For most up to date publications, visit our google scholar page.
  • Alon Shaiber, Amy D Willis, Tom O Delmont, Simon Roux, Lin-Xing Chen, Abigail C Schmid, Mahmoud Yousef, Andrea R Watson, Karen Lolans, Ozcan C Esen, Sonny TM Lee, Nora Downey, Hilary G Morrison, Floyd Dewhirst, Jessica L Mark Welch, A. Murat Eren. (2020) Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome. Genome Biol 21, 292. https://doi.org/10.1186/s13059-020-02195-w
  • Jun Miyoshi, Sonny T.M. Lee, Megan Kennedy, Mora Puertolas, Mary Frith, Jason C. Koval, Sawako Miyoshi, Dionysios A. Antonopoulos, Vanessa Leone, Eugene B. Chang. (2020). Metagenomic alterations in gut microbiota precede and predict onset of colitis in the IL10 gene-deficient murine model. Cellular and Molecular Gastroenterology and Hepatology https://doi.org/10.1016/j.jcmgh.2020.08.008
  • Sonny TM Lee, Jiun-Yan Ding, Pei-Wen Chiang, Mike Dyall-Smith, Sen-Lin Tang. (2020). Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica. MicrobiologyOpen. ​DOI: 10.1002/mbo3.1016.
  • Jun Miyoshi,  Vanessa Leone,  Sawako Miyoshi,  Lee Sonny T.M.,  Aki Sakatani, A Murat Eren, Eugene Chang. (2019) Peripartum antibiotic exposure induces persistence gut dysbiosis, impairs the development of immune tolerance, and increases risk for inflammatory bowel disease in genetically susceptible offspring. Gastroenterology 156(3):S101. DOI:10.1053/j.gastro.2019.01.235
  • Tom O. Delmont, Christopher Quince, Alon Shaiber, Özcan C. Esen, Lee Sonny T.M., Sebastian Lücker, A. Murat Eren. Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in the surface ocean. Nature Microbiology. Doi:https://doi.org/10.1038/s41564-018-0176-9
  • Lee Sonny T.M., Keshavmurthy S., Fontana Silvia, Takuma Mezaki, Chou W.H., Tang S.L., Chen A. (2018) Transcriptomic response in Acropora muricata under acute temperature stress follows preconditioned seasonal temperature fluctuations. BMC Research Notes. 11:119; doi: 10.1186/s13104-018-3230-z​
  • Lee Sonny T.M., Stacy A. Kahn, Tom O. Delmont, Alon Shaiber, Özcan C. Esen, Nathaniel A. Hubert, Hilary G. Morrison, Dionysios A. Antonopoulos, David T. Rubin, A. Murat Eren. (2017) Tracking microbial colonization in Fecal Microbiota Transplantation experiments via genome-resolved metagenomics. Microbiome. 5:50; doi: 10.1186/s40168-017-0270-x
  • Lee Sonny T.M., Davy S., Tang S.L. and Kench P.  (2017) Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata. Sci. Rep. 7, 43600; doi: 10.1038/srep43600
  • T.L. Yang, Lee Sonny T.M., P.Y. Tsai, C.J. Tan , T.Y. Fan. (2017) Spatial and depth variation in benthic community structure of a coral reef island, Hsiaoliuchiu, Taiwan. Platax 14: 1-20.
  • Yang S.H., Tseng C.H., Huang C.R., Chen C.P., Tandon K., Lee Sonny T.M., Chiang P.W., Shiu J.H., Chen Allen C.L., Tang S.L. (2017) Long term survey is necessary to reveal various shifts of microbial composition in corals. Frontiers in Microbiology. 13;8:1094. doi: 10.3389/fmicb.2017.01094.
  • Lee Sonny T.M., Davy S., Tang S.L. and Kench P.  (2016) Mucus sugar content shapes the bacterial community structure in thermally stressed Acropora muricata. Frontiers in Microbiology 7:371. doi: 10.3389/fmicb.2016.00371
  • Yang S.H., Lee Sonny T.M., Huang C.R., Tseng C.H., Chiang P.W., Chen C.P., Chen H.J., Tang S.L. (2016) Prevalence of potential nitrogen-fixing, green sulphur bacteria in the skeleton of reef-building coral Isopora palifera. Limnology and Oceanography DOI: 10.1002/lno.10277
  • Lee Sonny T.M., Davy S., Tang S.L., Fan T.Y. and Kench P.  (2015) Successive shifts in the microbial community of the surface mucus layer and tissues of the coral Acropora muricata under thermal stress. FEMS Microbiology Ecology 91 (12): fiv142. doi: 10.1093/femsec/fiv142
  • Lee Sonny T.M., Kelly M., Langlois T.J. and Costello M. (2015) Baseline seabed habitat and biotope mapping for a proposed marine reserve. PeerJ  DOI 10.7717/peerj.1446

Preprints
  • Soumyadev Sarkar, Kaitlyn Ward, Janet K. Jansson, Sonny T.M. Lee. (2020). Detection of stress functional responses in bacterial populations under dry soil conditions show potential microbial mechanisms to resist drought conditions. bioRxiv 2020.09.30.320879; doi: https://doi.org/10.1101/2020.09.30.320879
  • Jun Miyoshi, Sawako Miyoshi, Tom O Delmont, Candace Cham, Sonny TM Lee, Aki Sakatani, Karen Yang, Yue Shan, 
    Evan Kiefl, Mahmoud Yousef, Sean Crosson, Mitchell Sogin, Dionysios A Antonopoulos, A Murat Eren, Vanessa Leone, Eugene B Chang. (2020) Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis. bioRxiv 2020.03.11.987412; doi: https://doi.org/10.1101/2020.03.11.987412