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Joy Bergelson

TitleResearch Professor
InstitutionUniversity of Chicago
DepartmentEcology and Evolution
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    We study the ecology and evolution of plant – pathogen interactions, focusing primarily on Arabidopsis thaliana and the bacteria that reside within it. Our approach is interdisciplinary – we draw upon tools from molecular genetics, molecular evolution, computation, field biology, chemistry and population genetics to understand how ecological interactions shape evolutionary dynamics. The lab typically contains a mixture of graduate students, postdoctoral fellows, undergraduate students and technicians, who enjoy working with a diverse set of students and collaborators from around the world. Many of our field experiments are performed locally, at our new field station in Michigan, or abroad, at sites in Sweden and France.

    Collapse Biography 
    Collapse education and training
    Brown University, Rhode IslandScB 06/1984Biology
    University of York, York, UKMPhil06/1986Ecology
    University of Washington, Seattle, WAPhD11/1990Zoology
    Collapse awards and honors
    2018Elected National Academy of Science
    2017James D Watson Professor, University of Chicago
    2017BSD Distinguished Faculty Award, University of Chicago
    2010Louis Block Professor, University of Chicago
    2005Cheung Kong Honorary Professor, Nanjing University
    2004Fellow, American Association for the Advancement of Science
    1993Packard Fellowship, Packard Foundation
    1993Young Investigator Award, American Society of Naturalists
    1993Presidential Faculty Fellow, National Science Foundation
    1990NATO Fellow in Biological Sciences
    1986NSF Graduate Fellowship, National Science Foundation
    1984Marshall Scholarship, Marshall Foundation
    1984Sigma Xi Honor Society, Brown University chapter
    1983Phi Beta Kappa Honor Society, Brown University chapter

    Collapse Research 
    Collapse research activities and funding
    R01GM083068     (BERGELSON, JOY M)Aug 1, 2008 - Jun 30, 2014
    NIH
    The Molecular Basis of Local Adaptation in Arabidopsis thaliana
    Role: Principal Investigator
    R01GM062504     (BERGELSON, JOY M)Mar 1, 2001 - Feb 28, 2006
    NIH
    EVOLUTIONARY DYNAMICS OF GENE-FOR-GENE SYSTEMS
    Role: Principal Investigator
    R01GM057994     (BERGELSON, JOY M)Jul 1, 1998 - Jun 30, 2010
    NIH
    Evolutionary Genetics of R Loci in Arabidopsis
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Karasov TL, Neumann M, Leventhal L, Symeonidi E, Shirsekar G, Hawks A, Monroe G, Pathodopsis Team, Exposito-Alonso M, Bergelson J, Weigel D, Schwab R. Continental-scale associations of Arabidopsis thaliana phyllosphere members with host genotype and drought. Nat Microbiol. 2024 Oct; 9(10):2748-2758. PMID: 39242816; PMCID: PMC11457713.
      Citations:    Fields:    Translation:AnimalsCells
    2. Kennedy MS, Freiburger A, Cooper M, Beilsmith K, St George ML, Kalski M, Cham C, Guzzetta A, Ng SC, Chan FK, Rubin D, Henry CS, Bergelson J, Chang EB. Diet outperforms microbial transplant to drive microbiome recovery post-antibiotics. bioRxiv. 2024 Aug 01. PMID: 39211181; PMCID: PMC11361181.
      Citations:    
    3. Backman T, Latorre SM, Symeonidi E, Muszynski A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A phage tail-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria. Science. 2024 06 14; 384(6701):eado0713. PMID: 38870284; PMCID: PMC11404688.
      Citations: 5     Fields:    Translation:Cells
    4. Backman T, Latorre SM, Symeonidi E, Muszynski A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria. bioRxiv. 2024 Feb 02. PMID: 38352526; PMCID: PMC10862724.
      Citations:    
    5. Dooley KD, Henry LP, Bergelson J, Dooley KD, Henry LP, Bergelson J. Impact of timing on the invasion of synthetic bacterial communities. ISME J. 2024 Jan 08; 18(1). PMID: 39498487; PMCID: PMC11605641.
      Citations:    Fields:    Translation:AnimalsCells
    6. Dooley KD, Bergelson J. Richness and density jointly determine context dependence in bacterial interactions. iScience. 2024 Jan 19; 27(1):108654. PMID: 38188527; PMCID: PMC10770726.
      Citations: 1     
    7. Oldstone-Jackson C, Huang F, Bergelson J. Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field. Front Plant Sci. 2023; 14:1276472. PMID: 38023837; PMCID: PMC10663345.
      Citations: 1     
    8. Shapiro JS, Chang HC, Tatekoshi Y, Zhao Z, Waxali ZS, Hong BJ, Chen H, Geier JA, Bartom ET, De Jesus A, Nejad FK, Mahmoodzadeh A, Sato T, Ramos-Alonso L, Romero AM, Martinez-Pastor MT, Jiang SC, Sah-Teli SK, Li L, Bentrem D, Lopaschuk G, Ben-Sahra I, O'Halloran TV, Shilatifard A, Puig S, Bergelson J, Koivunen P, Ardehali H. Iron drives anabolic metabolism through active histone demethylation and mTORC1. Nat Cell Biol. 2023 10; 25(10):1478-1494. PMID: 37749225; PMCID: PMC11407783.
