Doctor of Philosophy (Ph.D.), Institute for Molecular Bioscience, University of Queensland, Australia
Bioinformatic Analyst (Evans lab), Salk Institute for Biological Studies, La Jolla, San Diego, USA
- Nuclear Receptor mechanism in digestive-related diseases including liver cancer and pancreatic cancer
- Application of Next-Generation Sequencing technologies and Machine-Learning / AI for disease model development
- Integration of multi-omics (genetics, epigenetics, metagenome, metabolome) to understand complex disease progression
My primary research interests lie in the application of “Bioinformatics” and “Molecular biology” techniques to the study of many diseases, particularly those linked with inflammation, such as fibrosis, NASH, and cancer. While working as a postdoc in Dr. Evans' group at the Salk Institute, I widened the scope of my research to include cutting-edge bioinformatics, such as the creation of a “Machine-Learning”-based diagnostic model for inflammatory metabolic disorders. I developed a metagenomic analysis pipeline for investigating liver cirrhosis patient feces samples under the direction of Drs. Evans and Downes at the Salk and Dr. Loomba at UC San Diego. This method successfully isolated 19 species that can differentiate between fibrosis and cirrhosis phases (diagnostic accuracy of 0.91 AUC; Oh et al., Cell Metabolism, 2020 & 2021). Supporting the value of a stool-based diagnostic test for advanced fibrosis or cirrhosis in high-risk populations, this microbiome-derived prediction signature was verified with external metagenome datasets from geographically and culturally varied cohorts.
At the level of a single cell with multi-omic technologies, our lab will investigate the mechanism of Nuclear Receptor activation/inactivation in conjunction with gut-liver crosstalk or gut-pancreas association via micro-organisms and metabolites.
Choi JH*, Oh TG*, Jung HW, Park KY, Shin HM, Jo TH, Chanda D, Hong SJ, Kim J, Jung MK, Syoj, Ayami Matsushima T, Kang DS, Kim PH, Mun JY, Cho SJ, Lee IK, Bapat SP, Zheng Y, Liddle C, Yu RT, Atkins AA, Downe M, Yoshihara E, Evans RM, and Suh JM. Estrogen-Related Receptor γ maintains pancreatic acinar cell function and identity by regulating cellular metabolism. Gastroenterology. 2022 Jul;163(1):239-256 (*Joint First author)
Kim JY, Wang L, Sladky VC, Oh TG, Liu J, Trinh K, Eichin F, Downes M, Hosseini M, Jacotot ED, Evans RM, Villunger A, Karin M. PIDDosome-SCAP crosstalk controls high fructose diet dependent transition from simple steatosis to steatohepatitis. Cell Metabolism. 2022 Aug 23:S1550-4131(22)00348-5.
Oh TG, Kim SM, Atkins AR, Yu RT, Downes M, Evans RM, Loomba R. Proton pump inhibitor use status does not modify the microbiome signature for cirrhosis. Cell Metabolism. 2021 Mar 2;33(3):457. DOI: 10.1016/j.cmet.2021.02.013.
Oh TG, Kim SM, Caussy C, Fu T, Guo J, Bassirian S, Singh S, Madamba EV, Bettencourt R, Richards L, Raffatellu M, Dorrestein PC, Yu RT, Atkins AR, Huan T, Brenner DA, Sirlin CB, Knight R, Downes M, Evans RM, Loomba R. A Universal Gut-Microbiome-Derived Signature Predicts Cirrhosis. Cell Metabolism. 2020 Nov 3;32(5):878-888.e6.
Yoshihara E, O’Connor C, Gasser E, Wei Z, Oh TG, Tseng TW, Wang D, Cayabyab F, Dai Y, Yu RT, Liddle C, Atkins AR, Downes M, Evans RM. Immune evasive human islet-like organoids ameliorate diabetes. Nature. 2020 Oct;586(7830):606-611.
Fu T, Coulter S, Yoshihara E, Oh TG, Fang S, Cayabyab F, Zhu Q, Zhang T, Leblanc M, Liu S, He M, Waizenegger W, Gasser E, Schnabl B, Atkins A, Yu R, Knight R, Liddle C, Downes M, Evans RM. FXR regulates intestinal cancer stem cell proliferation. Cell. 2019 Feb 21;176(5):1098-1112.e18.
Complete List of Publications: