Our research focuses on (i) functional genomics and biology of tRNA including microbiomes and (ii) epitranscriptomics including microbiome-host interactions.
tRNA biology: Translational regulation relies on the dynamic properties of tRNA that constantly change to facilitate response and adaptation to new environments and to control gene expression. We developed high throughput sequencing technologies that measure tRNA abundance, charging and modifications in one single sequencing library. We are investigating the roles of tRNA in translational control and extra-translational functions in mammalian cells.
Microbiome: We also developed tRNA-seq as another approach for microbiome characterization. Standard microbiome characterizations include 16S-seq or shotgun metagenomics. Although powerful, these DNA-based methods do not directly report the microbiome activity such as dynamic gene expression which requires the studies of RNA in the microbiome. Our microbiome tRNA-seq results show extensive variations of tRNA abundance and modification patterns in microbiomes from different sources. We also show that tRNA modification dynamics in the microbiome correlates with tuning the expression of specific microbial proteins, indicating that tRNA-seq can provide new insights in microbiome biology. We are further developing this approach to explore the potentials of tRNA-seq to study microbiomes from humans and from the oceans.
Epitranscriptomics: Over 100 types of post-transcriptional RNA modifications have been identified in thousands of sites in the transcriptome. They include methylation of bases and the ribose backbone, rotation and reduction of uridine, base deamination, addition of ring structures and carbohydrate moieties, and so on. mRNA modifications are involved in cell differentiation, proliferation, and many other cellular functions and human diseases. Some mRNA modifications can also be removed by cellular enzymes, resulting in the dynamic regulation of their functions. We are investigating the function and mechanisms of mRNA modifications such as N6-methyladenosine (m6A) in the regulation of gene expression. For example, we discovered that m6A modification can alter the local mRNA structure to regulate binding of mRNA binding proteins transcriptome-wide (m6A switch), resulting in changes in mRNA abundance and alternative splicing.
Microbiome-host interactions through epitranscriptomics: We are working on elucidating the function of mammalian host mRNA and tRNA modifications in response to the gut microbiome. We found that microbiome reprograms the host m6A modifications transcriptome-wide in a tissue-dependent manner, suggesting that this dynamic epitranscriptomic mark is used in yet unknown ways in microbiome response. We also found that a microbiome dependent, host tRNA modification alters the cellular small RNA pool, suggesting yet another pathway of microbiome response through RNA modifications.
University of Colorado at Boulder
Boulder, CO
postdoctoral - Biochemistry
1993
Yale University
New Haven, CT
Ph.D. - Biophysics/Biochemistry
1990
University des Saarlands
Germany
BS/MS - Chemistry
1986
Transarterial Chemoembolization Plus Thermal Ablation in Unresectable Hepatocellular Carcinoma: The Phase 3 TORCH Randomized Clinical Trial.
Transarterial Chemoembolization Plus Thermal Ablation in Unresectable Hepatocellular Carcinoma: The Phase 3 TORCH Randomized Clinical Trial. JAMA Oncol. 2026 09 01; 12(9):980-989.
PMID: 42530948
Low-dose bevacizumab plus atezolizumab enhances transarterial chemoembolization in HCC via correcting vascular-immune niche dysfunction.
Low-dose bevacizumab plus atezolizumab enhances transarterial chemoembolization in HCC via correcting vascular-immune niche dysfunction. J Hepatol. 2026 Jul 31.
PMID: 42537705
Paternal preconceptional metformin exposure induces metabolic dysregulation in offspring.
Paternal preconceptional metformin exposure induces metabolic dysregulation in offspring. Cell Discov. 2026 Jul 01; 12(1).
PMID: 42380093
A transfer RNA inosine modification drives genome-wide synonymous recoding across human commensal bacterial families.
A transfer RNA inosine modification drives genome-wide synonymous recoding across human commensal bacterial families. PNAS Nexus. 2026 Jun; 5(6):pgag187.
PMID: 42273404
Preterm Birth International Collaborative Australasia Branch: Expert Consensus on Diagnosis and Treatment of Neonatal Lactose Intolerance (2025).
Preterm Birth International Collaborative Australasia Branch: Expert Consensus on Diagnosis and Treatment of Neonatal Lactose Intolerance (2025). Pediatr Discov. 2026 Mar; 4(1):e70044.
PMID: 42021958
Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications.
Enzyme-mediated alkynylation enables transcriptome-wide identification of pseudouridine modifications. Nat Commun. 2026 Mar 23; 17(1).
PMID: 41872172
ITK-targeted immune remodeling enhanced the efficacy of anti-CD19 CAR-T cell therapy.
ITK-targeted immune remodeling enhanced the efficacy of anti-CD19 CAR-T cell therapy. Cell Death Discov. 2026 Mar 06; 12(1).
PMID: 41792111
Spatiotemporal Organization of PTK7 Diffusion on Cell Surface Facilitates Tumor Invasion and Migration.
Spatiotemporal Organization of PTK7 Diffusion on Cell Surface Facilitates Tumor Invasion and Migration. Adv Sci (Weinh). 2026 May; 13(26):e17876.
PMID: 41782379
Predicting short-term mortality in severe cirrhosis: An interpretable machine learning model integrating routine clinical indicators.
Predicting short-term mortality in severe cirrhosis: An interpretable machine learning model integrating routine clinical indicators. PLoS One. 2026; 21(3):e0328952.
PMID: 41774736
Decoding human tRNA modifications and crosstalk by enhanced single-read analysis.
Decoding human tRNA modifications and crosstalk by enhanced single-read analysis. Genome Biol. 2026 Feb 20; 27(1).
PMID: 41721424
American Association for the Advancement of Science (AAAS) Fellow
2015
NIH Director’s Pioneer award
2011 - 2016
NIH EUREKA award
2009 - 2013
American Cancer Society, Junior Faculty Research Award
1995 - 1997
Cancer Research Foundation, Raymond F. Zelko Young Investigator
1994
Damon Runyon-Walter Winchell Cancer Research Fund
1991 - 1993