Publications
The full list of publications is available on Dr. Liao’s Google Scholar page. For the following selected publications, Dr. Liao is highlighted in bold, marked with an asterisk (*) for co-first authors, and marked with a hashtag (#) for corresponding authors.
Mathematical modeling of microbial metabolism and physiology
Liao C*, Priyanka P*, Lai YH*, Rao CV, Lu T. How does Escherichia coli allocate proteome?. ACS Synthetic Biology. 2024 Aug 9.
Chen C*, Liao C*, 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, Xavier JB. Evolution and regulation of microbial secondary metabolism. eLife. 2022 Nov 21;11:e76119.
Yan J, Estanbouli H, Liao C, Kim W, Monk JM, Rahman R, Kamboj M, Palsson BO, Qiu W, Xavier JB. Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection. PLoS Computational Biology. 2019 Dec 20;15(12):e1007562.
Liao C, Blanchard AE, 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, Lu T. Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by Clostridium acetobutylicum. PNAS. 2015 Jul 7;112(27):8505-10.
Ecological network inference and community modeling
Liu H*, Liao C*, Wu L, Tang J, Chen J, Lei C, Zheng L, Zhang C, Liu YY, Xavier J, Dai L. Ecological dynamics of the gut microbiome in response to dietary fiber. The ISME Journal. 2022 Aug;16(8):2040-2055.
Liao C, Wang T, Maslov S, Xavier JB. Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. PLoS Computational Biology. 2020 Aug 18;16(8):e1008135.
Liao C, Xavier JB, Zhu Z. Enhanced inference of ecological networks by parameterizing ensembles of population dynamics models constrained with prior knowledge. BMC Ecology. 2020 Jan 8;20(1):3.
Gut microbiome in human health and disease
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, 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, 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.
Schluter J, Djukovic A, Taylor BP, Yan J, Duan C, Hussey GA, Liao C, Sharma S, Fontana E, Amoretti LA, Wright RJ, Dai A, Peled JU, Taur Y, Perales M-A, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Xavier JB. The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia. Cell Host & Microbe. 2023 Jul 12;31(7):1126-1139.e6.
Nguyen C, Markey K, Miltiadous O, Dai A, Waters N, Sadeghi K, Fei T, Shouval R, Taylor BP, Liao C, Slingerland JB, Slingerland AE, Clurman AG, Maloy MA, Bohannon L, Giardina PA, Brereton DG, Armijo GK, Fontana E, Gradissimo A, Guyrkcoza B, Sung AD, Chao NJ, Devlin SM, Taur Y, Giralt SA, Perales M-A, Xavier JB, Pamer EG, Peled JU, Gomes ALC, van den Brink MRM. High resolution analyses of associations between medications, microbiome and mortality in cancer patients. Cell. 2023 Jun 8;186(12):2705-2718.e17.
Yan J, Liao C, Taylor BP, Fontana E, Amoretti LA, Wright RJ, Littmann ER, Dai A, Waters N, Peled JU, Taur Y, Perales M-A, Siranosian BA, Bhatt AS, van den Brink MRM, Pamer EG, Schluter J, Xavier JB. A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients. Scientific Data. 2022 May 18;9(1):219.
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, Xavier JB. Compilation of longitudinal microbiota data and hospitalome from hematopoietic cell transplantation patients. Scientific Data. 2021 Mar 2;8(1):71.