Publications
The full list of publications is available on Dr. Liao’s Google Scholar page. For the following selected publications, asterisks (*) indicate co-first authors and hashtags (#) indicate corresponding authors.
Microbial metabolism, metabolomics, and isotope tracing
Puerner C, Morelli KA, Kerkaert JD, Jones JT, Quinn KG, DeMichaelis N, Vellanki S, Liao C and Cramer RA. Transcriptional and metabolic modeling analyses of developing Aspergillus fumigatus biofilms reveal metabolic shifts required for biofilm maturation. mSphere. 2025 Nov 28;10(12):e00752-25.
Liao C*, Priyanka P*, Lai YH*, Rao CV and Lu T. How does Escherichia coli allocate proteome?. ACS Synthetic Biology. 2024 Aug 9.
Chen C*, Liao C* and Liu YY. Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning. Nature Communications. 2023 Apr 25;14(1):2375.
Santamaria G*, Liao C*, Lindberg C, Chen Y, Wang Z, Rhee K, Pinto FR, Yan J and Xavier JB. Evolution and regulation of microbial secondary metabolism. eLife. 2022 Nov 21;11:e76119.
Liao C, Blanchard AE and Lu T. An integrative circuit-host modelling framework for predicting synthetic gene network behaviours. Nature Microbiology. 2017 Dec;2(12):1658-1666.
Liao C, Seo SO, Celik V, Liu H, Kong W, Wang Y, Blaschek H, Jin YS and Lu T. Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum. PNAS. 2015 Jul 7;112(27):8505-10.
Gut microbiome ecology and host-microbe interactions
Zhang H and Liao C#. Illuminating the functional dark matter of the gut microbiome. Cell Host & Microbe. 2026 Jan 14;34(1):12-14.
Zhai B*, Liao C*, Jaggavarapu S*, Tang Y*, Rolling T, Ning Y, Sun T, Bergin SA, Gjonbalaj M, Miranda E, Baby NE, Bader O, Taur Y, Butler G, Zhang L, Xavier JB, Weiss DS and Hohl TM. Echinocandin heteroresistance causes prophylaxis failure and facilitates breakthrough Candida parapsilosis infection. Nature Medicine. 2024 Aug 2.
Liao C*, Rolling T*, Djukovic A*, Fei T, Mishra V, Liu H, Lindberg C, Dai L, Zhai B, Peled JU, van den Brink MR, Hohl TM and Xavier JB. Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes. Nature Microbiology. 2024 May 2;9:1555–1565.
Liu H*, Liao C*, Wu L, Tang J, Chen J, Lei C, Zheng L, Zhang C, Liu YY, Xavier J and Dai L. Ecological dynamics of the gut microbiome in response to dietary fiber. The ISME Journal. 2022 Aug;16(8):2040-2055.
Liao C, Taylor BP, Ceccarani C, Fontana E, Amoretti LA, Wright RJ, Gomes ALC, Peled JU, Taur Y, Perales MA, van den Brink MRM, Littmann E, Pamer EG, Schluter J and Xavier JB. Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Scientific Data. 2021 Mar 2;8(1):71.
Liao C, Wang T, Maslov S and Xavier JB. Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. PLoS Computational Biology. 2020 Aug 18;16(8):e1008135.