      Citations: 7     Fields:    Translation:Cells
    9. Kennedy MS, 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, Chang EB. Dynamic genetic adaptation of Bacteroides thetaiotaomicron during murine gut colonization. Cell Rep. 2023 08 29; 42(8):113009. PMID: 37598339; PMCID: PMC10528517.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    10. Gloss AD, Steiner MC, Novembre J, Bergelson J. The design of mapping populations: Impacts of geographic scale on genetic architecture and mapping efficacy for defense and immunity. Curr Opin Plant Biol. 2023 08; 74:102399. PMID: 37307746; PMCID: PMC10441534.
      Citations: 2     Fields:    
    11. Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. Curr Opin Syst Biol. 2023 Jun; 34:None. PMID: 37287906; PMCID: PMC10242548.
      Citations: 2     
    12. Brachi B, Filiault D, Whitehurst H, Darme P, Le Gars P, Le Mentec M, Morton TC, Kerdaffrec E, Rabanal F, Anastasio A, Box MS, Duncan S, Huang F, Leff R, Novikova P, Perisin M, Tsuchimatsu T, Woolley R, Dean C, Nordborg M, Holm S, Bergelson J. Plant genetic effects on microbial hubs impact host fitness in repeated field trials. Proc Natl Acad Sci U S A. 2022 07 26; 119(30):e2201285119. PMID: 35867817; PMCID: PMC9335298.
      Citations: 24     Fields:    Translation:Animals
    13. Gloss AD, Morton TC, Laurin PJ, Bergelson J, Vergnol A, Roux F. Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity. Philos Trans R Soc Lond B Biol Sci. 2022 07 18; 377(1855):20200512. PMID: 35634919; PMCID: PMC9149790.
      Citations: 11     Fields:    Translation:Animals
    14. Huang Y, Chen J, Dong C, Sosa D, Xia S, Ouyang Y, Fan C, Li D, Mortola E, Long M, Bergelson J. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. Plant Cell. 2022 02 03; 34(2):802-817. PMID: 34875081; PMCID: PMC8824575.
      Citations: 12     Fields:    Translation:AnimalsCells
    15. Bergelson J, Brachi B, Roux F, Vailleau F. Assessing the potential to harness the microbiome through plant genetics. Curr Opin Biotechnol. 2021 08; 70:167-173. PMID: 34126329.
      Citations: 11     Fields:    Translation:AnimalsCells
    16. Bergelson J, Kreitman M, Petrov DA, Sanchez A, Tikhonov M. Functional biology in its natural context: A search for emergent simplicity. Elife. 2021 06 07; 10. PMID: 34096867; PMCID: PMC8184206.
      Citations: 19     Fields:    Translation:HumansAnimals
    17. Bergelson J, Rubio B, Fernandez O, Cosson P, Berton T, Caballero M, Lion R, Roux F, Gibon Y, Schurdi-Levraud V. Metabolic Profile Discriminates and Predicts Arabidopsis Susceptibility to Virus under Field Conditions. Metabolites. 2021 Apr 09; 11(4). PMID: 33918649; PMCID: PMC8069729.
      Citations: 1     
    18. Beilsmith K, Perisin M, Bergelson J. Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development. mBio. 2021 01 19; 12(1). PMID: 33468687; PMCID: PMC7845642.
      Citations: 15     Fields:    Translation:AnimalsCells
    19. Koskella B, Bergelson J. The study of host-microbiome (co)evolution across levels of selection. Philos Trans R Soc Lond B Biol Sci. 2020 09 28; 375(1808):20190604. PMID: 32772660; PMCID: PMC7435161.
      Citations: 31     Fields:    
    20. MacQueen A, Tian D, Chang W, Holub E, Kreitman M, Bergelson J. Population Genetics of the Highly Polymorphic RPP8 Gene Family. Genes (Basel). 2019 09 08; 10(9). PMID: 31500388; PMCID: PMC6771003.
      Citations: 9     Fields:    Translation:Animals
    21. Bergelson J, Mittelstrass J, Horton MW. Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome. Sci Rep. 2019 01 10; 9(1):24. PMID: 30631088; PMCID: PMC6328596.
      Citations: 64     Fields:    Translation:AnimalsCells
    22. Beilsmith K, Thoen MPM, Brachi B, Gloss AD, Khan MH, Bergelson J. Genome-wide association studies on the phyllosphere microbiome: Embracing complexity in host-microbe interactions. Plant J. 2019 01; 97(1):164-181. PMID: 30466152.
      Citations: 30     Fields:    Translation:Animals
    23. Rubio B, Cosson P, Bergelson J, Caballero M, Revers F, Roux F, Schurdi-Levraud V. Genome-wide association study reveals new loci involved in Arabidopsis thaliana and Turnip mosaic virus (TuMV) interactions in the field. New Phytol. 2019 03; 221(4):2026-2038. PMID: 30282123.
