The University of Chicago Header Logo

Seppe Kuehn

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentEcology and Evolution
AddressChicago IL 60637
vCardDownload vCard

    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.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    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. Sinha V, Kuehn S. Hierarchical control of bacterial growth efficiency by substrate and taxonomy. bioRxiv. 2026 Jul 29. PMID: 42619735; PMCID: PMC13483885.
      Citations:    
    2. Yousef M, Lee KK, Tang J, Mullen P, Charisopoulos V, Willett R, Kuehn S. Epistatic interactions inform rational design of synthetic microbial communities for bioremediation. Nat Microbiol. 2026 Jul; 11(7):1995-2007. PMID: 42373819; PMCID: PMC13323053.
      Citations:    Fields:    Translation:CellsPHPublic Health
    3. Chakraverti-Wuerthwein MS, Domenig A, Kuehn S. Phylogenetic coherence in microbiome composition across environmental gradients. bioRxiv. 2026 Jun 10. PMID: 42327301; PMCID: PMC13277947.
      Citations:    
    4. Kuehn S. Global epistasis in ecosystems arises from resource constraints. bioRxiv. 2026 May 15. PMID: 42182413; PMCID: PMC13192798.
      Citations:    
    5. Schmitt MS, Lee KK, Bunbury F, Landsittel JA, Vitelli V, Kuehn S. Learning functional groups in complex microbiomes. ArXiv. 2026 Mar 03. PMID: 41822155; PMCID: PMC12976935.
      Citations:    
    6. Schmitt MS, Lee KK, Bunbury F, Landsittel JA, Vitelli V, Kuehn S. Learning functional groups in complex microbiomes. bioRxiv. 2026 Mar 03. PMID: 41867766; PMCID: PMC13001407.
      Citations:    
    7. Oliveira RA, McSpadden E, Pandey B, Lee K, Yousef M, Chen RY, Triebold C, Haro F, Aksianiuk V, Patel R, Shriram K, Ramanujam R, Kuehn S, Raman AS. Statistical design of a synthetic microbiome that suppresses diverse gut pathogens. bioRxiv. 2025 Dec 31. PMID: 41502951; PMCID: PMC12773023.
      Citations:    
    8. Wang L, Kuehn S, Tikhonov M. Learning the mechanism of collective microbial function via random community-media pairing. bioRxiv. 2025 Nov 27. PMID: 41394740; PMCID: PMC12699405.
      Citations:    
    9. Lee KK, Liu S, Crocker K, Wang J, Huggins DR, Tikhonov M, Mani M, Kuehn S. Functional regimes define soil microbiome response to environmental change. Nature. 2025 08; 644(8078):1028-1038. PMID: 40670792; PMCID: PMC12390847.
      Citations: 6     Fields:    Translation:CellsPHPublic Health
    10. Chen X, Crocker K, Kuehn S, Walczak AM, Mora T. Inferring Resource Competition in Microbial Communities from Time Series. PRX Life. 2025 Apr-Jun; 3(2). PMID: 42052147; PMCID: PMC13120769.
      Citations:    
    11. Chen X, Crocker K, Kuehn S, Walczak AM, Mora T. Inferring resource competition in microbial communities from time series. bioRxiv. 2025 May 02. PMID: 39829848; PMCID: PMC11741390.
      Citations:    
    12. Chen X, Crocker K, Kuehn S, Walczak AM, Mora T. Inferring resource competition in microbial communities from time series. ArXiv. 2025 May 02. PMID: 39867430; PMCID: PMC11759850.
      Citations:    
    13. Yousef M, Lee KK, Tang J, Charisopoulos V, Willett R, Kuehn S. Collective Microbial Effects Drive Toxin Bioremediation and Enable Rational Design. bioRxiv. 2025 Mar 28. PMID: 40196698; PMCID: PMC11974898.
