CV

Education

• B.S. in Computational Biology, National University of Singapore, 2014
• Ph.D in Computer Science, National University of Singapore, 2019
  • Bioinformatics specialist, Genome Institute of Singapore, 2014-2019 (concurrent with Ph.D)

Postdoctoral training

• Postdoctoral Fellow, Genome Institute of Singapore, 2019-2020
• Research Associate, Genome Institute of Singapore, 2019-2020
• Postdoctoral Fellow, Massachusetts General Hospital, 2020-2024
  • Harvard Medical School
  • Broad Institute

Faculty appointment

• Instructor in Medicine, Massachusetts General Hospital, 2025-present
  • Harvard Medical School

Honors and Prizes

• Harvard Chinese Life Science Annual Distinguished Research Award, 2024
• GIS Graduate Student Prize, 2018
• Honor List of Student Tutors, 2018

Editorial Activities

Ad hoc reviewer for: Nature Communications, Microbiome, Nucleic Acid Research, BMC Microbiology, BMC Genomics, GigaScience, iMeta, Journal of Genetics and Genomics, Journal of Bioinformatics and Computational Biology, NPJ biofilms, PLos Computational Biology, Scientific Reports

Selected publications

INC-Seq: accurate single molecule reads using nanopore sequencing

C Li, et al. (2016). "INC-Seq: accurate single molecule reads using nanopore sequencing." Gigascience . 5(1).

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data

C Li, et al. (2019). "An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data." Microbiome . 7(1).

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

K R Chng, C Li, D Bertrand et al. (2020). "Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment." Nature Medicine. 26(6).

Atopic dermatitis microbiomes stratify into ecologic dermotypes enabling microbial virulence and disease severity

A Tay, C Li, T Nandi, et al. (2021). "Atopic dermatitis microbiomes stratify into ecologic dermotypes enabling microbial virulence and disease severity" Journal of Allergy and Clinical Immunology. 147(4).

BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data

C Li, et al. (2021). "BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data." PLoS Computational Biology . 17(9).

Genetic vulnerability to Crohn’s disease reveals a spatially resolved epithelial restitution program

T Nakata, C Li, et al. (2023). "Genetic vulnerability to Crohn’s disease reveals a spatially resolved epithelial restitution program." Science Translational Medicine. 15(719).

Gut microbiome and metabolome profiling in Framingham Heart Study reveals cholesterol-metabolizing bacteria linked with lower cardiovascular risk

C Li, et al. (2024). "Gut microbiome and metabolome profiling in Framingham Heart Study reveals cholesterol-metabolizing bacteria linked with lower cardiovascular risk." Cell . 8674(24).

Spatially restricted immune and microbiota-driven adaptation of the gut

T Mayassi, C Li, et al. (2024). "Spatially restricted immune and microbiota-driven adaptation of the gut" Nature ."