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portfolio
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publications
Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota
Published in Environmental Microbiology Reports, volume 8, issue 3, pages 399-406, 2016
Using whole-genome sequencing over nearly two years, this study identified a stable, highly diverse community of both resident and transient Lactobacillus species and strains in a healthy subject’s gut, including 16 never-before-seen in human feces.
Health and Disease Imprinted in the Time Variability of the Human Microbiome
Published in mSystems, volume 2, e00144-16, 2017
By analyzing published 16S rRNA and shotgun metagenomic sequencing data over time, this study developed a fluctuation scaling law to describe temporal changes and quantify the path toward disease in the gut microbiota.
Time series analysis of the microbiota of children suffering from acute infectious diarrhea and their recovery after treatment
Published in Frontiers in Microbiology, volume 9, 1230, 2018
After children with rotavirus-induced diarrhea were treated with the probiotic Saccharomyces boulardii CNCM I-745, their gut microbiota diversity initially decreased but then recovered over 30 days, mirroring their clinical improvement, which was evident by the cessation of diarrhea by day 3, and demonstrating a shift from a highly variable, diseased state to a stable, healthy one.
Oxidative stress in the oral cavity is driven by individual-specific bacterial communities
Published in NPJ Biofilms and Microbiomes, volume 4, issue 1, 29, 2018
This study investigates the role of individual-specific bacterial communities in driving oxidative stress in the oral cavity.
Host-microbe-drug-nutrient screen identifies bacterial effectors of metformin therapy
Published in Cell, volume 178, issue 6, pages 1299-1312.e29, 2019
Metformin, a first-line therapy for type 2 diabetes and a promising anti-aging drug, exerts its effects through interactions with gut microbes and diet, as revealed by a high-throughput four-way screen using E. coli and C. elegans models, identifying microbial agmatine as a key regulator of metformin’s impact on host lipid metabolism and lifespan.
The role of the microbiome in drug response
Published in Annual Review of Pharmacology and Toxicology, volume 60, pages 417-435, 2020
This review outlines current evidence, experimental tools, and computational methods showing that the microbiota acts as a key mediator of drug effects (both benefits and side effects) for treatments of mental disorders, type 2 diabetes, and cancer.
Mechanical properties measured by atomic force microscopy define health biomarkers in ageing C. elegans
Published in Nature Communications, volume 11, issue 1, 1043, 2020
By applying Atomic Force Microscopy (AFM) to measure nanoscale biomechanical properties in aging C. elegans, this study found that longer lifespan doesn’t always coincide with extended healthspan, though insulin signaling and bacterial physiology interventions successfully increased both.
Transcriptome analysis of Caenorhabditis elegans lacking heme peroxidase SKPO-1 reveals an altered response to Enterococcus faecalis
Published in G3 Genes|Genomes|Genetics, volume 11, issue 2, jkaa055, 2021
Loss of the peroxidase gene skpo−1 in C. elegans was shown by RNA sequencing and Atomic Force Microscopy to cause upregulation of cuticle development genes, resulting in a leaky, misaligned cuticle and failure to upregulate environmental sensors, which explains its increased susceptibility to the pathogen E. faecalis.
C. elegans: A biosensor for host-microbe interactions
Published in Lab Animal, volume 50, pages 127–135, 2021
The nematode C. elegans serves as a powerful model organism to investigate the complex, poorly understood mechanisms of microbe–host interactions by leveraging its extensive genetic tools with deep phenotyping.
Development and implementation of a scalable and versatile test for COVID-19 diagnostics in rural communities
Published in Nature Communications, volume 12, 4400, 2021
Developement of a highly sensitive and adaptable RT-qPCR-based SARS-CoV-2 test to rapidly supplement COVID-19 testing needs, especially in rural and underserved communities, by 3D printing critical supplies and creating a cold-chain-independent transport media.
Increased fidelity of protein synthesis extends lifespan
Published in Cell Metabolism, volume 33, issue 11, pages 2288-2300. e12, 2021
Introduction of a specific RPS23 ribosomal protein mutation (Lysine → Arginine) from hyperthermophilic archaea into yeast, worms, and flies, finds that the resulting increase in translation accuracy significantly extended lifespan and promoted heat shock resistance. The anti-aging drugs like rapamycin reduce translation errors, suggesting a unified mechanism for diverse longevity interventions targeting translation accuracy.
Reducing Dietary Protein Enhances the Antitumor Effects of Chemotherapy through Immune-Mediated Mechanisms
Published in Molecular Cancer Therapies, volume 24, issue 7, pages 1099-1110, 2025
This review outlines current evidence, experimental tools, and computational methods showing that the microbiota acts as a key mediator of drug effects (both benefits and side effects) for treatments of mental disorders, type 2 diabetes, and cancer.
Chemotherapy modulation by a cancer-associated microbiota metabolite
Published in Cell Systems, volume 16, issue 9, pages 101397, 2025
This study that I led identifies a microbiome-derived metabolite that inhibits cancer cell proliferation and synergizes with the chemotherapeutic agent 5-fluorouracil, highlighting its potential as a co-adjuvant in cancer treatment.
talks
Talk 1 on Relevant Topic in Your Field
Published:
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
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Teaching experience 2
Workshop, University 1, Department, 2015
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