For an up-to-date list, as well as links to articles, please see my Google Scholar page.

* co-first authors         + co-corresponding authors

Preprint

Zhao S*, Lieberman TD*+, Poyet M, Groussin M, Gibbons SM, Xavier RJ, Alm EJ+.  “Adaptive evolution within the gut microbiome of individual people” bioRxiv (link)

 

Key publications

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. Covered widely, including: Nature Reviews GeneticsNational Geographic blog, ArsTechnia, Rich Lenski’s blog

 

Others

Chung HC, Lieberman TD, Vargas S, Flett KB, McAdam AJ, Priebe GP, Kishony R. (2017). “Global and local selection acting on the pathogen Stenotrophomonas maltophilia in the human lung.” Nature Communications, doi:10.1038/ncomms14078.

Stone LK, Baym M, Lieberman TD, Chait R, Clardy C, Kishony R. (2016). “Compounds that select against the tetracycline resistance efflux pump.” Nature Chemical Biology, doi: 10.1038/nchembio.2176.

Wang KK, Stone LK, Lieberman TD, Shavit M, Baasov T and Kishony R. (2016). “A hybrid drug limits resistance by evading the action of the multiple antibiotic resistance pathway.” Molecular Biology and Evolution, doi: 10.1093/molbev/msv243.

Kim S, Lieberman TD, Kishony R. (2014) “Alternating antibiotic treatments constrain evolutionary paths to multi-drug resistance.” PNAS, doi: 10.1073/pnas.1409800111.

Wintermute EH, Lieberman TD, Silver PA. (2013). “An objective function exploiting suboptimal solutions in metabolic networks.” BMC Systems Biology, doi: 10.1186/1752- 0509-7-98.

Skurnik D, Davis MR Jr., Benedett D, Moravec KL, Cywes-Bentley C, Roux D, Traficante DC, Walsh RL, Maira-Litràn T, Cassidy SK, Hermos CR, Martin TR, Thakkallapalli EL, Vargas SO, McAdam AJ, Lieberman TD, Kishony R, LiPuma JJ, Pier GB, Goldberg JB, Priebe, GP. (2012). “Targeting pan-resistant bacteria with antibodies to a broadly conserved surface polysaccharide expressed during infection.” Journal of Infectious Diseases, doi: 10.1093/infdis/jis254.

Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, Silver PA. (2011). “Towards a Synthetic Chloroplast.” PLOS ONE, doi: 10.1371/journal.pone.0018877.