Publications from the Systems Engineering group, Department of Engineering Science, University of Oxford
Systems Engineering
Selected Publications
Most Recent Publications
Discovery of dietary polyphenols targeting the autoinducer-2 quorum sensing system of pathogenic bacteria.
Wu S, Zhang P, Wang M, Xiao X, Jin H et al. (2026), Gut Microbes, 18(1), 2726629
BibTeX
@article{discoveryofdiet-2026/12,
title={Discovery of dietary polyphenols targeting the autoinducer-2 quorum sensing system of pathogenic bacteria.},
author={Wu S, Zhang P, Wang M, Xiao X, Jin H et al.},
journal={Gut Microbes},
volume={18},
pages={2726629},
publisher={Taylor & Francis},
year = "2026"
}
Wind energy potential assessment for China using long short-term memory-delta and spatial–temporal optimization
Gao J, Huang W, Yang A & Qian Y (2026), Energy Conversion and Management, 367, 121940
BibTeX
@article{windenergypoten-2026/11,
title={Wind energy potential assessment for China using long short-term memory-delta and spatial–temporal optimization},
author={Gao J, Huang W, Yang A & Qian Y},
journal={Energy Conversion and Management},
volume={367},
pages={121940},
publisher={Elsevier},
year = "2026"
}
Predictive modelling of CHO cell culture using enzyme-constrained genome-scale metabolic models coupled with empirical regression
Wee H, Qiu S, Angione C, Ye H, Odeleye AOO et al. (2026), Biochemical Engineering Journal, 235, 110325
BibTeX
@article{predictivemodel-2026/11,
title={Predictive modelling of CHO cell culture using enzyme-constrained genome-scale metabolic models coupled with empirical regression},
author={Wee H, Qiu S, Angione C, Ye H, Odeleye AOO et al.},
journal={Biochemical Engineering Journal},
volume={235},
pages={110325},
publisher={Elsevier},
year = "2026"
}
Response to “Caution: Fundamental data quality issues underlying intelligent prediction of enzyme optimal pH”
Qiu S & Yang A (2026), Briefings in Bioinformatics, 27(5), bbag537
BibTeX
@article{responsetocauti-2026/9,
title={Response to “Caution: Fundamental data quality issues underlying intelligent prediction of enzyme optimal pH”},
author={Qiu S & Yang A},
journal={Briefings in Bioinformatics},
volume={27},
pages={bbag537},
publisher={Oxford University Press (OUP)},
year = "2026"
}
Carbon Dioxide Uptake and Storage in Construction Materials: Mechanisms, Theoretical Capacity, and Global Potential
Chen L & Yang A (2026), INTERNATIONAL JOURNAL OF JOURNALISM AND MEDIA STUDIES, 2(2)
BibTeX
@article{carbondioxideup-2026/6,
title={Carbon Dioxide Uptake and Storage in Construction Materials: Mechanisms, Theoretical Capacity, and Global Potential},
author={Chen L & Yang A},
journal={INTERNATIONAL JOURNAL OF JOURNALISM AND MEDIA STUDIES},
volume={2},
publisher={Wiley},
year = "2026"
}
Response to “Addressing flaws in the Seq2Topt dataset for the prediction of enzyme optimal temperature”
Qiu S & Yang A (2026), Briefings in Bioinformatics, 27(3)
BibTeX
@article{responsetoaddre-2026/5,
title={Response to “Addressing flaws in the Seq2Topt dataset for the prediction of enzyme optimal temperature”},
author={Qiu S & Yang A},
journal={Briefings in Bioinformatics},
volume={27},
number={bbag283},
publisher={Oxford University Press},
year = "2026"
}
Substituting fossil fuels in cement production with solar energy to reduce carbon emissions
Williams F & Yang A (2026), Renewable Energy, 260, 125227
BibTeX
@article{substitutingfos-2026/3,
title={Substituting fossil fuels in cement production with solar energy to reduce carbon emissions},
author={Williams F & Yang A},
journal={Renewable Energy},
volume={260},
pages={125227},
publisher={Elsevier},
year = "2026"
}
Electrochemical direct air capture with intermittent renewable energy: techno-economic insights from solar-driven electrodialysis systems
Liu G, Zhang Y, Lin M & Yang A (2026), EES Solar
BibTeX
@article{electrochemical-2026/2,
title={Electrochemical direct air capture with intermittent renewable energy: techno-economic insights from solar-driven electrodialysis systems},
author={Liu G, Zhang Y, Lin M & Yang A},
journal={EES Solar},
publisher={Royal Society of Chemistry},
year = "2026"
}
Proteome constrained metabolic modeling of Sus scrofa muscle stem cells for cultured meat production
Qiu S, Kratochvilova E, Huang WE, Cui Z, Agnew T et al. (2026), Metabolic Engineering
BibTeX
@article{proteomeconstra-2026/1,
title={Proteome constrained metabolic modeling of Sus scrofa muscle stem cells for cultured meat production},
author={Qiu S, Kratochvilova E, Huang WE, Cui Z, Agnew T et al.},
journal={Metabolic Engineering},
publisher={Elsevier BV},
year = "2026"
}
Machine learning for enzyme catalytic activity: current progress and future horizons
Qiu S, Saeed H, Leonard W, Li F & Yang A (2026), Briefings in Bioinformatics, 27(1)
BibTeX
@article{machinelearning-2026/1,
title={Machine learning for enzyme catalytic activity: current progress and future horizons},
author={Qiu S, Saeed H, Leonard W, Li F & Yang A},
journal={Briefings in Bioinformatics},
volume={27},
number={bbag002},
publisher={Oxford University Press},
year = "2026"
}
Towards decarbonizing the supply chain of dairy industry: current practice and emerging strategies