      Citations: 15     Fields:    Translation:AnimalsCells
    24. Nallu S, Hill JA, Don K, Sahagun C, Zhang W, Meslin C, Snell-Rood E, Clark NL, Morehouse NI, Bergelson J, Wheat CW, Kronforst MR. The molecular genetic basis of herbivory between butterflies and their host plants. Nat Ecol Evol. 2018 09; 2(9):1418-1427. PMID: 30076351; PMCID: PMC6149523.
      Citations: 25     Fields:    Translation:Animals
    25. Wang M, Meyer C, Lee H, McPeek MS, Bergelson J, Roux F, Bartoli C, Huard-Chauveau C, Roby D. Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes. Proc Natl Acad Sci U S A. 2018 06 12; 115(24):E5440-E5449. PMID: 29848634; PMCID: PMC6004472.
      Citations: 28     Fields:    Translation:AnimalsCells
    26. . The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genetics. 2018; 2(14):e1007155.
    27. Setzer C, Slovak R, Brachi B, Chen J, Busch W, Bergelson J, Ness RW, Exposito-Alonso M, Becker C, Schuenemann VJ, Reiter E, Hagmann J, Grimm DG, Krause J, Burbano HA, Weigel D. The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genet. 2018 02; 14(2):e1007155. PMID: 29432421; PMCID: PMC5825158.
      Citations: 53     Fields:    Translation:Animals
    28. Vitalis R, Bouchez O, Vidal M, Bergelson J, Frachon L, Libourel C, Villoutreix R, Carrère S, Glorieux C, Huard-Chauveau C, Navascués M, Gay L, Baron E, Amsellem L, Le Corre V, Roby D, Roux F. Author Correction: Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nat Ecol Evol. 2018 01; 2(1):194. PMID: 29208992.
      Citations:    Fields:    
    29. Karasov TL, Barrett L, Hershberg R, Bergelson J. Similar levels of gene content variation observed for Pseudomonas syringae populations extracted from single and multiple host species. PLoS One. 2017; 12(9):e0184195. PMID: 28880925; PMCID: PMC5589212.
      Citations: 4     Fields:    Translation:AnimalsCells
    30. . Similar levels of gene content variation observed for Pseudomonas syringae populations extracted from single and multiple host species. PLoS ONE. 2017; 9(12):e0184195.
    31. . Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nature Ecology & Evolution. 2017; 1(1):1551-1561.
    32. Vitalis R, Bouchez O, Vidal M, Bergelson J, Frachon L, Libourel C, Villoutreix R, Carrère S, Glorieux C, Huard-Chauveau C, Navascués M, Gay L, Baron E, Amsellem L, Le Corre V, Roby D, Roux F. Intermediate degrees of synergistic pleiotropy drive adaptive evolution in ecological time. Nat Ecol Evol. 2017 Oct; 1(10):1551-1561. PMID: 29185515.
      Citations: 48     Fields:    Translation:Animals
    33. Herman JJ, Bergelson J, Karasov TL, Chae E. Mechanisms to Mitigate the Trade-Off between Growth and Defense. Plant Cell. 2017 Apr; 29(4):666-680. PMID: 28320784; PMCID: PMC5435432.
      Citations: 181     Fields:    Translation:Animals
    34. MacQueen A, Sun X, Bergelson J. Genetic architecture and pleiotropy shape costs of Rps2-mediated resistance in Arabidopsis thaliana. Nat Plants. 2016 07 18; 2:16110. PMID: 27428524; PMCID: PMC4968571.
      Citations: 14     Fields:    Translation:Animals
    35. Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, O'Neil R, O'Malley RC, Quarless DX, 1001 Genomes Consortium, Schork NJ, Nordborg M, Ecker JR, Wang C, Bemm F, Becker C, Weigel D. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell. 2016 Jul 14; 166(2):492-505. PMID: 27419873; PMCID: PMC5172462.
      Citations: 315     Fields:    Translation:AnimalsCells
    36. Vetter M, Karasov TL, Bergelson J. Differentiation between MAMP Triggered Defenses in Arabidopsis thaliana. PLoS Genet. 2016 06; 12(6):e1006068. PMID: 27336582; PMCID: PMC4919071.
      Citations: 12     Fields:    Translation:AnimalsCells
    37. Bergelson J, Buckler ES, Ecker JR, Nordborg M, Weigel D. A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants. Plant Cell. 2016 Mar; 28(3):606-9. PMID: 26956491; PMCID: PMC4826003.
      Citations: 19     Fields:    Translation:Animals
    38. MacQueen A, Bergelson J. Modulation of R-gene expression across environments. J Exp Bot. 2016 Mar; 67(7):2093-105. PMID: 26983577; PMCID: PMC4793800.
      Citations: 24     Fields:    Translation:Animals
    39. Zhang X, Yang S, Wang J, Jia Y, Huang J, Tan S, Zhong Y, Wang L, Gu L, Chen JQ, Pan Q, Bergelson J, Tian D. A genome-wide survey reveals abundant rice blast R genes in resistant cultivars. Plant J. 2015 Oct; 84(1):20-28. PMID: 26248689; PMCID: PMC4591205.
