| Kennedy, M, Freiburger, A, Cooper, M, Beilsmith, K, St. George, M, Kalski, M, Cham, C, Guzetta, A, Ng, SC, Chan, F, Rubin, D, Henry, CS, Bergelson*, J and EB Chang*. 2025. Diet outperforms microbial transplant to drive microbiome recovery in mice. Nature, in press. |
| Weiner, B, Maerkle, H, Laderman, E, Demirjian, C and J Bergelson. 2025. A physical model links structure and function in the plant immune system. Proceedings of the National Academy of Science, in press. |
| Henry,LP and J Bergelson. 2025. Ecologically informed microbiome engineering. Nature Microbiology, in press. |
| Dooley, K and J Bergelson. 2024. “Richness and density jointly determine context dependence in bacterial interactions.” iScience 27(1): 108654. https://doi.org/10.1016/j.isci.2023.108654. |
| Backman, T, Latorre, SM, Symeonidi, E, Muszynski, A, Bleak, E, Eads, L, Martinez-Koury, I, Som, S, Hawks, A, Gloss, AD, Belnap, D, Manuel, AM, Deutschbauer, AM, Bergelson, J, Azadi, P, Burbano, HA and T Karasov. 2024. “A phage-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria.” Science 384 (6701): ado713. DOI: 10.1126/science.ado0713. |
| Karasov, TL, Neumann, M, Leventhal, L, Symeonidi, E, Shirsekar, G, Hawks, A, Monroe, G, PATHODOPSIS Team, Exposito Alonso, M, Bergelson, J, Weigel, D and R Schwab. 2024. “Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought.” Nature Microbiology, https://doi.org/10.1038/s41564-024-01773-z. |
| Gloss, AD, Steiner, MC, Novembre, J and J Bergelson. 2023. “The design of mapping populations: impacts of geographic scale on genetic architecture and mapping efficiency for defense and immunity.” Current Opinion in Plant Biology 74: 102399. https://doi.org/10.1016/j.pbi.2023.102399. |
| Henry, LP and J Bergelson. 2023. “Evolutionary implications of host genetic control for engineering beneficial microbiomes.” Current Opinion in Systems Biology 34: 1004555. https://doi.org/10.1016/j.coisb.2023.100455. |
| Kennedy, M, Zhang, M, DeLeon, O, Bissell, J, Trigodet, F, Lolans, K, Temelkova, S, Carroll, KT, Fiebig, A, Deutschbauer, A, Sidebottom, AM, Lake, J, Henry, C, Rice, PA, Bergelson, J and EB Chang. 2023. “Dynamic genetic adaptation of Bacteroides thetaiotaomicron murine gut colonization.” Cell Reports 42(8): 113009. https://doi.org/10.1016/j.celrep.2023.113009. |
| Brachi, B, Filiault, D, Whitehurst, H, Darme, P, Le Gars, P, Lemantec, M, Morton, T, Kerdafrec, E, Rabanal, F, Anastasio, A, Box, M, Duncan, S, Huang, F, Leff, R, Novikova, P, Perisin, M, Tsuchimatsu, R, Woolley, R, Dean, C, Nordborg, M, Holmes, S and J Bergelson. 2022. “Plant genetic effects on microbial hubs impact host fitness in repeated field trials.” PNAS 119(30): e2201285119. https://doi.org/10.1073/pnas.2201285119. |
| Bergelson, J, Brachi, B, Roux, F and F Vailleau. 2021. “Assessing the potential to harness the microbiome through plant genetics.” Current Opinions in Biotechnology 70:167-173.https://doi.org/10.1016/j.copbio.2021.05.007. |
| Bergelson, J, Kreitman, K, Petrov, D, Sanchez, A and M Tikhonov. 2021. “Functional biology in its natural context: a search for emergent simplicity.” eLife 10:e67646. https://doi.org/10.7554/eLife.67646. |
| Koskella, B and J Bergelson. 2020. “The study of host microbiome (co)evolution across levels of selection.” Philosophical Transactions of the Royal Society B 375(1808): DOI:10.1098/rstb.2019.0604. https://doi.org/10.1098/rstb.2019.0604. |
| Bergelson, Joy, Jana Mittelstrass, and Matthew W. Horton. 2019. “Characterizing Both Bacteria and Fungi Improves Understanding of the Arabidopsis Root Microbiome.” Scientific Reports 9 (1): 24. https://doi.org/10.1038/s41598-018-37208-z. |
| Wang, Miaoyan, Fabrice Roux, Claudia Bartoli, Carine Huard-Chauveau, Christopher Meyer, Hana Lee, Dominique Roby, Mary Sara McPeek, and Joy Bergelson. 2018. “Two-Way Mixed-Effects Methods for Joint Association Analysis Using Both Host and Pathogen Genomes.” Proceedings of the National Academy of Sciences 115 (24): E5440–49. https://doi.org/10.1073/pnas.1710980115. |
