Quantitative Evolutionary Microbiology Laboratory

Center for Advanced Biotechnology and Medicine | Rutgers University

Publications

See here for Michael’s Google Scholar page.

Publications from the lab

(Underline marks lab members)

  • Held NA, Manhart M. (2024) “Are microbes colimited by multiple resources?” EcoEvoRxiv preprint, doi:10.32942/X2SK6W.
  • Held NA, Krishna A, Crippa D, Dragan A, Manhart M. (2023) “Nutrient colimitation is a quantitative, dynamic property of microbial populations.” bioRxiv preprint, doi:10.1101/2023.09.27.559472.
  • 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:j.coisb.2023.100470. (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.
  • Gould E et al. (150 authors including Manhart M) (2023) “Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology.” EcoEvoRxiv preprint, doi:10.32942/X2GG62.
  • 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)
  • 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 Royal 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)
  • 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)