      Citations: 25     Fields:    Translation:Animals
    40. Perisin M, Vetter M, Gilbert JA, Bergelson J. 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. ISME J. 2016 Apr; 10(4):1020-4. PMID: 26359911; PMCID: PMC4796925.
      Citations: 11     Fields:    Translation:AnimalsCells
    41. Brachi B, Meyer CG, Platt A, Morton TC, Roux F, Bergelson J, Villoutreix R. Coselected genes determine adaptive variation in herbivore resistance throughout the native range of Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2015 Mar 31; 112(13):4032-7. PMID: 25775585; PMCID: PMC4386350.
      Citations: 52     Fields:    Translation:Animals
    42. Meyer RC, Schneeberger K, Altmann T, Bergelson J, Hagmann J, Becker C, Müller J, Stegle O, Wang G, Fitz J, Borgwardt K, Weigel D. Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet. 2015 Jan; 11(1):e1004920. PMID: 25569172; PMCID: PMC4287485.
      Citations: 77     Fields:    Translation:AnimalsCells
    43. Luo GZ, MacQueen A, Zheng G, Duan H, Dore LC, Lu Z, Liu J, Chen K, Jia G, Bergelson J, He C. Unique features of the m6A methylome in Arabidopsis thaliana. Nat Commun. 2014 Nov 28; 5:5630. PMID: 25430002; PMCID: PMC4248235.
      Citations: 228     Fields:    Translation:Animals
    44. Horton MW, Bodenhausen N, Beilsmith K, Meng D, Muegge BD, Subramanian S, Vetter MM, Nordborg M, Gordon JI, Bergelson J, Vilhjálmsson BJ. Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nat Commun. 2014 Nov 10; 5:5320. PMID: 25382143; PMCID: PMC4232226.
      Citations: 154     Fields:    Translation:Animals
    45. Li P, Filiault D, Box MS, Kerdaffrec E, van Oosterhout C, Wilczek AM, Schmitt J, McMullan M, Bergelson J, Nordborg M, Dean C. Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana. Genes Dev. 2014 Aug 01; 28(15):1635-40. PMID: 25035417; PMCID: PMC4117938.
      Citations: 60     Fields:    Translation:Animals
    46. Karasov TL, Kniskern JM, Gao L, DeYoung BJ, Ding J, Dubiella U, Lastra RO, Nallu S, Roux F, Innes RW, Barrett LG, Hudson RR, Bergelson J. The long-term maintenance of a resistance polymorphism through diffuse interactions. Nature. 2014 Aug 28; 512(7515):436-440. PMID: 25043057; PMCID: PMC4696508.
      Citations: 96     Fields:    Translation:AnimalsCells
    47. Karasov TL, Horton MW, Bergelson J. Genomic variability as a driver of plant-pathogen coevolution? Curr Opin Plant Biol. 2014 Apr; 18:24-30. PMID: 24491596; PMCID: PMC4696489.
      Citations: 44     Fields:    Translation:Animals
    48. Bodenhausen N, Falk KL, Kästner J, Schramm K, Paetz C, Vassão DG, Reichelt M, von Knorre D, Bergelson J, Erb M, Gershenzon J, Meldau S. The role of glucosinolates and the jasmonic acid pathway in resistance of Arabidopsis thaliana against molluscan herbivores. Mol Ecol. 2014 Mar; 23(5):1188-1203. PMID: 24313595; PMCID: PMC5147714.
      Citations: 41     Fields:    Translation:Animals
    49. Huard-Chauveau C, Perchepied L, Debieu M, Rivas S, Kroj T, Kars I, Bergelson J, Roux F, Roby D. An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsis. PLoS Genet. 2013; 9(9):e1003766. PMID: 24068949; PMCID: PMC3772041.
      Citations: 57     Fields:    Translation:AnimalsCells
    50. Roby D, Bergelson J, Brachi B, Villoutreix R, Faure N, Hautekèete N, Piquot Y, Pauwels M, Cuguen J, Roux F. Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana. Mol Ecol. 2013 Aug; 22(16):4222-4240. PMID: 23875782.
      Citations: 42     Fields:    Translation:Animals
    51. Bergelson J, Brachi B, Faure N, Cuguen J, Roux F. Genome-wide association mapping of flowering time in Arabidopsis thaliana in nature: genetics for underlying components and reaction norms across two successive years. Acta Bot Gall. 2013 Jul 01; 160(3-4):205-219. PMID: 24470785; PMCID: PMC3901435.
      Citations: 8     
    52. Bodenhausen N, Horton MW, Bergelson J. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One. 2013; 8(2):e56329. PMID: 23457551; PMCID: PMC3574144.
      Citations: 288     Fields:    Translation:AnimalsCells
    53. Vetter MM, Kronholm I, He F, Reymond M, Bergelson J, Robatzek S, de Meaux J, Häweker H. Flagellin perception varies quantitatively in Arabidopsis thaliana and its relatives. Mol Biol Evol. 2012 Jun; 29(6):1655-67. PMID: 22319159.
      Citations: 36     Fields:    Translation:AnimalsCells
    54. Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, Muliyati NW, Platt A, Sperone FG, Nordborg M, Borevitz JO, Bergelson J, Vilhjálmsson BJ. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet. 2012 Jan 08; 44(2):212-6. PMID: 22231484; PMCID: PMC3267885.