| Karasov, Talia L., Eunyoung Chae, Jacob J. Herman, and Joy Bergelson. 2017. “Mechanisms to Mitigate the Trade-Off between Growth and Defense.” The Plant Cell 29 (4): 666–80. https://doi.org/10.1105/tpc.16.00931. |
| Frachon, Léa, Cyril Libourel, Romain Villoutreix, Sébastien Carrère, Cédric Glorieux, Carine Huard-Chauveau, Miguel Navascués, et al. 2017. “Intermediate Degrees of Synergistic Pleiotropy Drive Adaptive Evolution in Ecological Time.” Nature Ecology & Evolution 1 (10): 1551. https://doi.org/10.1038/s41559-017-0297-1. |
| Vetter, Madlen, Talia L. Karasov, and Joy Bergelson. 2016. “Differentiation between MAMP Triggered Defenses in Arabidopsis Thaliana.” PLOS Genet 12 (6): e1006068. https://doi.org/10.1371/journal.pgen.1006068. |
| MacQueen, Alice, Xiaoqin Sun, and Joy Bergelson. 2016. “Genetic Architecture and Pleiotropy Shape Costs of Rps2-Mediated Resistance in Arabidopsis Thaliana.” Nature Plants 2 (July): 16110. https://doi.org/10.1038/nplants.2016.110. |
| Brachi, Benjamin, Christopher G. Meyer, Romain Villoutreix, Alexander Platt, Timothy C. Morton, Fabrice Roux, and Joy Bergelson. 2015. “Coselected Genes Determine Adaptive Variation in Herbivore Resistance throughout the Native Range of Arabidopsis Thaliana.” Proceedings of the National Academy of Sciences 112 (13): 4032–37. https://doi.org/10.1073/pnas.1421416112. |
| Karasov, Talia L., Joel M. Kniskern, Liping Gao, Brody J. DeYoung, Jing Ding, Ullrich Dubiella, Ruben O. Lastra, et al. 2014. “The Long-Term Maintenance of a Resistance Polymorphism through Diffuse Interactions.” Nature 512 (7515): 436–40. https://doi.org/10.1038/nature13439. |
| Horton, Matthew W., Natacha Bodenhausen, Kathleen Beilsmith, Dazhe Meng, Brian D. Muegge, Sathish Subramanian, M. Madlen Vetter, et al. 2014. “Genome-Wide Association Study of Arabidopsis Thaliana Leaf Microbial Community.” Nature Communications 5 (November). https://doi.org/10.1038/ncomms6320. |
| Luo, Guan-Zheng, Alice MacQueen, Guanqun Zheng, Hongchao Duan, Louis C. Dore, Zhike Lu, Jun Liu, et al. 2014. “Unique Features of the M6A Methylome in Arabidopsis Thaliana.” Nature Communications 5 (November). https://doi.org/10.1038/ncomms6630. |
| Bodenhausen, Natacha, Matthew W. Horton, and Joy Bergelson. 2013. “Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis Thaliana.” PLoS ONE 8 (2). https://doi.org/10.1371/journal.pone.0056329. |
| Horton, Matthew W., Angela M. Hancock, Yu S. Huang, Christopher Toomajian, Susanna Atwell, Adam Auton, N. Wayan Muliyati, et al. 2012. “Genome-Wide Patterns of Genetic Variation in Worldwide Arabidopsis Thaliana Accessions from the RegMap Panel.” Nature Genetics 44 (2): 212–16. https://doi.org/10.1038/ng.1042. |
| Hu, Tina T., Pedro Pattyn, Erica G. Bakker, Jun Cao, Jan-Fang Cheng, Richard M. Clark, Noah Fahlgren, et al. 2011. “The Arabidopsis Lyrata Genome Sequence and the Basis of Rapid Genome Size Change.” Nature Genetics 43 (5): 476–81. https://doi.org/10.1038/ng.807. |
| Hancock, Angela M., Benjamin Brachi, Nathalie Faure, Matthew W. Horton, Lucien B. Jarymowycz, F. Gianluca Sperone, Chris Toomajian, Fabrice Roux, and Joy Bergelson. 2011. “Adaptation to Climate Across the Arabidopsis Thaliana Genome.” Science 334 (6052): 83–86. https://doi.org/10.1126/science.1209244. |
| Barrett, Luke G., Thomas Bell, Greg Dwyer, and Joy Bergelson. 2011. “Cheating, Trade-Offs and the Evolution of Aggressiveness in a Natural Pathogen Population.” Ecology Letters 14 (11): 1149–57. https://doi.org/10.1111/j.1461-0248.2011.01687.x. |
| Bergelson, Joy, and Fabrice Roux. 2010. “Towards Identifying Genes Underlying Ecologically Relevant Traits in Arabidopsis Thaliana.” Nature Reviews Genetics 11 (12): 867–79. https://doi.org/10.1038/nrg2896. |