      Citations:    
    14. Crocker K, Skwara A, Kannan R, Murugan A, Kuehn S. Microbial functional guilds respond cohesively to rapidly fluctuating environments. bioRxiv. 2025 Feb 15. PMID: 39974892; PMCID: PMC11838272.
      Citations:    
    15. Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Author Correction: Environmentally dependent interactions shape patterns in gene content across natural microbiomes. Nat Microbiol. 2025 Feb; 10(2):599. PMID: 39623069.
      Citations:    Fields:    
    16. Crocker K, Skwara A, Kannan R, Murugan A, Kuehn S. Timescale of environmental change modulates metabolic guild cohesion in microbial communities. ISME J. 2025 Jan 02; 19(1). PMID: 40843988; PMCID: PMC12448442.
      Citations:    Fields:    Translation:Cells
    17. Gopalakrishnappa C, Li Z, Kuehn S. Environmental modulators of algae-bacteria interactions at scale. Cell Syst. 2024 09 18; 15(9):838-853.e13. PMID: 39236710; PMCID: PMC11412779.
      Citations: 3     Fields:    Translation:Cells
    18. Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Environmentally dependent interactions shape patterns in gene content across natural microbiomes. Nat Microbiol. 2024 Aug; 9(8):2022-2037. PMID: 38977908; PMCID: PMC11386527.
      Citations: 11     Fields:    Translation:CellsPHPublic Health
    19. Lee KK, Liu S, Crocker K, Huggins DR, Tikhonov M, Mani M, Kuehn S. Functional regimes define the response of the soil microbiome to environmental change. bioRxiv. 2024 May 28. PMID: 38559185; PMCID: PMC10980070.
      Citations:    
    20. Li Z, Selim A, Kuehn S. Statistical prediction of microbial metabolic traits from genomes. PLoS Comput Biol. 2023 12; 19(12):e1011705. PMID: 38113208; PMCID: PMC10729968.
      Citations: 9     Fields:    Translation:HumansCells
    21. Crocker K, Lee KK, Chakraverti-Wuerthwein M, Li Z, Tikhonov M, Mani M, Gowda K, Kuehn S. Global patterns in gene content of soil microbiomes emerge from microbial interactions. bioRxiv. 2023 Nov 15. PMID: 38014336; PMCID: PMC10680560.
      Citations:    
    22. Skwara A, Gowda K, Yousef M, Diaz-Colunga J, Raman AS, Sanchez A, Tikhonov M, Kuehn S. Statistically learning the functional landscape of microbial communities. Nat Ecol Evol. 2023 11; 7(11):1823-1833. PMID: 37783827; PMCID: PMC11088814.
      Citations: 32     Fields:    Translation:Humans
    23. Li Z, Sinha V, Kuehn S. Constraints on microbial metabolic complexity. Nat Microbiol. 2023 Oct; 8(10):1756-1757. PMID: 37679599.
      Citations:    Fields:    
    24. Prabhakara KH, Kuehn S. Algae drive convergent bacterial community assembly at low dilution frequency. iScience. 2023 Jun 16; 26(6):106879. PMID: 37275519; PMCID: PMC10238937.
      Citations: 3     
    25. Sanchez A, Bajic D, Diaz-Colunga J, Skwara A, Vila JCC, Kuehn S. The community-function landscape of microbial consortia. Cell Syst. 2023 02 15; 14(2):122-134. PMID: 36796331.
      Citations: 33     Fields:    
    26. Gowda K, Kuehn S. Microbial biofilms: An ecological tale of Jekyll and Hyde. Curr Biol. 2022 12 19; 32(24):R1349-R1351. PMID: 36538887.
      Citations:    Fields:    
    27. Gowda K, Ping D, Mani M, Kuehn S. Genomic structure predicts metabolite dynamics in microbial communities. Cell. 2022 02 03; 185(3):530-546.e25. PMID: 35085485.
      Citations: 54     Fields:    Translation:Cells
    28. Gopalakrishnappa C, Gowda K, Prabhakara KH, Kuehn S. An ensemble approach to the structure-function problem in microbial communities. iScience. 2022 Feb 18; 25(2):103761. PMID: 35141504; PMCID: PMC8810406.
