List of publications
See here for Michael's Google Scholar page, NCBI bibliography, and ORCID record. For personal publication lists of individual lab members, see links in the list of current lab members.
Publications from the lab
(Underlined author names are QEM Lab members; papers resulting from projects primarily led by the QEM Lab usually have Michael as last author. Other papers represent collaborations and may not correspond to major projects in the QEM Lab.)
- Corral López R, Bonachela JA, Dominguez-Bello MG, Manhart M, Levin SA, Blaser MJ, Muñoz MA. (2026) "Imbalance in gut microbial interactions as a marker of health and disease." Science 391:890-895. doi:10.1126/science.ady1729. (PDF, press coverage in
Rutgers Today,
NPR,
The Scientist,
Inside Precision Medicine,
Bioengineer.org,
Medical Xpress,
Nutrition Insight,
Scienmag,
Time.News,
Healthcare in Europe)
- Ramoneda J, Vinod DP, Ma Y, Ruan C, Schmidt J, Manhart M, Angst DC, Johnson DR. (2026) "Plasmid transfer and loss probabilities interactively determine antibiotic resistance spread in surface-associated bacterial biomass." bioRxiv preprint, doi:10.64898/2026.01.08.698332.
- Gould E et al. (310 authors including Manhart M) (2025) "Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology." BMC Biol 23:35. doi:10.1186/s12915-024-02101-x. (PDF)
- Fink JW, Manhart M. (2024) "Quantifying microbial fitness in high-throughput experiments." eLife 13:RP102635. doi:10.7554/eLife.102635.1. (PDF, code)
- Held NA, Krishna A, Crippa D, Battaje RR, Devaux AJ, Dragan A, Manhart M. (2024) "Nutrient colimitation is a quantitative, dynamic property of microbial populations." Proc Natl Acad Sci USA 120:e2207295120. doi:10.1073/pnas.2400304121. (PDF, code)
- Held NA, Manhart M. (2024) "Are microbes colimited by multiple resources?" Curr Opin Microbiol 80:102509. doi:10.1016/j.mib.2024.102509. (In special issue on "Microbial Systems and Synthetic Biology") (PDF)
- Fink JW, Manhart M. (2023) "How do microbes grow in nature? The role of population dynamics in microbial ecology and evolution." Curr Opin Syst Biol 36:100470. doi:10.1016/j.coisb.2023.100470. (In special issue on "Systems Ecology and Evolution") (PDF)
- Ramoneda J, Ma Y, Schmidt J, Manhart M, Angst DC, Johnson DR. (2023) "Physical contacts between sparse biofilms promote plasmid transfer and generate functional novelty." bioRxiv preprint, doi:10.1101/2023.02.01.526699.
- Fink JW, Held NA, Manhart M. (2023) "Microbial population dynamics decouple growth response from environmental nutrient concentration." Proc Natl Acad Sci USA 120:e2207295120. doi:10.1073/pnas.2207295120. (PDF, data)
- Manhart M, Bonhoeffer S. (2021) "The search for universality in evolutionary landscapes: Comment on ‘From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics’ by Susanna Manrubia, José A. Cuesta, et al." Phys Life Rev 39:76–78. doi:10.1016/j.plrev.2021.08.004. (PDF)
- Gorter FA, Manhart M, Ackermann M. (2020) "Understanding the evolution of interspecies interactions in microbial communities." Phil Trans R Soc B 375:20190256. doi:10.1098/rstb.2019.0256. (In special issue on "Conceptual challenges in microbial community ecology") (PDF)
- Lin J, Manhart M, Amir A. (2020) "Evolution of microbial growth traits under serial dilution." Genetics 215:767-777. doi:10.1534/genetics.120.303149. (PDF)
- Kheir Gouda M, Manhart M, Balázsi G. (2019) "Evolutionary regain of lost gene circuit function." Proc Natl Acad Sci USA 116:25162-25171. doi:10.1073/pnas.1912257116. (PDF)
Earlier publications from Michael
- Jasinska W,* Manhart M,* Lerner J, Gauthier L, Serohijos AWR, Bershtein S. (2020) "Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution." Nat Ecol Evol 4:437-452 doi:10.1038/s41559-020-1103-z. (* equal contribution) (PDF)
- Kion-Crosby WB, Manhart M, Morozov AV. (2019) "Inferring biophysical models of evolution from genome-wide patterns of codon usage." bioRxiv preprint doi:10.1101/578815.
