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).
CV
Education
- B.S. in Computational Biology, National University of Singapore, 2014
- Ph.D in Computer Science, National University of Singapore, 2019
Work experience
- Bioinformatics specialist, Genome Institute of Singapore, 2014-2019 (concurrent with Ph.D)
- Postdoctoral Fellow, Genome Institute of Singapore, 2019-2020
- Research Associate, Genome Institute of Singapore, 2019-2020
- Research Fellow, Massachusetts General Hospital and Broad Institute, 2020-Present
Selected publications
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 ."