli, G., Martin, E. W., Holehouse, A. S., Boothby, T. C. (2021) Tardigrade CAHS Proteins Act as Molecular Swiss Army Knives to Mediate Desiccation Tolerance Through Multiple Mechanisms. bioRxiv.  DOI: 10.1101/2021.08.16.456555

Marks, R. A., Farrant, J. M., Nicholas McLetchie, D., VanBuren, R. (2021) Unexplored dimensions of variability in vegetative desiccation tolerance. Am. J. Bot. 108, 346–358. PMID: 33421106

Moses, D., Guadalupe, K., Yu, F., Flores, E., Perez, A., McAnelly, R., Shamoon, N. M., Cuevas-Zepeda, E., Merg, A., Martin, E. W., Holehouse, A. S., Sukenik, S. (2021) Hidden structure in disordered proteins is adaptive to intracellular changes. bioRxiv. DOI: 10.1101/2021.11.24.469609

2020

Moses, D., Yu, F., Ginell, G. M., Shamoon, N. M., Koenig, P. S., Holehouse, A. S., Sukenik, S. (2020) Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment. J. Phys. Chem. Lett. 11, 10131–10136. PMID: 33191750

Pardo, J., Man Wai, C., Chay, H., Madden, C. F., Hilhorst, H. W. M., Farrant, J. M., VanBuren, R. (2020) Intertwined signatures of desiccation and drought tolerance in grasses. Proc. Natl. Acad. Sci. U. S. A. 117, 10079–10088. PMID: 32327609

2017-2019

Boothby, T. C., Tapia, H., Brozena, A. H., Piszkiewicz, S., Smith, A. E., Giovannini, I., Rebecchi, L., Pielak, G. J., Koshland, D., Goldstein, B. (2017) Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. Mol. Cell 65, 975–984.e5. PMID: 28306513
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Exposito-Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H. A., Weigel, D. (2018) Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana. Nat Ecol Evol 2, 352–358. PMID: 29255303

Fleming, M. B., Richards, C. M., Walters, C. (2017) Decline in RNA integrity of dry-stored soybean seeds correlates with loss of germination potential. J. Exp. Bot. 68, 2219–2230. PMID: 28407071

Koshland D. and Tapia, H. (2019) Desiccation tolerance: an unusual window into stress biology. MBoC 30, 737–741. PMID: 30870092