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publications

INC-Seq: accurate single molecule reads using nanopore sequencing

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

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

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

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

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

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

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

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

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

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

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

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

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

Spatially restricted immune and microbiota-driven adaptation of the gut

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