Publications

28. Epistatic interactions drive microbial community bioremediation and enable rational design. Mahmoud Yousef, Kiseok Keith Lee, Jonathan Tang, Vasileios Charisopoulos, Rebecca Willett, Seppe Kuehn bioRxiv. Data and Code.

27. Microbial functional guilds respond cohesively to rapidly fluctuating environments. Kyle Crocker, Abigail Skwara, Rathi Kannan, Arvind Murugan, Seppe Kuehn. biorXiv. Submitted (2025). Data and Code.

26. Inferring resource competition in microbial communities from time series. Xiaowen Chen, Kyle Crocker, Seppe Kuehn, Aleksandra M Walczak, Thierry Mora. arXiv. In revision. (2025). Data and Code.

25. Functional regimes define the response of the soil microbiome to environmental change. Kiseok Lee, Siqi Liu, Kyle Crocker, Mikhail Tikhonov, Madhav Mani, and Seppe Kuehn. biorxiv. Data and Code.

24. Statistical design of a synthetic microbiome that clears a multi-drug resistant gut pathogen. Rita A. Oliveira, Bipul Pandey, Kiseok Lee, Mahmoud Yousef, Robert Y. Chen, Conrad Triebold, Emma McSpadden, Fidel Haro, Valeryia Aksianiuk, Ramaswamy Ramanujam, Eric Pamer, Seppe Kuehn, Arjun S. Raman. biorxiv

23. Constraints on microbial metabolic complexity. Vaibhhav Sinha, Zeqian Li, Seppe Kuehn. Nature Microbiology. 8,–1757 (2023). PDF.

22. Robustness of microbiome function. Kiseok Lee, Yeonwoo Park, Seppe Kuehn. Current Opinions in Systems Biology. PDF.

21. Statistically learning the functional landscape of microbial communities. Abigail Skwara, Karna Gowda, Mahmoud Yousef, Juan Diaz-Colunga, Arjun S Raman, Alvaro Sanchez, Mikhail Tikhonov, Seppe Kuehn. Nature Ecology & Evolution. 7, 1823–1833 (2023). PDF. Data and Code.

20. Statistical prediction of microbial metabolic traits from genomes. Zeqian Li, Ahmed Selim, Seppe Kuehn. PLoS Comp. Biol. 2023. PDF. Data and Code.

19. Genomic patterns in the global soil microbiome emerge from microbial interactions. Kyle Crocker, Milena Chakraverti-Wuerthwein, Zeqian Li, Madhav Mani, Karna Gowda, Seppe Kuehn. Nature Microbiology. (2024) PDF Code and Data.

18. Environmental modulators of algae-bacteria interactions at scale Chandana Gopalakrishnappa, Zeqian Li, and Seppe Kuehn. Cell Systems, 2024. PDF. Data and Code. Cover feature.

Commentary by Calatrava, Kilonzo, Hom. PDF.

17. Microbial biofilms: An ecological tale of Jekyll and Hyde. Karna Gowda and Seppe Kuehn. Dispatch for Current Biology. PDF.

Commentary on work by Wilbert and Newman. PDF.

16. Algae drive convergent bacterial community assembly when nutrients are scarce. Kaumudi H. Prabhakara and Seppe Kuehn. iScience. 26, 6, 16 2023, 106879. PDF. bioRxiv. 16S data. Analyzed data.

15. The community-function landscape of microbial consortia. Alvaro Sanchez, Djordje Bajic, Juan Diaz,-Colunga, Abigail Skwara, and Seppe Kuehn. (Invited review, submitted). Cell Systems (2023) PDF.

14. Genomic structure predicts metabolite dynamics in microbial communities. Karna Gowda, Derek Ping, Madhav Mani, and Seppe Kuehn. Cell. 185. 1-17. 2022. PDF. Data and Code.

Dispatch in Current Biology: PDF.

UChicago news.

Northwestern News.

Phys.org

EurekaAlert

12. Commentary on Waddington's landscapes. Seppe Kuehn. Cell Systems. 2022. (pdf)

12. An ensemble approach to the structure-function problem in microbial communities. Chandana Gopalakrishnappa, Karna Gowda, Kaumudi Prabhakara and Seppe Kuehn. (Invited review) iScience, 2022

11. Closed microbial communities self-organize to persistently cycle carbon. Luis Miguel de Jesus Astacio*, Kaumudi H. Prabhakara*, Zeqian Li, Harry Mickalide, and Seppe Kuehn. PNAS. 2021. *Equal contribution. PDF. Data

10. Evolution of generalists by phenotypic plasticity. David T. Fraebel, Karna Gowda, Madhav Mani, and Seppe Kuehn. iScience. 23, 11, 101678. 2020.