      Citations: 249     Fields:    Translation:Animals
    55. Poroyko V, Morowitz M, Bell T, Ulanov A, Wang M, Donovan S, Bao N, Gu S, Hong L, Alverdy JC, Bergelson J, Liu DC. Diet creates metabolic niches in the "immature gut" that shape microbial communities. Nutr Hosp. 2011 Nov-Dec; 26(6):1283-95. PMID: 22411374.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    56. Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, Toomajian C, Roux F, Bergelson J. Adaptation to climate across the Arabidopsis thaliana genome. Science. 2011 Oct 07; 334(6052):83-6. PMID: 21980108.
      Citations: 270     Fields:    Translation:Animals
    57. Barrett LG, Bell T, Dwyer G, Bergelson J. Cheating, trade-offs and the evolution of aggressiveness in a natural pathogen population. Ecol Lett. 2011 Nov; 14(11):1149-57. PMID: 21951910; PMCID: PMC3190666.
      Citations: 33     Fields:    Translation:AnimalsCells
    58. Anastasio AE, Platt A, Horton M, Grotewold E, Scholl R, Borevitz JO, Nordborg M, Bergelson J. Source verification of mis-identified Arabidopsis thaliana accessions. Plant J. 2011 Aug; 67(3):554-66. PMID: 21481029.
      Citations: 37     Fields:    Translation:Animals
    59. Huang YS, Horton M, Seren U, Meng D, Meyer C, Ali Amer M, Borevitz JO, Bergelson J, Nordborg M, Vilhjálmsson BJ. Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies. Database (Oxford). 2011; 2011:bar014. PMID: 21609965; PMCID: PMC3243604.
      Citations: 2     Fields:    Translation:Animals
    60. Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, Fahlgren N, Fawcett JA, Grimwood J, Gundlach H, Haberer G, Hollister JD, Ossowski S, Ottilar RP, Salamov AA, Schneeberger K, Spannagl M, Wang X, Yang L, Nasrallah ME, Bergelson J, Carrington JC, Gaut BS, Schmutz J, Mayer KF, Van de Peer Y, Grigoriev IV, Nordborg M, Weigel D, Guo YL. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 2011 May; 43(5):476-81. PMID: 21478890; PMCID: PMC3083492.
      Citations: 425     Fields:    Translation:AnimalsCells
    61. Bergelson J, Roux F. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet. 2010 Dec; 11(12):867-79. PMID: 21085205.
      Citations: 140     Fields:    Translation:Animals
    62. Li Y, Huang Y, Bergelson J, Nordborg M, Borevitz JO. Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2010 Dec 07; 107(49):21199-204. PMID: 21078970; PMCID: PMC3000268.
      Citations: 152     Fields:    Translation:Animals
    63. Baxter I, Brazelton JN, Yu D, Huang YS, Lahner B, Yakubova E, Li Y, Bergelson J, Borevitz JO, Nordborg M, Vitek O, Salt DE. A coastal cline in sodium accumulation in Arabidopsis thaliana is driven by natural variation of the sodium transporter AtHKT1;1. PLoS Genet. 2010 Nov 11; 6(11):e1001193. PMID: 21085628; PMCID: PMC2978683.
      Citations: 154     Fields:    Translation:Animals
    64. Kniskern JM, Barrett LG, Bergelson J. Maladaptation in wild populations of the generalist plant pathogen Pseudomonas syringae. Evolution. 2011 Mar; 65(3):818-30. PMID: 21044058; PMCID: PMC3053089.
      Citations: 20     Fields:    
    65. Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RA, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D, Todesco M. Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature. 2010 Jun 03; 465(7298):632-6. PMID: 20520716; PMCID: PMC3055268.
      Citations: 156     Fields:    
    66. Traw MB, Bergelson J. Plant immune system incompatibility and the distribution of enemies in natural hybrid zones. Curr Opin Plant Biol. 2010 Aug; 13(4):466-71. PMID: 20494612.
      Citations: 7     Fields:    Translation:AnimalsCells
    67. Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, Bergelson J, Cuguen J, Roux F, Brachi B. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet. 2010 May 06; 6(5):e1000940. PMID: 20463887; PMCID: PMC2865524.
      Citations: 196     Fields:    Translation:AnimalsCells
    68. Atwell S, Huang YS, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone AM, Hu TT, Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JD, Michael T, Nemri A, Roux F, Salt DE, Tang C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz JO, Bergelson J, Nordborg M, Vilhjálmsson BJ. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature. 2010 Jun 03; 465(7298):627-31. PMID: 20336072; PMCID: PMC3023908.
      Citations: 820     Fields:    
    69. Platt A, Horton M, Huang YS, Li Y, Anastasio AE, Mulyati NW, Agren J, Bossdorf O, Byers D, Donohue K, Dunning M, Holub EB, Hudson A, Loudet O, Roux F, Warthmann N, Weigel D, Rivero L, Scholl R, Nordborg M, Bergelson J, Borevitz JO, Le Corre V. The scale of population structure in Arabidopsis thaliana. PLoS Genet. 2010 Feb 12; 6(2):e1000843. PMID: 20169178; PMCID: PMC2820523.