| Atwell, Susanna, Yu S Huang, Bjarni J Vilhjálmsson, Glenda Willems, Matthew Horton, Yan Li, Dazhe Meng, et al. 2010. “Genome-Wide Association Study of 107 Phenotypes in Arabidopsis Thaliana Inbred Lines.” Nature 465 (7298): 627–31. https://doi.org/10.1038/nature08800. |
| Platt, Alexander, Matthew Horton, Yu S Huang, Yan Li, Alison E Anastasio, Ni Wayan Mulyati, Jon Agren, et al. 2010. “The Scale of Population Structure in Arabidopsis Thaliana.” PLoS Genetics 6 (2): e1000843. https://doi.org/10.1371/journal.pgen.1000843. |
| Todesco, Marco, Sureshkumar Balasubramanian, Tina T Hu, M Brian Traw, Matthew Horton, Petra Epple, Christine Kuhns, et al. 2010. “Natural Allelic Variation Underlying a Major Fitness Trade-off in Arabidopsis Thaliana.” Nature 465 (7298): 632–36. https://doi.org/10.1038/nature09083. |
| Tian, Dacheng, Qiang Wang, Pengfei Zhang, Hitoshi Araki, Sihai Yang, Martin Kreitman, Thomas Nagylaki, Richard Hudson, Joy Bergelson, and Jian-Qun Chen. 2008. “Single-Nucleotide Mutation Rate Increases Close to Insertions/Deletions in Eukaryotes.” Nature 455 (7209): 105–8. https://doi.org/10.1038/nature07175. |
| Bakker, Erica G, Christopher Toomajian, Martin Kreitman, and Joy Bergelson. 2006. “A Genome-Wide Survey of R Gene Polymorphisms in Arabidopsis.” The Plant Cell 18 (8): 1803–18. https://doi.org/10.1105/tpc.106.042614. |
| Nordborg, Magnus, Tina T Hu, Yoko Ishino, Jinal Jhaveri, Christopher Toomajian, Honggang Zheng, Erica Bakker, et al. 2005. “The Pattern of Polymorphism in Arabidopsis Thaliana.” PLoS Biology 3 (7): e196. https://doi.org/10.1371/journal.pbio.0030196. |
| Wichmann, Gale, and Joy Bergelson. 2004. “Effector Genes of Xanthomonas Axonopodis Pv. Vesicatoria Promote Transmission and Enhance Other Fitness Traits in the Field.” Genetics 166 (2): 693–706. doi: 10.1534/genetics.166.2.693. |
| Jakob, Katrin, Erica M Goss, Hitoshi Araki, Tam Van, Martin Kreitman, and Joy Bergelson. 2002. “Pseudomonas Viridiflava and P. Syringae–Natural Pathogens of Arabidopsis Thaliana.” Molecular Plant-Microbe Interactions : MPMI 15 (12): 1195–1203. https://doi.org/10.1094/MPMI.2002.15.12.1195. |
| Tian, Dacheng, Hitoshi Araki, Eli Stahl, Joy Bergelson, and Martin Kreitman. 2002. “Signature of Balancing Selection in Arabidopsis.” Proceedings of the National Academy of Sciences of the United States of America 99 (17): 11525–30. https://doi.org/10.1073/pnas.172203599. |
| Bergelson, Joy, Martin Kreitman, Eli A. Stahl, and Dacheng Tian. 2001. “Evolutionary Dynamics of Plant R-Genes.” Science 292 (5525): 2281–85. https://doi.org/10.1126/science.1061337. |
| Stahl, Eli A., Greg Dwyer, Rodney Mauricio, Martin Kreitman, and Joy Bergelson. 1999. “Dynamics of Disease Resistance Polymorphism at the Rpm1 Locus of Arabidopsis.” Nature 400 (6745): 667–71. https://doi.org/10.1038/23260. |
| Bergelson, Joy, Colin B. Purrington, and Gale Wichmann. 1998. “Promiscuity in Transgenic Plants.” Nature 395 (6697): 25–25. https://doi.org/10.1038/25626. |
| Newman, Jonathan A., Joy Bergelson, and Alan Grafen. 1997. “Blocking Factors and Hypothesis Tests in Ecology: Is Your Statistics Text Wrong?” Ecology 78 (5): 1312–20. https://doi.org/10.1890/0012-9658(1997)078[1312:BFAHTI]2.0.CO;2. |
| Bergelson, Joy, and Colin B. Purrington. 1996. “Surveying Patterns in the Cost of Resistance in Plants.” The American Naturalist 148 (3): 536–58. https://www.jstor.org/stable/2463302. |
| Bergelson, Joy. 1994. “The Effects of Genotype and the Environment on Costs of Resistance in Lettuce.” The American Naturalist 143 (2): 349–59. https://www.jstor.org/stable/2462647. |
| Exposito-Alonso, Moises, Claude Becker, Verena J. Schuenemann, Ella Reiter, Claudia Setzer, Radka Slovak, Benjamin Brachi, et al. 2018. “The Rate and Potential Relevance of New Mutations in a Colonizing Plant Lineage.” PLOS Genetics 14 (2): e1007155. https://doi.org/10.1371/journal.pgen.1007155. |