For an up-to-date list, including links, please see Tami’s Google Scholar page.

* co-first authors         + co-corresponding authors

Pre-print papers

Alexandra J. Poret, Matthew M. Schaefers, Christina Merakou, Kathryn E. Mansour, Georgia K. Lagoudas, Ashley R. Cross, Joanna B. Goldberg, Roy Kishony, Ahmed Z. Uluer, Alexander J. McAdam, Paul C. Blainey, Sara O. Vargas, Tami D. Lieberman, Gregory P. Priebe (2024). “De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen”, bioRxiv, doi:

Jacob S. Baker, Evan Qu, Christopher P. Mancuso, A. Delphine Tripp, Arolyn Conwill, Tami D. Lieberman (2024). “Highly-resolved within-species dynamics in the human facial skin microbiome”, bioRxiv, doi:

Veda D. Khadka, Laura Markey, Magalie Boucher, Tami D. Lieberman (2023). “Commensal skin bacteria exacerbate inflammation and delay skin healing”, bioRxiv, doi:

Paul A. Torrillo, Tami D. Lieberman (2023). “Reversions mask the contribution of adaptive evolution in microbiomes”, bioRxiv, doi:

Published papers

Felix M. Key, Veda D. Khadka, Carolina Romo-González, Kimbria J. Blake, Liwen Deng, Tucker C. Lynn, Jean C. Lee, Isaac M. Chiu, Maria Teresa García-Romero+, Tami D. Lieberman+ (2023). “On-person adaptive evolution of Staphylococcus aureus during treatment for atopic dermatitis”, Cell Host and Microbe, doi:

Leonid Kruglyak, Andreas Beyer, Joshua S. Bloom, Jan Grossbach, Tami D. Lieberman, Chris P. Mancuso, Matthew S. Rich, Gavin J. Sherlock, Erik J. van Nimwegen, and Craig D. Kaplan. (2023). “Insufficient evidence for non-neutrality of synonymous mutations.” Nature. doi: 10.1101/2022.07.14.500130

Sameer Gupta*, Alexandra J Poret*, David Hashemi, Amarachi Eseonu, H Yu Sherry, Jonathon D’Gama, Victor A Neel+, Tami D Lieberman+ (2022). “Cutaneous surgical wounds have distinct microbiomes from intact skin”, Microbiology Spectrum doi: 10.1128/spectrum.03300-22

Arolyn Conwill, Anne C. Kuan, Ravalika Damerla, Alexandra J. Poret, Jacob S. Baker, A. Delphine Tripp, Eric J. Alm, Tami D. Lieberman (2022). “Anatomy promotes neutral coexistence of strains in the human skin microbiome”, Cell Host and Microbe, doi: 10.1016/j.chom.2021.12.007

Tami D. Lieberman (2022). Detecting bacterial adaptation within individual microbiomes. Philosophical Transactions of the Royal Society B, doi: 10.1098/rstb.2021.0243

V. D. Khadka*, F. M. Key*, C. Romo-González, A. Martínez-Gayosso, B. L. Campos-Cabrera, A. Gerónimo-Gallegos, T. C. Lynn, C. Durán-Mckinster, R. Coria-Jiménez, T. D. Lieberman+, M. T. Garcia-Romero+. (2021) “The Skin Microbiome of Patients With Atopic Dermatitis Normalizes Gradually During Treatment” Frontiers in Cellular and Infection Microbiology, doi: 10.3389/fcimb.2021.720674

J. E. Lemieux, K. J. Siddle, B. M. Shaw, C. Loreth, S. F. Schaffner, ….., T. D. Lieberman, ….., B. L. MacInnis. (2020) “Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events” Science , doi: doi: 10.1126/science.abe3261

M. Poyet, M. Groussin, S. M. Gibbons, J. Avila-Pacheco, X. Jiang, ….., T. D. Lieberman, ….., R. J. Xavier & E. J. Alm (2019). “A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research” Nature Medicine, doi:

Zhao S*, Lieberman TD*+, Poyet M, Groussin M, Gibbons SM, Xavier RJ, Alm EJ+ (2019).  “Adaptive evolution within gut microbiomes of healthy people” Cell Host and Microbe, doi:

Featured papers pre 2018

Lieberman TD (2018). “Seven Billion Microcosms: Evolution within Human Microbiome.” mSystems, doi: (invited perspective)

Lieerman TD, Wilson D, Misra R, Xiong LL, Moodley P, Cohen T, Kishony R. (2016). “Genomic diversity in autopsy samples reveals within-host dissemination of HIV- associated Mycobacterium tuberculosis.” Nature Medicine, doi: 10.1038/nm.4205.

Baym M, Lieberman TD, Kelsic ED, Chait R, Gross M, Yelin I, Kishony R. (2016). “Spatiotemporal microbial evolution on antibiotic landscapes.” Science, doi: 10.1126/science.aag0822. Associated video: The Evolution of Bacteria on a “Mega-Plate” Petri Dish 

Baym M*, Kryazhimskiy S*, Lieberman TD*, Chung H*, Desai MM, Kishony R. (2015). “Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes.” PLOS ONE, doi: 10.1371/journal.pone.0128036

Lieberman TD, Flett KB, Yelin I, Martin TR, McAdam AJ, Priebe GP, Kishony R. (2014). “Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures.” Nature Genetics, doi: 10.1038/ng.2848.   Coverage: Nature Genetics, Harvard Medical School

Lieberman TD*, Michel JB*, Aingaran M, Potter-Bynoe G, Roux D, Davis MR, Skurnik D, Lieby N, LiPuma JJ, Goldberg JB, McAdam AJ, Priebe GP, Kishony R. (2011). “Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes.” Nature Genetics, doi: 10.1038/ng.997. Coverage: Nature Reviews GeneticsNational Geographic blog, ArsTechnica, Rich Lenski’s blog