      Citations: 166     Fields:    
    70. Roux F, Gao L, Bergelson J. Impact of initial pathogen density on resistance and tolerance in a polymorphic disease resistance gene system in Arabidopsis thaliana. Genetics. 2010 May; 185(1):283-91. PMID: 20142437; PMCID: PMC2870963.
      Citations: 12     Fields:    Translation:Animals
    71. Horton M, Bodenhausen N, Bergelson J. MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences. Bioinformatics. 2010 Feb 15; 26(4):568-9. PMID: 20007739.
      Citations: 13     Fields:    Translation:Cells
    72. Li X, Bergelson J, Chapple C. The ARABIDOPSIS accession Pna-10 is a naturally occurring sng1 deletion mutant. Mol Plant. 2010 Jan; 3(1):91-100. PMID: 19969522.
      Citations: 17     Fields:    Translation:Animals
    73. Gao L, Roux F, Bergelson J. Quantitative fitness effects of infection in a gene-for-gene system. New Phytol. 2009 Oct; 184(2):485-494. PMID: 19659661; PMCID: PMC4311775.
      Citations: 9     Fields:    
    74. Barrett LG, Kniskern JM, Bodenhausen N, Zhang W, Bergelson J. Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences. New Phytol. 2009 Aug; 183(3):513-529. PMID: 19563451.
      Citations: 65     Fields:    Translation:Animals
    75. Chen JQ, Wu Y, Yang H, Bergelson J, Kreitman M, Tian D. Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol. 2009 Jul; 26(7):1523-31. PMID: 19329651.
      Citations: 66     Fields:    Translation:HumansAnimals
    76. Tian D, Wang Q, Zhang P, Araki H, Yang S, Kreitman M, Nagylaki T, Hudson R, Bergelson J, Chen JQ. Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature. 2008 Sep 04; 455(7209):105-8. PMID: 18641631.
      Citations: 131     Fields:    Translation:HumansAnimalsCells
    77. Bakker EG, Traw MB, Toomajian C, Kreitman M, Bergelson J. Low levels of polymorphism in genes that control the activation of defense response in Arabidopsis thaliana. Genetics. 2008 Apr; 178(4):2031-43. PMID: 18245336; PMCID: PMC2323794.
      Citations: 29     Fields:    Translation:AnimalsCells
    78. Broeckling CD, Broz AK, Bergelson J, Manter DK, Vivanco JM. Root exudates regulate soil fungal community composition and diversity. Appl Environ Microbiol. 2008 Feb; 74(3):738-44. PMID: 18083870; PMCID: PMC2227741.
      Citations: 154     Fields:    Translation:AnimalsPHPublic Health
    79. Kniskern JM, Traw MB, Bergelson J. Salicylic acid and jasmonic acid signaling defense pathways reduce natural bacterial diversity on Arabidopsis thaliana. Mol Plant Microbe Interact. 2007 Dec; 20(12):1512-22. PMID: 17990959.
      Citations: 54     Fields:    Translation:AnimalsCells
    80. Araki H, Innan H, Kreitman M, Bergelson J. Molecular evolution of pathogenicity-island genes in Pseudomonas viridiflava. Genetics. 2007 Oct; 177(2):1031-41. PMID: 17720907; PMCID: PMC2034611.
      Citations: 4     Fields:    Translation:Cells
    81. Traw MB, Kniskern JM, Bergelson J. SAR increases fitness of Arabidopsis thaliana in the presence of natural bacterial pathogens. Evolution. 2007 Oct; 61(10):2444-9. PMID: 17725640.
      Citations: 21     Fields:    Translation:AnimalsCells
    82. Jakob K, Kniskern JM, Bergelson J. The role of pectate lyase and the jasmonic acid defense response in Pseudomonas viridiflava virulence. Mol Plant Microbe Interact. 2007 Feb; 20(2):146-58. PMID: 17313166.
      Citations: 13     Fields:    Translation:AnimalsCells
    83. Goss EM, Bergelson J. Fitness consequences of infection of Arabidopsis thaliana with its natural bacterial pathogen Pseudomonas viridiflava. Oecologia. 2007 May; 152(1):71-81. PMID: 17180370.
      Citations: 11     Fields:    Translation:AnimalsCells
    84. Goss EM, Bergelson J. Variation in resistance and virulence in the interaction between Arabidopsis thaliana and a bacterial pathogen. Evolution. 2006 Aug; 60(8):1562-73. PMID: 17017057.
      Citations: 19     Fields:    Translation:AnimalsCells
    85. Bakker EG, Toomajian C, Kreitman M, Bergelson J. A genome-wide survey of R gene polymorphisms in Arabidopsis. Plant Cell. 2006 Aug; 18(8):1803-18. PMID: 16798885; PMCID: PMC1533970.
      Citations: 150     Fields:    Translation:AnimalsCells
    86. Bakker EG, Stahl EA, Toomajian C, Nordborg M, Kreitman M, Bergelson J. Distribution of genetic variation within and among local populations of Arabidopsis thaliana over its species range. Mol Ecol. 2006 Apr; 15(5):1405-18. PMID: 16626462.