- Manhart M, Shakhnovich EI. (2018) "Growth tradeoffs produce complex microbial communities on a single limiting resource." Nat Commun 9:3214. doi:10.1038/s41467-018-05703-6. (PDF)
- Manhart M, Adkar BV, Shakhnovich EI. (2018) "Tradeoffs between microbial growth phases lead to frequency-dependent and non-transitive selection." Proc R Soc B 285:20172459. doi:10.1098/rspb.2017.2459. (PDF)
- Adkar BV, Manhart M, Bhattacharyya S, Tian J, Musharbash M, Shakhnovich EI. (2017) "Optimization of lag phase shapes the evolution of a bacterial enzyme." Nat Ecol Evol 1:0149. doi:10.1038/s41559-017-0149. (PDF)
- Springer SA, Manhart M, Morozov AV. (2016) "Separating spandrels from phenotypic targets of selection in adaptive molecular evolution." Evolutionary Biology, ed. P. Pontarotti. Springer: Switzerland. doi:10.1007/978-3-319-41324-2_18. (PDF)
- Manhart M, Kion-Crosby W, Morozov AV. (2015) "Path statistics, memory, and coarse-graining of continuous-time random walks on networks." J Chem Phys 143:214106. doi:10.1063/1.4935968. (PDF, code)
- Bershtein S, Serohijos AWR, Bhattacharyya S, Manhart M, Choi J-M, Mu W, Zhou J, Shakhnovich EI. (2015) "Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria." PLoS Genet 11:e1005612. doi:10.1371/journal.pgen.1005612. (PDF)
- González C, Ray JCJ, Manhart M, Adams RM, Nevozhay D, Morozov AV, Balázsi G. (2015) "Stress-response balance drives the evolution of a network module and its host genome." Mol Syst Biol 11:827. doi:10.15252/msb.20156185. (PDF)
- Manhart M, Morozov AV. (2015) "Scaling properties of evolutionary paths in a biophysical model of protein adaptation." Phys Biol 15:045001. doi:10.1088/1478-3975/12/4/045001. (In special issue on "Evolution of Biological Molecules and Networks") (PDF)
- Manhart M, Morozov AV. (2015) "Protein folding and binding can emerge as evolutionary spandrels through structural coupling." Proc Natl Acad Sci USA 112:1797-1802. doi:10.1073/pnas.1415895112. (PDF, press coverage)
- Haldane A, Manhart M, Morozov AV. (2014) "Biophysical Fitness Landscapes for Transcription Factor Binding Sites." PLoS Comput Biol 10:e1003683. doi:10.1371/journal.pcbi.1003683. (PDF)
- Manhart M, Morozov AV. (2014) "Statistical Physics of Evolutionary Trajectories on Fitness Landscapes." First-Passage Phenomena and Their Applications, eds. R. Metzler, G. Oshanin, and S. Redner. World Scientific: Singapore. doi:10.1142/9789814590297_0017. (PDF)
- Manhart M, Morozov AV. (2013) "Path-Based Approach to Random Walks on Networks Characterizes How Proteins Evolve New Functions." Phys Rev Lett 111:088102. doi:10.1103/PhysRevLett.111.088102. (Editors’ Suggestion) (PDF)
- Manhart M, Haldane A, Morozov AV. (2012) "A universal scaling law determines time reversibility and steady state of substitutions under selection." Theor Popul Biol 82:66-76. doi:10.1016/j.tpb.2012.03.007. (PDF)
- Izaguirre E, Manhart M, Wacker JG. (2010) "Bigger, Better, Faster, More at the LHC." J High Energ Phys 12:1-25. doi:10.1007/JHEP12(2010)030. (PDF)
