(1) Ruan, Y.; Tang, H.; Cai, T.; Du, X.; Liu, T.; Wang, X.; Wang, P. Efficient genetic manipulation of Shewanella through targeting defense islands. Applied and Environmental Microbiology 2025, 91 (4), e02499-02424.

(2) Baimanov, D.; Wang, J.; Liu, Y.; Zheng, P.; Yu, S.; Liu, F.; Wang, J.; Boraschi, D.; Zhao, Y.; Chen, C. Identification of cell receptors responsible for recognition and binding of lipid nanoparticles. Journal of the American Chemical Society 2025, 147 (9), 7604-7616.

(3) Wu, J.; Bai, X.; Yan, L.; Baimanov, D.; Cong, Y.; Quan, P.; Cai, R.; Guan, Y.; Bu, W.; Lin, B. Selective regulation of macrophage lipid metabolism via nanomaterials’ surface chemistry. Nature Communications 2024, 15 (1), 8349.

(4) Wang, P.; Du, X.; Zhao, Y.; Wang, W.; Cai, T.; Tang, K.; Wang, X. Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria. Applied and Environmental Microbiology 2024, 90 (4), e00095-00024.

(5) Cong, Y.; Qiao, R.; Wang, X.; Ji, Y.; Yang, J.; Baimanov, D.; Yu, S.; Cai, R.; Zhao, Y.; Wu, X. Protein corona-mediated inhibition of nanozyme activity: impact of protein shape. Journal of the American Chemical Society 2024, 146 (15), 10478-10488.

(6) Cai, R.; Baimanov, D.; Yuan, H.; Xie, H.; Yu, S.; Zhang, Z.; Yang, J.; Zhao, F.; You, Y.; Guan, Y. Protein corona-directed cellular recognition and uptake of polyethylene nanoplastics by macrophages. Environmental Science & Technology 2024, 58 (32), 14158-14168.

(7) Baimanov, D.; Song, Z.; Zhang, Z.; Sun, L.; Yuan, Q.; Huang, W.; Gao, Y.; Wang, L.; Zhang, Z. Preferred lung accumulation of polystyrene nanoplastics with negative charges. Nano Letters 2024, 24 (41), 12857-12865.

(8) Baimanov, D.; Li, S.; Gao, X. J.; Cai, R.; Liu, K.; Li, J.; Liu, Y.; Cong, Y.; Wang, X.; Liu, F. A phosphatase-like nanomaterial promotes autophagy and reprograms macrophages for cancer immunotherapy. Chemical Science 2024, 15 (28), 10838-10850.

(9) Wu, C.; Guarnieri, M.; Xiong, W. FreeFlux: A Python Package for Time-Efficient Isotopically Nonstationary Metabolic Flux Analysis. ACS Synthetic Biology 2023, 12 (9), 2707-2714.

(10) Tang, T.; Duan, Z.; Baimanov, D.; Bai, X.; Liu, X.; Wang, L.; Wang, Z.; Guan, J. Synergy between isolated Fe and Co sites accelerates oxygen evolution. Nano Research 2023, 16 (2), 2218-2223.

(11) Lo, J.; Wu, C.; Humphreys, J. R.; Yang, B.; Jiang, Z.; Wang, X.; Maness, P.; Tsesmetzis, N.; Xiong, W. Thermodynamic and Kinetic Modeling Directs Pathway Optimization for Isopropanol Production in a Gas-Fermenting Bacterium. mSystems 2023, 8 (2), e01274-01222.

(12) Jiang, Y.; Baimanov, D.; Jin, S.; Cheuk-Fung Law, J.; Zhao, P.; Tang, J.; Peng, J.; Wang, L.; Leung, K. S.-Y.; Sheng, W. In situ turning defects of exfoliated Ti3C2 MXene into Fenton-like catalytic active sites. Proceedings of the National Academy of Sciences 2023, 120 (1), e2210211120.

(13) Cai, T.; Tang, H.; Du, X.; Wang, W.; Tang, K.; Wang, X.; Liu, D.; Wang, P. Genomic Island-Encoded Diguanylate Cyclase from Vibrio alginolyticus Regulates Biofilm Formation and Motility in Pseudoalteromonas. Microorganisms 2023, 11 (11), 2725.