      Citations: 32     Fields:    Translation:AnimalsCells
    87. Araki H, Tian D, Goss EM, Jakob K, Halldorsdottir SS, Kreitman M, Bergelson J. Presence/absence polymorphism for alternative pathogenicity islands in Pseudomonas viridiflava, a pathogen of Arabidopsis. Proc Natl Acad Sci U S A. 2006 Apr 11; 103(15):5887-92. PMID: 16581904; PMCID: PMC1458668.
      Citations: 31     Fields:    Translation:AnimalsCells
    88. Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M, Aranzana MJ. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet. 2005 Nov; 1(5):e60. PMID: 16292355; PMCID: PMC1283159.
      Citations: 173     Fields:    Translation:Animals
    89. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J. The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol. 2005 Jul; 3(7):e196. PMID: 15907155; PMCID: PMC1135296.
      Citations: 442     Fields:    Translation:Animals
    90. Wichmann G, Ritchie D, Kousik CS, Bergelson J. Reduced genetic variation occurs among genes of the highly clonal plant pathogen Xanthomonas axonopodis pv. vesicatoria, including the effector gene avrBs2. Appl Environ Microbiol. 2005 May; 71(5):2418-32. PMID: 15870329; PMCID: PMC1087534.
      Citations: 14     Fields:    Translation:Cells
    91. Goss EM, Kreitman M, Bergelson J. Genetic diversity, recombination and cryptic clades in Pseudomonas viridiflava infecting natural populations of Arabidopsis thaliana. Genetics. 2005 Jan; 169(1):21-35. PMID: 15489535; PMCID: PMC1448860.
      Citations: 19     Fields:    Translation:AnimalsCells
    92. Cipollini D, Enright S, Traw MB, Bergelson J. Salicylic acid inhibits jasmonic acid-induced resistance of Arabidopsis thaliana to Spodoptera exigua. Mol Ecol. 2004 Jun; 13(6):1643-53. PMID: 15140107.
      Citations: 66     Fields:    Translation:AnimalsCells
    93. Korves T, Bergelson J. A novel cost of R gene resistance in the presence of disease. Am Nat. 2004 Apr; 163(4):489-504. PMID: 15122498.
      Citations: 21     Fields:    Translation:AnimalsCells
    94. Wichmann G, Bergelson J. Effector genes of Xanthomonas axonopodis pv. vesicatoria promote transmission and enhance other fitness traits in the field. Genetics. 2004 Feb; 166(2):693-706. PMID: 15020460; PMCID: PMC1470734.
      Citations: 36     Fields:    Translation:AnimalsCells
    95. Traw MB, Bergelson J. Interactive effects of jasmonic acid, salicylic acid, and gibberellin on induction of trichomes in Arabidopsis. Plant Physiol. 2003 Nov; 133(3):1367-75. PMID: 14551332; PMCID: PMC281631.
      Citations: 121     Fields:    Translation:AnimalsCells
    96. Korves TM, Bergelson J. A developmental response to pathogen infection in Arabidopsis. Plant Physiol. 2003 Sep; 133(1):339-47. PMID: 12970499; PMCID: PMC196610.
      Citations: 41     Fields:    Translation:AnimalsCells
    97. Traw MB, Kim J, Enright S, Cipollini DF, Bergelson J. Negative cross-talk between salicylate- and jasmonate-mediated pathways in the Wassilewskija ecotype of Arabidopsis thaliana. Mol Ecol. 2003 May; 12(5):1125-35. PMID: 12694277.
      Citations: 21     Fields:    Translation:AnimalsCells
    98. Tian D, Traw MB, Chen JQ, Kreitman M, Bergelson J. Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature. 2003 May 01; 423(6935):74-7. PMID: 12721627.
      Citations: 294     Fields:    Translation:AnimalsCells
    99. Mauricio R, Stahl EA, Korves T, Tian D, Kreitman M, Bergelson J. Natural selection for polymorphism in the disease resistance gene Rps2 of Arabidopsis thaliana. Genetics. 2003 Feb; 163(2):735-46. PMID: 12618410; PMCID: PMC1462445.
      Citations: 68     Fields:    Translation:Animals
    100. Cipollini DF, Busch JW, Stowe KA, Simms EL, Bergelson J. Genetic variation and relationships of constitutive and herbivore-induced glucosinolates, trypsin inhibitors, and herbivore resistance in Brassica rapa. J Chem Ecol. 2003 Feb; 29(2):285-302. PMID: 12737259.
      Citations: 7     Fields:    Translation:Animals
    101. Jakob K, Goss EM, Araki H, Van T, Kreitman M, Bergelson J. Pseudomonas viridiflava and P. syringae--natural pathogens of Arabidopsis thaliana. Mol Plant Microbe Interact. 2002 Dec; 15(12):1195-203. PMID: 12481991.
      Citations: 31     Fields:    Translation:AnimalsCells
    102. Tian D, Araki H, Stahl E, Bergelson J, Kreitman M. Signature of balancing selection in Arabidopsis. Proc Natl Acad Sci U S A. 2002 Aug 20; 99(17):11525-30. PMID: 12172007; PMCID: PMC123289.
