*=co-first authors, †=corresponding authors, ☯=undergraduate author

  1. J. Lopez, S. McKeithen-Mead, H. Shi, T. Nguyen, K.C. Huang†, and B.H. Good†. Abundance measurements reveal the balance between lysis and lysogeny in the human gut microbiome. biorxiv 2024.09.27.614587 (2024).

  2. Lyulina, A.S.*, Z. Liu* and B.H. Good. Linkage equilibrium between rare mutations. Genetics iyae145, early online (2024).

  3. Vasquez, K.S.*, D.P.G.H. Wong*, M.F. Pedro, F.B. Yu, S. Jain, X. Meng, S.K. Higginbottom, B.C. DeFelice, N. Neff, A.S. Bhatt, C. Tropini, K.B. Xavier, J.L. Sonnenburg†, B.H. Good†, and K.C. Huang†. Within-host evolution and strain transmission of a human gut symbiont across ecological scales. biorXiv 2024.02.17.580834 (2024).

  4. McEnany, J.D. and B.H. Good. Predicting the first steps of evolution in randomly assembled communities. Nature Communications 15: 8495 (2024).

  5. Xue, K.S.†, S.J. Walton, D.A. Goldman☯, M.L. Morrison, A.J. Verster, A.B. Parrott☯, F.B. Yu, N. Neff, N.A. Rosenberg, B.D. Ross, D.A. Petrov, K.C. Huang, B.H. Good†, and D. Relman†. Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation. biorXiv 2023.09.26.559480 (2023).

  6. Ferrare, J.T. and B.H. Good. Evolution of evolvability in rapidly evolving populations. Nature Ecology & Evolution s41559-024-02527-0 (2024).

  7. B.H. Good. Limited codiversification of the gut microbiota with humans. biorXiv 2022.10.27.514143 (2022).

  8. Wong, D.P.G.H. and B.H. Good. Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking. Nature Communications 15: 1605 (2024).

  9. Liu, Z. and B.H. Good. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biology 22(2): e3002472 (2024).

  10. B.H. Good†, L.B. Rosenfeld☯. Eco-evolutionary feedbacks in the human gut microbiome. Nature Communications 74: 7146 (2023).

  11. Dapa, T*, D.P.G.H.Wong*, K.S. Vasquez, K.B. Xavier†, K.C. Huang†, and B.H. Good†. Within-host evolution of the gut microbiome. Current Opinion in Microbiology 71: 102258 (2023).

  12. Ascensao, J.A., K.M. Wetmore, B.H. Good, A.P. Arkin, O. Hallatschek. Quantifying the local adaptive landscape of a nascent bacterial community. Nature Communications 14: 248 (2023).

  13. Ghosh, O.M. and B.H. Good. Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota. PNAS 119(28): e2114931119 (2022).

  14. Melissa, M.J., B.H. Good, D.S. Fisher, and M.M. Desai, Population genetics of polymorphism and divergence in rapidly evolving populations. Genetics 221(4): iyac053 (2022).

  15. P.Y. Ho, B.H. Good†, and K.C. Huang†. Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas. eLife 11:e75168 (2022).

  16. B.H. Good, Linkage disequilibrium between rare mutations. Genetics 220(4): iyac004 (2022).

  17. Vasquez, K.S., L. Willis, N. Cira, K.M. Ng, M.F. Pedro, A. Aranda-Díaz, M. Ranjendram, F.B. Yu, S.K. Higginbottom, N. Neff, G. Sherlock, K.B. Xavier, S. Quake, J. Sonnenburg, B.H. Good†, and K.C. Huang†. Quantifying rapid bacterial evolution and transmission within the mouse intestine. Cell Host & Microbe 29(9): 1454-1468.e4 (2021).

  18. Roodgar, M.*, B. H. Good*†, N.R. Garud, S. Martis, M. Avula, W. Zhou, S. Lancaster, H. Lee, A. Babveyh, S. Nesamoney, K. S. Pollard†, and M. P. Snyder†. Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Genome Research 31: 1433-1446 (2021).

  19. Garud, N. R.*†, B. H. Good*†, O. Hallatschek, and K. S. Pollard. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biology 17(1):e3000102 (2019).

    See Primer article by I. Gordo.

  20. Good, B.H.† and O. Hallatschek. Effective models and the search for quantitative principles in microbial evolution. Current Opinion in Microbiology 45:203-212 (2018).

  21. Good, B. H.†, S. Martis, and O. Hallatschek. Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources. PNAS 115:E10407-E10416 (2018).

  22. Cvijovic, I., B. H. Good, and M. M. Desai. The effect of strong purifying selection on genetic diversity. Genetics 209:1235-1278 (2018).

  23. Good, B. H.*, M. J. McDonald*, J. E. Barrick, R. E. Lenski, and M. M. Desai. The Dynamics of Molecular Evolution Over 60,000 Generations. Nature 551:45-50 (2017).

    See News and Views article by J. Plotkin.

  24. Good, B. H. and M. M. Desai. Evolution of mutation rates in rapidly adapting asexual populations. Genetics 204:1249-1266 (2016).

  25. Cvijovic, I.*, B. H. Good*, E. R. Jerison, and M. M. Desai. Fate of a mutation in a fluctuating environment. PNAS 112:E5021-E5028 (2015).

  26. Rice, D. P., B. H. Good, and M. M. Desai. The evolutionarily stable distribution of fitness effects. Genetics 200:321-329 (2015).

  27. Good, B. H. and M. M. Desai. The impact of macroscopic epistasis on long-term evolutionary dynamics. Genetics 199:177-190 (2015).

  28. Good, B. H. and M. M. Desai. Deleterious passengers in adapting populations. Genetics 198:1183-1208 (2014).

  29. Frenkel, E., B.H. Good, and M. M. Desai. The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations. Genetics 196:1217-1226 (2014).

  30. Good, B. H., A.M. Walczak, R. A. Neher, and M. M. Desai. Genetic diversity in the interference selection limit. PLoS Genetics 10:e1004222 (2014).

  31. Good, B. H. and M. M. Desai. Fluctuations in fitness distributions and the effects of weak selection on sequence evolution. Theoretical Population Biology 85:86-102 (2013).

  32. Good, B. H., I. M. Rouzine, D. J. Balick, O. Hallatschek, and M. M. Desai. Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. PNAS 109:4950-4955 (2012).

    See commentary article by M. Lässig

  33. Good, B. H., Y.-A. de Montjoye, and A. Clauset. The performance of modularity maximization in practical contexts. Physical Review E 81, 046106 (2010)