(14) Baimanov, D.; Wang, L.; Liu, K.; Pan, M.; Cai, R.; Yuan, H.; Huang, W.; Yuan, Q.; Zhou, Y.; Chen, C. Stereoselective coronas regulate the fate of chiral gold nanoparticles in vivo. Nanoscale Horizons 2023, 8 (7), 859-869.

(15) Zhu, X.; Jack, J.; Leininger, A.; Yang, M.; Bian, Y.; Lo, J.; Xiong, W.; Tsesmetzis, N.; Ren, Z. J. Syngas mediated microbial electrosynthesis for CO₂ to acetate conversion using Clostridium ljungdahlii. Resources, Conservation and Recycling 2022, 184.

(16) Zhao, Y.; Wang, W.; Yao, J.; Wang, X.; Liu, D.; Wang, P. the HipAB toxin–antitoxin system stabilizes a composite genomic island in Shewanella putrefaciens CN-32. Frontiers in Microbiology 2022, 13, 858857.

(17) Zhang, G.; Cong, Y.; Liu, F.-L.; Sun, J.; Zhang, J.; Cao, G.; Zhou, L.; Yang, W.; Song, Q.; Wang, F.; Liu K.; Qu, J.; Wang, J.; He, M.; Feng, S.; Baimanov, D.; et al. A nanomaterial targeting the spike protein captures SARS-CoV-2 variants and promotes viral elimination. Nature Nanotechnology 2022, 17 (9), 993-1003.

(18) Wu, C.; Yu, J.; Guarnieri, M.; Xiong, W. Computational Framework for Machine-Learning-Enabled ¹³C Fluxomics. ACS Synth. Biol. 2022, 11 (1), 103-115.

(19) Wang, W.; Tang, K.; Wang, P.; Zeng, Z.; Xu, T.; Zhan, W.; Liu, T.; Wang, Y.; Wang, X. The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction. Nature Ecology & Evolution 2022, 6 (8), 1132-1144.

(20) Wang, P.; Zhao, Y.; Wang, W.; Lin, S.; Tang, K.; Liu, T.; Wood, T. K.; Wang, X. Mobile genetic elements used by competing coral microbial populations increase genomic plasticity. The ISME Journal 2022, 16 (9), 2220-2229.

(21) Sebesta, J.; Xiong, W.; Guarnieri, M. T.; Yu, J. Biocontainment of genetically engineered algae. Frontiers in Plant Science 2022, 13, 839446.

(22) Lo, J.; Humphreys, J. R.; Magnusson, L.; Wachter, B.; Urban, C.; Hebdon, S. D.; Xiong, W.; Chou, K. J.; Ching Maness, P. Acetogenic production of 3-Hydroxybutyrate using a native 3-Hydroxybutyryl-CoA Dehydrogenase. Frontiers in Microbiology 2022,13:948369.

(23) Hu, Q.; Hu, H.; Cui, L.; Li, Z.; Svedruzic, D.; Blackburn, J. L.; Beard, M. C.; Ni, J.; Xiong, W.; Gao, X. Ultrafast electron transfer in Au–cyanobacteria hybrid for solar to chemical production. ACS Energy Letters 2022, 8 (1), 677-684.

(24) Hameed, S.; Baimanov, D.; Li, X.; Liu, K.; Wang, L. Synchrotron radiation-based analysis of interactions at the nano–bio interface. Environmental Science: Nano 2022, 9 (9), 3152-3167.

(25) Cong, Y.; Baimanov, D.; Zhou, Y.; Chen, C.; Wang, L. Penetration and translocation of functional inorganic nanomaterials into biological barriers. Advanced Drug Delivery Reviews 2022, 191, 114615.

(26) Baimanov, D.; Wang, J.; Zhang, J.; Liu, K.; Cong, Y.; Shi, X.; Zhang, X.; Li, Y.; Li, X.; Qiao, R. In situ analysis of nanoparticle soft corona and dynamic evolution. Nature Communications 2022, 13 (1), 5389.

(27) Wei, Y.; Gao, X.; Zhao, F.; Baimanov, D.; Cong, Y.; Jiang, Y.; Hameed, S.; Ouyang, Y.; Gao, X.; Lin, X. Induced autophagy of macrophages and the regulation of inflammatory effects by perovskite nanomaterial LaNiO₃. Frontiers in Immunology 2021, 12, 676773.

