Published in Nature, 2024
Molecular cartography of mouse gut
Recommended citation: T Mayassi, C Li, et al. (2024). "Spatially restricted immune and microbiota-driven adaptation of the gut" Nature ." https://www.nature.com/articles/s41586-024-08216-z
Published in Cell, 2024
Oscillibacter metabolizes cholesterol in the gut
Recommended citation: 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). https://www.cell.com/cell/fulltext/S0092-8674(24)00305-2
Published in Science Translational Medicine, 2023
HGFAC variant characterization.
Recommended citation: 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). https://www.science.org/doi/abs/10.1126/scitranslmed.adg5252
Published in PLoS Computational Biology, 2021
An EM algorithm for inferring microbial community model from cross-sectional microbiome data.
Recommended citation: C Li, et al. (2021). "BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data." PLoS Computational Biology . 17(9). https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009343
Published in Journal of Allergy and Clinical Immunology, 2021
Identify microbial signatures on AD skin that are predictive of disease fate.
Recommended citation: 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). https://www.sciencedirect.com/science/article/abs/pii/S0091674920313993
Published in Nature Medicine, 2020
Characterization of hospital microbiome.
Recommended citation: 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). https://www.nature.com/articles/s41591-020-0894-4
Published in Microbiome, 2019
An EM algorithm for inferring microbial community model from longitudinal microbiome data.
Recommended citation: C Li, et al. (2019). "An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data." Microbiome . 7(1). https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0729-z
Published in Gigascience, 2016
Constructing accurate nanopore sequencing reads
Recommended citation: C Li, et al. (2016). "INC-Seq: accurate single molecule reads using nanopore sequencing." Gigascience . 5(1). https://academic.oup.com/gigascience/article/5/1/s13742-016-0140-7/2720995