For an up-to-date list, including links, please see Tami’s Google Scholar page.
* co-first authors + co-corresponding authors
Pre-prints
Evan B. Qu, Jacob S. Baker, Laura Markey, Veda D. Khadka, Christopher P. Mancuso, A. Delphine Tripp, Tami D. Lieberman (2025). “Intraspecies associations from strain-rich metagenome samples.” bioRxiv, doi:
https://doi.org/10.1101/2025.02.07.636498
Samuel Degregori, Melissa B. Manus, Evan B. Qu, Calen P. Mendall, Jacob S. Baker, Lydia M. Hopper, Katherine R. Amato+, Tami D. Lieberman+ (2025). “The microbiome of the human facial skin is unique compared to that of other hominids.” bioRxiv, doi:
https://doi.org/10.1101/2025.01.22.634396
Christopher P. Mancuso, Jacob S. Baker, Evan Qu, A. Delphine Tripp, Ishaq O. Balogun, Tami D. Lieberman (2024). “Intraspecies warfare restricts strain coexistence in human skin microbiomes.” bioRxiv, doi:
https://doi.org/10.1101/2024.05.07.592803
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:
https://doi.org/10.1101/2024.02.06.579193
Jacob S. Baker, Evan Qu, Christopher P. Mancuso, A. Delphine Tripp, Arolyn Conwill, Tami D. Lieberman (2024). “Previously hidden intraspecies dynamics underlie the apparent stability of two important skin microbiome species.” bioRxiv, doi: https://doi.org/10.1101/2024.01.10.575018
Published papers
Paul A. Torrillo, Tami D. Lieberman (2024). “Reversions mask the contribution of adaptive evolution in microbiomes.” eLife, doi: https://doi.org/10.7554/eLife.93146
Veda D. Khadka*, Laura Markey*, Magalie Boucher, Tami D. Lieberman (2024). “Commensal skin bacteria exacerbate inflammation and delay skin healing.” Journal of Investigative Dermatology, doi: https://doi.org/10.1016/j.jid.2024.03.033
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: https://doi.org/10.1016/j.chom.2023.03.009
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: doi.org/10.1038/s41591-019-0
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: https://doi.org/10.1016/j.chom.2019.03.007
Featured papers pre-2018
Lieberman TD (2018). “Seven Billion Microcosms: Evolution within Human Microbiome.” mSystems, doi: https://doi.org/10.1128/mSystems.00171-17. (invited perspective)
Lieberman 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 Genetics, National Geographic blog, ArsTechnica, Rich Lenski’s blog