(28) Ni, S.; Li, B.; Tang, K.; Yao, J.; Wood, T. K.; Wang, P.; Wang, X. Conjugative plasmid-encoded toxin–antitoxin system PrpT/PrpA directly controls plasmid copy number. Proceedings of the National Academy of Sciences 2021, 118 (4), e2011577118.

(29) Li, Z.; Wu, C.; Gao, X.; Addison, B.; Shinde, S.; Wang, X.; Chen, X.; Yu, J.; Svedruzic, D.; Blackburn, J. L.; Xiong, W. Exogenous electricity flowing through cyanobacterial photosystem I drives CO₂ valorization with high energy efficiency. Energy & Environmental Science 2021, 14 (10), 5480-5490.

(30) Henard, C. A.; Wu, C.; Xiong, W.; Henard, J. M.; Davidheiser-Kroll, B.; Orata, F. D.; Guarnieri, M. T. Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RubisCO) Is Essential for Growth of the Methanotroph Methylococcus capsulatus Strain Bath. Appl Environ Microbiol 2021, 87 (18), e0088121.

(31) Del Cerro, C.; Erickson, E.; Dong, T.; Wong, A. R.; Eder, E. K.; Purvine, S. O.; Mitchell, H. D.; Weitz, K. K.; Xiong, W.; Markillie, L. M.; Burnet, M. C. Intracellular pathways for lignin catabolism in white-rot fungi. Proceedings of the National Academy of Sciences 2021, 118 (9), e2017381118.

(32) Arnolds, K. L.; Dahlin, L. R.; Ding, L.; Wu, C.; Yu, J.; Xiong, W.; Zuniga, C.; Suzuki, Y.; Zengler, K.; Linger, J. G.; et al. Biotechnology for secure biocontainment designs in an emerging bioeconomy. Current Opinion in Biotechnology 2021, 71, 25-31.

(33) Wu, C.; Jiang, H.; Kalra, I.; Wang, X.; Cano, M.; Maness, P.; Yu, J.; Xiong, W. A generalized computational framework to streamline thermodynamics and kinetics analysis of metabolic pathways. Metabolic Engineering 2020, 57, 140-150.

(34) Wu, C.; Cano, M.; Gao, X.; Lo, J.; Maness, P.; Xiong, W. A quantitative lens on anaerobic life: leveraging the state-of-the-art fluxomics approach to explore clostridial metabolism. Current Opinion in Biotechnology 2020, 64, 47-54.

(35) Lo, J.; Humphreys, J. R.; Jack, J.; Urban, C.; Magnusson, L.; Xiong, W.; Gu, Y.; Ren, Z. J.; Maness, P.-C. The Metabolism of Clostridium ljungdahlii in Phosphotransacetylase Negative Strains and Development of an Ethanologenic Strain. Frontiers in Bioengineering and Biotechnology 2020, 8:560726.

(36) Dong, T.; Wang, B.; Xiong, W.; Sweeney, N.; Pienkos, P. T.; Yu, J. System-Level Optimization to Improve Biofuel Potential via Genetic Engineering and Hydrothermal Liquefaction. ACS Sustainable Chemistry & Engineering 2020, 8 (7), 2753-2762.

(37) Baimanov, D.; Wu, J.; Chu, R.; Cai, R.; Wang, B.; Cao, M.; Tao, Y.; Liu, J.; Guo, M.; Wang, J. Immunological responses induced by blood protein coronas on two-dimensional MoS₂ nanosheets. ACS Nano 2020, 14 (5), 5529-5542.

(38) Wu, C.; Herold, R. A.; Knoshaug, E. P.; Wang, B.; Xiong, W.; Laurens, L. M. Fluxomic analysis reveals central carbon metabolism adaptation for diazotroph Azotobacter vinelandii ammonium excretion. Scientific reports 2019, 9 (1), 13209.

(39) Wu, C.; Chen, C.-h.; Lo, J.; Michener, W.; Maness, P.; Xiong, W. EMUlator: An Elementary Metabolite Unit (EMU) Based Isotope Simulator Enabled by Adjacency Matrix. Frontiers in Microbiology 2019, 10.