      Citations: 108     Fields:    Translation:AnimalsCells
    103. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D. The extent of linkage disequilibrium in Arabidopsis thaliana. Nat Genet. 2002 Feb; 30(2):190-3. PMID: 11780140.
      Citations: 176     Fields:    Translation:HumansAnimals
    104. Bergelson J, Kreitman M, Stahl EA, Tian D. Evolutionary dynamics of plant R-genes. Science. 2001 Jun 22; 292(5525):2281-5. PMID: 11423651.
      Citations: 194     Fields:    Translation:AnimalsCells
    105. Bergelson J, Dwyer G, Emerson JJ. Models and data on plant-enemy coevolution. Annu Rev Genet. 2001; 35:469-99. PMID: 11700291.
      Citations: 42     Fields:    Translation:Animals
    106. Juenger T, Bergelson J. The evolution of compensation to herbivory in scarlet gilia, Ipomopsis aggregata: herbivore-imposed natural selection and the quantitative genetics of tolerance. Evolution. 2000 Jun; 54(3):764-77. PMID: 10937251.
      Citations: 29     Fields:    Translation:Animals
    107. Shonle I, Bergelson J. Evolutionary ecology of the tropane alkaloids of Datura stramonium L. (Solanaceae). Evolution. 2000 Jun; 54(3):778-88. PMID: 10937252.
      Citations: 34     Fields:    Translation:Animals
    108. Juenger T, Bergelson J. Factors limiting rosette recruitment in scarlet gilia, Ipomopsis aggregata: seed and disturbance limitation. Oecologia. 2000 May; 123(3):358-363. PMID: 28308590.
      Citations: 5     Fields:    
    109. Kotanen PM, Bergelson J. Effects of simulated grazing on different genotypes of Bouteloua gracilis: how important is morphology? Oecologia. 2000 Apr; 123(1):66-74. PMID: 28308745.
      Citations: 2     Fields:    
    110. Stahl EA, Dwyer G, Mauricio R, Kreitman M, Bergelson J. Dynamics of disease resistance polymorphism at the Rpm1 locus of Arabidopsis. Nature. 1999 Aug 12; 400(6745):667-71. PMID: 10458161.
      Citations: 221     Fields:    Translation:AnimalsCells
    111. Purrington CB, Bergelson J. Exploring the Physiological Basis of Costs of Herbicide Resistance in Arabidopsis thaliana. Am Nat. 1999 Jul; 154(S1):S82-S91. PMID: 29586706.
      Citations: 12     Fields:    
    112. Nordborg M, Bergelson J. The effect of seed and rosette cold treatment on germination and flowering time in some Arabidopsis thaliana (Brassicaceae) ecotypes. Am J Bot. 1999 Apr; 86(4):470-5. PMID: 10205066.
      Citations: 26     Fields:    
    113. Juenger T, Bergelson J. PAIRWISE VERSUS DIFFUSE NATURAL SELECTION AND THE MULTIPLE HERBIVORES OF SCARLET GILIA, IPOMOPSIS AGGREGATA. Evolution. 1998 Dec; 52(6):1583-1592. PMID: 28565335.
      Citations: 19     Fields:    
    114. Bergelson J, Stahl E, Dudek S, Kreitman M. Genetic variation within and among populations of Arabidopsis thaliana. Genetics. 1998 Mar; 148(3):1311-23. PMID: 9539444; PMCID: PMC1460032.
      Citations: 52     Fields:    Translation:Animals
    115. Purrington CB, Bergelson J. Fitness consequences of genetically engineered herbicide and antibiotic resistance in Arabidopsis thaliana. Genetics. 1997 Mar; 145(3):807-14. PMID: 9055089; PMCID: PMC1207864.
      Citations: 19     Fields:    Translation:Animals
    116. Rees M, Bergelson J. Asymmetric Light Competition and Founder Control in Plant Communities. J Theor Biol. 1997 Feb 07; 184(3):353-358. PMID: 31940744.
      Citations: 2     Fields:    
    117. Bergelson J, Purrington CB, Palm CJ, López-Gutiérrez JC. Costs of resistance: a test using transgenic Arabidopsis thaliana. Proc Biol Sci. 1996 Dec 22; 263(1377):1659-63. PMID: 9025313.
      Citations: 21     Fields:    Translation:Animals
    118. Purrington CB, Bergelson J. Assessing weediness of transgenic crops: industry plays plant ecologist. Trends Ecol Evol. 1995 Aug; 10(8):340-2. PMID: 21237062.
      Citations: 1     Fields:    
    119. Bergelson J. Details of local dispersion improve the fit of neighborhood competition models. Oecologia. 1993 Aug; 95(2):299-302. PMID: 28312956.
      Citations:    Fields:    
    120. Bergelson J, Crawley MJ. The effects of grazers on the performance of individuals and populations of scarlet gilia, Ipomopsis aggregata. Oecologia. 1992 Jun; 90(3):435-444. PMID: 28313533.
      Citations: 5     Fields:    
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