Focusing on yeast, mutiple state of art techonologies including systematic integration of multi-scale omics, machine learning to develop the next generation of whole-cell models, which will be as a strong platform to promote the research in system biology and synthetic biology.
By combining rational prediction from metabolic models with quantitative analysis of proteomics, fluxomics and metabolomics, we will accelerate the development of high-performance industrial strains by remodeling the distribution of resource and fluxes within the target cell factories.
In a sytematic way, we will explore the evolutionary origin of yeast diverse metabolic function and traits through the integrative analysis from model prediction, comparative genomics and physiological study.
H Lu* (co-corresponding author), L Xiao, W Liao, X Yan, J Nielsen*. Cell factory design with advanced metabolic modelling empowered by artificial intelligence. Metabolic Engineering, 2024.07
Yuan L, Lu H* (co-corresponding author), Li F, Nielsen J and Kerkhoven* EJ. HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer. Briefings in Bioinformatics, 2023: 1–7.
Lu H, Kerkhoven EJ, Nielsen J. Multiscale models quantifying yeast physiology: towards a whole-cell model. Trends in Biotechnology, 2022, 40(3):291-305.
Lu H#, Li F#, Yuan L#, Domenzain I, Yu R, Wang H, Li G, Chen Y, Ji B, Kerkhoven EJ, Nielsen J*. Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. Molecular Systems Biology, 2021(17):e10427.
Lu H#, Li F#, Sánchez BJ, Zhu Z, Li G, Domenzain I, Marcišauskas S, Anton PM, Lappa D, Lieven C, Beber ME, Sonnenschein N, Kerkhoven EJ, Nielsen J*. A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nature Communications, 2019, 10 (1):1-13.
Lu H, Chen Y, Nielsen J, Kerkhoven EJ. Kinetic Models of Metabolism. Metabolic Engineering: Concepts and Applications, 2021 (13): 153-170. Book chapter.
Lu H, Liu X, Huang M*, Xia J, Chu J*, Zhuang Y, Zhang S, Noorman H. Integrated isotope-assisted metabolomics and (13)C metabolic flux analysis reveals metabolic flux redistribution for high glucoamylase production by Aspergillus niger. Microb Cell Fact, 2015(14):147.
Lu H, Cao W, Ouyang L, Xia J, Huang M* , Chu J*, Zhuang Y, Zhang S, Noorman H. Comprehensive reconstruction and in silico analysis of Aspergillus niger genome-scale metabolic network model that accounts for 1210 ORFs. Biotechnology and Bioengineering, 2017, 114(3):685-695.
Lu H#, Cao W#, Liu X, Sui Y, Ouyang L*, Xia J, Huang M, Zhuang Y, Zhang S, Noorman H, Chu J*. Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspergillus niger under industrial enzyme production condition. Sci Rep, 2018, 8(1):14404.
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