9. Hitchhiking, collapse and contingency in phage infections of migrating bacterial populations. Derek Ping, Tong Wang, David Fraebel, Sergei Maslov, Kim Sneppen and Seppe Kuehn. The ISME Journal . (2020)

8. Higher order interaction inhibits bacterial invasion of a phototroph-predator microbial community. Harry Mickalide & Seppe Kuehn. Cell Systems. (9) 6. p. 521-533. (2019). PDF. Data and Code. Cover feature. Commentary from Alvaro Sanchez.

7. Massively Parallel Screening of Synthetic Microbial Communities. Jared Kehe, Anthony Kulesa, Anthony Ortiz, Cheri Ackerman, Gowtham Thakku, Daniel Sellers, Seppe Kuehn, Jeff Gore, Jonathan Friedman, Paul C. Blainey. PNAS. 116 (26) 12804-12809 (2019)

6. Biophysical constraints determine the selection of phenotypic fluctuations during directed evolution. Hong-yan Shih, Harry Mickalide, David T. Fraebel, Nigel Goldenfeld and Seppe Kuehn. Physical Biology, 15 (6) 2018.

5 Frequency and amplitude dependent population dynamics during cycles of feast and famine. Jason Merritt and Seppe Kuehn. Physical Review Letters. 121, 098101 (2018). arXiv. Image analysis code.

4. Dynamic structure of locomotor behavior in walking fruit flies. Alexander Y. Katsov, Limor Freifeld, Mark Horowitz, Seppe Kuehn, and Thomas R. Clandinin. eLife. (2017)

3. Environment determines evolutionary trajectory in a constrained phenotypic space. David Fraebel, Harry Mickalide, Diane Schnitkey, Jason Merritt, Thomas E. Kuhlman, and Seppe Kuehn. eLife. (2017);10.7554/eLife.24669

2. Quantitative high-throughput population dynamics in continuous-culture by automated microscopy. Jason Merritt and Seppe Kuehn. Scientific Reports. 6, 33173. (2016).

1. When communities collide. Jason Merritt and Seppe Kuehn. eLife 2016;5:e18753

Postdoc

Strongly deterministic population dynamics in closed microbial communities. Zak Frentz*, Seppe Kuehn* and Stanislas Leibler. Physical Review X 5, 041014 (2015)

Behavioral diversity in microbes and low dimensional phenotypic spaces. David Jordan*, Seppe Kuehn*, Eleni Ketifori and Stanislas Leibler. PNAS 110 (34) 14018-14023 (2013).

Microbial population dynamics by digital in-line holographic microscopy.
Zak Frentz*, Seppe Kuehn*, Doeke Hekstra, and Stanislas Leibler, Review of Scientific Instruments 81, 084301 (2010).

Ph.D.
Quantifying Electric Field Gradient Fluctuations over Polymers Using Ultrasensitive Cantilevers. Showkat M. Yazdanian, Nikolas Hoepker, Seppe Kuehn, Roger F. Loring and John A. Marohn. Nano Lett. 9 (6) 2273–2279 (2009).

Advances in Mechanical Detection of Magnetic Resonance. Seppe Kuehn, Steven A. Hickman, and John A. Marohn. J. Chemical Physics. 128 (5) 052208 (2008).

Dielectric Fluctuations and the Origins of Noncontact Friction. Seppe Kuehn, Roger F. Loring, and John A. Marohn, Physical Review Letters 96, 156103 (2006).

Noncontact Dielectric Friction. Seppe Kuehn, John A. Marohn, and Roger F. Loring, J. Physical Chemistry B Letters. 110 (30) 14525-14528 (2006).

Force-gradient detected nuclear magnetic resonance. Sean R. Garner, Seppe Kuehn, Jahan M. Dawlaty, Neil E. Jenkins, and John A. Marohn, Applied Physics Letters 84, 5091 (2004).

Batch fabrication and characterization of ultrasensitive cantilevers. Neil E. Jenkins, Lauren P. DeFlores, Jack Allen, Tse Nga Ng, Sean R. Garner, Seppe Kuehn, Jahan M. Dawlaty and John A. Marohn. J. Vacuum Science and Technology B. (22), 909 (2004).

The direct production of CO(v=1-9) in the reaction of O3P with the ethyl radical<br>Jonathan P. Reid.,Timothy P. Marcy, Seppe Kuehn, and Stephen R. Leone. J. Chemical Physics (113) (11) 4572-4580 (2000).