(40) Wang, P.; He, D.; Li, B.; Guo, Y.; Wang, W.; Luo, X.; Zhao, X.; Wang, X. Eliminating MCR-1-harbouring plasmids in clinical isolates using the CRISPR/Cas9 system. Journal of Antimicrobial Chemotherapy 2019, 74 (9), 2559-2565.

(41) Wang, B.; Dong, T.; Myrlie, A.; Gu, L.; Zhu, H.; Xiong, W.; Maness, P.; Zhou, R.; Yu, J. Photosynthetic production of the nitrogen-rich compound guanidine. Green Chemistry 2019, 21 (11), 2928-2937.

(42) Ren, J.; Cai, R.; Wang, J.; Daniyal, M.; Baimanov, D.; Liu, Y.; Yin, D.; Liu, Y.; Miao, Q.; Zhao, Y. Precision nanomedicine development based on specific opsonization of human cancer patient-personalized protein coronas. Nano Letters 2019, 19 (7), 4692-4701.

(43) Douchi, D.; Liang, F.; Cano, M.; Xiong, W.; Wang, B.; Maness, P.-C.; Lindblad, P.; Yu, J. Membrane-Inlet Mass Spectrometry Enables a Quantitative Understanding of Inorganic Carbon Uptake Flux and Carbon Concentrating Mechanisms in Metabolically Engineered Cyanobacteria. Frontiers in Microbiology 2019, 10:1356.

(44) Baimanov, D.; Cai, R.; Chen, C. Understanding the chemical nature of nanoparticle–protein interactions. Bioconjugate Сhemistry 2019, 30 (7), 1923-1937.

(45) Xiong, W.; Reyes, L. H.; Michener, W. E.; Maness, P. C.; Chou, K. J. Engineering cellulolytic bacterium Clostridium thermocellum to co-ferment cellulose- and hemicellulose-derived sugars simultaneously. Biotechnol Bioeng. 2018, 115 (7), 1755-1763.

(46) Xiong, W.; Lo, J.; Chou, K. J.; Wu, C.; Magnusson, L.; Dong, T.; Maness, P. Isotope-Assisted Metabolite Analysis Sheds Light on Central Carbon Metabolism of a Model Cellulolytic Bacterium Clostridium thermocellum. Front Microbiol. 2018, 9, 1947.

(47) Liu, J.; Shen, X.; Baimanov, D.; Wang, L.; Xiao, Y.; Liu, H.; Li, Y.; Gao, X.; Zhao, Y.; Chen, C. Immobilized ferrous ion and glucose oxidase on graphdiyne and its application on one-step glucose detection. ACS Applied Materials & Interfaces 2018, 11 (3), 2647-2654.

(48) Wen, Z.; Wang, P.; Sun, C.; Guo, Y.; Wang, X. Interaction of type IV toxin/antitoxin systems in cryptic prophages of Escherichia coli K-12. Toxins 2017, 9 (3), 77.

(49) Wang, P.; Zeng, Z.; Wang, W.; Wen, Z.; Li, J.; Wang, X. Dissemination and loss of a biofilm‐related genomic island in marine Pseudoalteromonas mediated by integrative and conjugative elements. Environmental Microbiology 2017, 19 (11), 4620-4637.

(50) Xiong, W.; Lin, P. P.; Magnusson, L.; Warner, L.; Liao, J. C.; Maness, P.-C.; Chou, K. J. CO₂-fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum. Proceedings of the National Academy of Sciences 2016, 113 (46), 13180-13185.

(51) Wang, P.; Zhu, Y.; Zhang, Y.; Zhang, C.; Xu, J.; Deng, Y.; Peng, D.; Ruan, L.; Sun, M. Mob/oriT, a mobilizable site-specific recombination system for unmarked genetic manipulation in Bacillus thuringiensis and Bacillus cereus. Microbial Cell Factories 2016, 15 (1), 108.

(52) Xiong, W.; Morgan, J. A.; Ungerer, J.; Wang, B.; Maness, P.-C.; Yu, J. The plasticity of cyanobacterial metabolism supports direct CO₂ conversion to ethylene. Nature Plants 2015, 1 (5), 1-7.