Ni H, Zeng H, Liu Z, Li W, Miao S et al. (2025), Carbon Neutrality, 4(1), 8-8
BibTeX
@article{towardsdecarbon-2025/12,
title={Towards decarbonizing the supply chain of dairy industry: current practice and emerging strategies},
author={Ni H, Zeng H, Liu Z, Li W, Miao S et al.},
journal={Carbon Neutrality},
volume={4},
pages={8-8},
publisher={Springer Nature},
year = "2025"
}
Unraveling risk dynamics in the urban food-energy-water system for sustainable management: A coupled model considering trivariate complexity
Li X, Zhang L, Yang A, Hao Y, Zhang P et al. (2025), Technological Forecasting and Social Change, 221, 124332-124332
BibTeX
@article{unravelingriskd-2025/12,
title={Unraveling risk dynamics in the urban food-energy-water system for sustainable management: A coupled model considering trivariate complexity},
author={Li X, Zhang L, Yang A, Hao Y, Zhang P et al.},
journal={Technological Forecasting and Social Change},
volume={221},
pages={124332-124332},
publisher={Elsevier},
year = "2025"
}
Process modelling and analysis of ikaite production for atmospheric CO2 removal through ocean alkalinity enhancement
Lu X, Millar R, Toutam P, Yang A, Foteinis S et al. (2025), Chemical Engineering Research and Design
BibTeX
@article{processmodellin-2025/12,
title={Process modelling and analysis of ikaite production for atmospheric CO2 removal through ocean alkalinity enhancement},
author={Lu X, Millar R, Toutam P, Yang A, Foteinis S et al.},
journal={Chemical Engineering Research and Design},
publisher={Elsevier},
year = "2025"
}
Deep Learning-Based Prediction of Enzyme Optimal pH and Design of Point Mutations to Improve Acid Resistance
Qiu S, Wang N-K, Lu Y, Gong J-S, Shi J-S et al. (2025), ACS Synthetic Biology, 14(12), 4897-4906
BibTeX
@article{deeplearningbas-2025/11,
title={Deep Learning-Based Prediction of Enzyme Optimal pH and Design of Point Mutations to Improve Acid Resistance},
author={Qiu S, Wang N-K, Lu Y, Gong J-S, Shi J-S et al.},
journal={ACS Synthetic Biology},
volume={14},
pages={4897-4906},
publisher={American Chemical Society},
year = "2025"
}
Proteome trade-off between primary and secondary metabolism shapes acid stress induced bacterial exopolysaccharide production
Qiu S, Yang A, Yang X, Ni H, Li W et al. (2025), Metabolic Engineering
BibTeX
@article{proteometradeof-2025/5,
title={Proteome trade-off between primary and secondary metabolism shapes acid stress induced bacterial exopolysaccharide production},
author={Qiu S, Yang A, Yang X, Ni H, Li W et al.},
journal={Metabolic Engineering},
publisher={Elsevier},
year = "2025"
}
Modeling and Feasibility Assessment of Mineral Carbonation Based on Biological pH Swing for Atmospheric CO 2 Removal
Zhang Y, Long S, Duret MT, Bullock LA, Lam P et al. (2025), ACS Sustainable Chemistry and Engineering, 13(19), 6972-6981
BibTeX
@article{modelingandfeas-2025/5,
title={Modeling and Feasibility Assessment of Mineral Carbonation Based on Biological pH Swing for Atmospheric CO 2 Removal},
author={Zhang Y, Long S, Duret MT, Bullock LA, Lam P et al.},
journal={ACS Sustainable Chemistry and Engineering},
volume={13},
pages={6972-6981},
publisher={American Chemical Society},
year = "2025"
}
Optimal phasing of tidal stream power around the British Isles and within the English Channel for green ammonia production
Driscoll H, Salmon N & Bañares-Alcántara R (2025), Renewable Energy, 241, 122335-122335
BibTeX
@article{optimalphasingo-2025/3,
title={Optimal phasing of tidal stream power around the British Isles and within the English Channel for green ammonia production},
author={Driscoll H, Salmon N & Bañares-Alcántara R},
journal={Renewable Energy},
volume={241},
pages={122335-122335},
publisher={Elsevier},
year = "2025"
}
Facilitating India’s Deep Decarbonisation Through Sector Coupling of Electricity with Green Hydrogen and Ammonia
Cesaro Z, Bramstoft R, Bañares-Alcántara R & Ives MC (2025), Energy Storage and Applications, 2(2)
BibTeX
@article{facilitatingind-2025/3,
title={Facilitating India’s Deep Decarbonisation Through Sector Coupling of Electricity with Green Hydrogen and Ammonia},
author={Cesaro Z, Bramstoft R, Bañares-Alcántara R & Ives MC},
journal={Energy Storage and Applications},
volume={2},
number={4},
publisher={MDPI},
year = "2025"
}
Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature
Qiu S, Hu B, Zhao J, Xu W & Yang A (2025), Briefings in Bioinformatics, 26(2)
BibTeX
@article{seqtoptasequenc-2025/3,
title={Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature},
author={Qiu S, Hu B, Zhao J, Xu W & Yang A},
journal={Briefings in Bioinformatics},
volume={26},
number={bbaf114},
publisher={Oxford University Press},
year = "2025"
}
Assessing the net carbon removal potential by a combination of direct air capture and recycled concrete aggregates carbonation
Chen L & Yang A (2025), Resources, Conservation and Recycling, 212
BibTeX
@article{assessingthenet-2025/1,
title={Assessing the net carbon removal potential by a combination of direct air capture and recycled concrete aggregates carbonation},
author={Chen L & Yang A},
journal={Resources, Conservation and Recycling},
volume={212},
year = "2025"
}