      Citations: 11     
    29. de Jesús Astacioa LM, Prabhakara KH, Li Z, Mickalide H, Kuehn S. Closed microbial communities self-organize to persistently cycle carbon. Proc Natl Acad Sci U S A. 2021 11 09; 118(45). PMID: 34740965; PMCID: PMC8609437.
      Citations: 16     Fields:    Translation:AnimalsCells
    30. Fraebel DT, Gowda K, Mani M, Kuehn S. Evolution of Generalists by Phenotypic Plasticity. iScience. 2020 Nov 20; 23(11):101678. PMID: 33163936; PMCID: PMC7600391.
      Citations: 10     
    31. Ping D, Wang T, Fraebel DT, Maslov S, Sneppen K, Kuehn S. Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations. ISME J. 2020 08; 14(8):2007-2018. PMID: 32358533; PMCID: PMC7367814.
      Citations: 16     Fields:    Translation:HumansCells
    32. Mickalide H, Kuehn S. Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community. Cell Syst. 2019 12 18; 9(6):521-533.e10. PMID: 31838145.
      Citations: 50     Fields:    Translation:AnimalsCells
    33. Kehe J, Kulesa A, Ortiz A, Ackerman CM, Thakku SG, Sellers D, Kuehn S, Gore J, Friedman J, Blainey PC. Massively parallel screening of synthetic microbial communities. Proc Natl Acad Sci U S A. 2019 06 25; 116(26):12804-12809. PMID: 31186361; PMCID: PMC6600964.
      Citations: 111     Fields:    Translation:CellsPHPublic Health
    34. Merritt J, Kuehn S. Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine. Phys Rev Lett. 2018 Aug 31; 121(9):098101. PMID: 30230885.
      Citations: 4     Fields:    Translation:Cells
    35. Shih HY, Mickalide H, Fraebel DT, Goldenfeld N, Kuehn S, Shih HY, Mickalide H, Fraebel DT, Goldenfeld N, Kuehn S. Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution. Phys Biol. 2018 07 27; 15(6):065003. PMID: 29762139.
      Citations: 3     Fields:    Translation:Cells
    36. Katsov AY, Freifeld L, Horowitz M, Kuehn S, Clandinin TR. Dynamic structure of locomotor behavior in walking fruit flies. Elife. 2017 07 25; 6. PMID: 28742018; PMCID: PMC5526672.
      Citations: 26     Fields:    Translation:Animals
    37. Fraebel DT, Mickalide H, Schnitkey D, Merritt J, Kuhlman TE, Kuehn S. Environment determines evolutionary trajectory in a constrained phenotypic space. Elife. 2017 03 27; 6. PMID: 28346136; PMCID: PMC5441876.
      Citations: 53     Fields:    Translation:Cells
    38. Merritt J, Kuehn S. Quantitative high-throughput population dynamics in continuous-culture by automated microscopy. Sci Rep. 2016 09 12; 6:33173. PMID: 27616752; PMCID: PMC5018735.
      Citations: 3     Fields:    Translation:Cells
    39. Merritt J, Kuehn S. When communities collide. Elife. 2016 07 15; 5. PMID: 27420812; PMCID: PMC4946875.
      Citations: 1     Fields:    
    40. Jordan D, Kuehn S, Katifori E, Leibler S. Behavioral diversity in microbes and low-dimensional phenotypic spaces. Proc Natl Acad Sci U S A. 2013 Aug 20; 110(34):14018-23. PMID: 23898201; PMCID: PMC3752258.
      Citations: 25     Fields:    Translation:Animals
    Kuehn's Networks
    Click the
    Explore
    buttons for more information and interactive visualizations!
    Concepts (74)
    Explore
    _
    Co-Authors (2)
    Explore
    _
    Similar People (60)
    Explore
    _
    Same Department Expand Description
    Explore
    _
    Physical Neighbors
    _