(53) Xiong, W.; Lee, T.-C.; Rommelfanger, S.; Gjersing, E.; Cano, M.; Maness, P.-C.; Ghirardi, M.; Yu, J. Phosphoketolase pathway contributes to carbon metabolism in cyanobacteria. Nature plants 2015, 2 (1), 1-8.

(54) Wang, P.; Yu, Z.; Li, B.; Cai, X.; Zeng, Z.; Chen, X.; Wang, X. Development of an efficient conjugation-based genetic manipulation system for Pseudoalteromonas. Microbial Cell Factories 2015, 14 (1), 11.

(55) Lee, T.-C.; Xiong, W.; Paddock, T.; Carrieri, D.; Chang, I.-F.; Chiu, H.-F.; Ungerer, J.; Hank Juo, S.-H.; Maness, P.-C.; Yu, J. Engineered xylose utilization enhances bio-products productivity in the cyanobacterium Synechocystis sp. PCC 6803. Metabolic Engineering 2015, 30, 179-189.

(56) Eckert, C.; Xu, W.; Xiong, W.; Lynch, S.; Ungerer, J.; Tao, L.; Gill, R.; Maness, P.-C.; Yu, J. Ethylene-forming enzyme and bioethylene production. Biotechnology for Biofuels 2014, 7 (1), 33.

(57) Wang, P.; Zhang, C.; Zhu, Y.; Deng, Y.; Guo, S.; Peng, D.; Ruan, L.; Sun, M. The resolution and regeneration of a cointegrate plasmid reveals a model for plasmid evolution mediated by conjugation and oriT site‐specific recombination. Environmental Microbiology 2013, 15 (12), 3305-3318.

(58) Xiong, W.; Liu, L.; Wu, C.; Yang, C.; Wu, Q. 13C-tracer and gas chromatography-mass spectrometry analyses reveal metabolic flux distribution in the oleaginous microalga Chlorella protothecoides. Plant Physiology 2010, 154 (2), 1001-1011.

(59) Xiong, W.; Gao, C.; Yan, D.; Wu, C.; Wu, Q. Double CO₂ fixation in photosynthesis-fermentation model enhances algal lipid synthesis for biodiesel production. Bioresour Technol. 2010, 101 (7), 2287-2293.

(60) Xiong, W.; Gao, C.; Yan, D.; Wu, C.; Wu, Q. Double CO₂ fixation in photosynthesis–fermentation model enhances algal lipid synthesis for biodiesel production. Bioresource technology 2010, 101 (7), 2287-2293.

(61) Gao, Y.; Xiong, W.; Li, X.-b.; Gao, C.-F.; Zhang, Y.-l.; Li, H.; Wu, Q.-y. Identification of the proteomic changes in Synechocystis sp. PCC 6803 following prolonged UV-B irradiation. Journal of Experimental Botany 2009, 60 (4), 1141-1154.

(62) Gao, Y.; Xiong, W.; He, M. J.; Tang, L.; Xiang, J. Y.; Wu, Q. Y. Action spectra of chlorophyll a biosynthesis in cyanobacteria: Dark-operative protochlorophyllide oxidoreductase-deficient mutants. Zeitschrift für Naturforschung C. A Journal of Biosciences 2009, 64 (1-2), 117-124.

(63) Gao, Y.; Cui, Y.; Xiong, W.; Li, X.; Wu, Q. Effect of UV‐C on algal evolution and differences in growth rate, pigmentation and photosynthesis between prokaryotic and eukaryotic algae. Photochemistry and Photobiology 2009, 85 (3), 774-782.

(64) Xiong, W.; Li, X.; Xiang, J.; Wu, Q. High-density fermentation of microalga Chlorella protothecoides in bioreactor for microbio-diesel production. Applied Microbiology and Biotechnology 2008, 78 (1), 29-36.

(65) Xiong, W.; He, M.; Li, X.; Gao, Y.; Wu, Q. Identification and biochemical properties of Dps (starvation‐induced DNA binding protein) from cyanobacterium Anabaena sp. PCC 7120. IUBMB Life 2008, 59 (10), 675-681.

(66) Gao, C.; Xiong, W.; Zhang, Y.; Yuan, W.; Wu, Q. Rapid quantitation of lipid in microalgae by time-domain nuclear magnetic resonance. J. Microbiol. Methods 2008, 75 (3), 437-440.