Synthetic Biology and Biomanufacturing at Texas A&M

Synthetic Biology and Biomanufacturing at Texas A&M

Publications

2023
  • X. Tao, A. Zhou, H. Ouyang, D. Wang, H. Matlock, J. Morgan, A. Ren, D. Mu, C. Pan, X. Zhu, A. Han, and J. Zhou,” Polyethylene degradation by a Rhodococcous strain isolated from naturally weathered plastic waste enrichment,” Environmental Science and Technology, Vol. 57, pp. 13901-13911, 2023

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  • S-I. Han, D. A. Sarkes, M. M. Hurley, R. Renberg, C.  Huang, Y. Li, J. P. Jahnke, J. J. Sumner, D. N. Stratis-Cullum, and A. Han, “Identification of Microorganisms that Bind Specifically to Target Materials of Interest using a Magnetophoretic Microfluidic Platform,” Applied Material Interface, Vol. 15 (9), pp. 11391-11402, 2023.
  • C. Huang, F. Guo, H. Wang, J. Olivares, J. Dalton, III, O. Belyanina, A. R. Wattam, C. A. Cucinell, A. W. Dickerman, Q. Qin, A. Han*, and P. de Figueiredo*, “An automated system for interrogating the evolution of microbial endosymbiosis,” Lab on a Chip, Vol. 23, pp. 671-683, 2023 (*Co-corresponding authors).
  • He, S., Gao, B., Sabnis, R., Sun, Q., RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning, Briefings in Bioinformatics, 2023, 24(1): bbac581.

2022
  • Huan Zhang, Man S. Kim, Jun Huang, Huijuan Yan, Tao Yang, Linlin Song, Wenying Yu, Won Bo Shim.  Transcriptome analysis of maize pathogen Fusarium verticillioides revealed FvLcp1, a secreted protein with type-D fungal LysM and chitin-binding domains, that plays important roles in pathogenesis and mycotoxin production. Microbiological Research, 2022, 265: 127195.

  • Zehua Zhou, Huijuan Yan, Man S. Kim, and Won Bo Shim.  Distinct function of Mediator subunits in fungal development, stress response and secondary metabolism in fungal phytopathogen Fusarium verticillioides. Phytopathology 2022, 112: 1730-1838.

  • J. Dai, C. Huang, H. Zhang, R. Samuel, Y. Li, A. Jayaraman, P. de Figueiredo, and A. Han, “Microfluidic Dielectrophoretic Method Enables On-Demand Spatial Arrangement of Bacteria-Encapsulated Agarose Gel Microparticles,” Analytical Chemistry, Vol. 94 (38), pp. 13197-13204, 2022.
  • H. Zhang, C. Huang, Y. Li, R. Gupte, R. Samuel, J. Dai, A. Guzman, R. Sabnis, P. de Figueiredo, and A. Han, “FIDELITY: A quality control system for droplet microfluidics,” Science Advances, eabc9108 (2022).
  • Y. Li, C. Huang, S. -I. Han, and A. Han, “Measurement of Dielectric Properties of Cells at Single-Cell Resolution Using Electrorotation,” Biomedical Microdevices, Vol. 24, 23, 2022. Published as Front Cover.

  • Hu, C. Y. , Murray, R. M. “Layered feedback control overcomes performance trade-off in synthetic biomolecular networks”. Nat Commun, 2022, 13, 5393

  • Ramos, E. K., Tsai, C. F., Jia, Y., Cao, Y., Manu, M., Taftaf, R., … & Liu, H. “Machine learning-assisted elucidation of CD81–CD44 interactions in promoting cancer stemness and extracellular vesicle integrity.” Elife, 2022, 11, e82669.
  • You, Y., & Shen, Y. Cross-modality and self-supervised protein embedding for compound–protein affinity and contact prediction. Bioinformatics, 2022, 38(Supplement_2), ii68-ii74.
  • Ardywibowo R, Huo Z, Wang Z, Mortazavi B, Huang S, Qian, X. “VariGrow: Variational Architecture Growing for Task-Agnostic Continual Learning based on Bayesian Novelty.”  The 39th International Conference on Machine Learning (ICML 2022), 2022.

   

  • Qian, L., Ouyang, H., Gordils-Valentin, L., Hong, J., Jayaraman, A., Zhu, X. “Identification of Gut Bacterial Enzymes for Keto-Reductive Metabolism of Xenobiotics” ACS Chem. Biol., 2022, 17(7), 1665–1671.

2021
  • S-I. Han*, D. A. Sarkes*, J. P. Jahnke, M. M. Hurley, V. M. Ugaz, R. Renberg, J. J. Sumner, D. N. Stratis-Cullum, and A. Han, “Discovery of Targeted Material Binding Microorganisms Using a Centrifugal Microfluidic Platform,” Advanced Materials Technologies, 2021, 6, 2100282. (*these authors contributed equally)

  • C. Huang*, H. Zhang*, S. -I. Han, and A. Han, “Cell Washing and Solution Exchange in Droplet Microfluidic Systems,” Analytical Chemistry, Vol. 93 (24), pp. 8622-8630, 2021. (*these authors contributed equally). The article was published as a cover image article.

  • Niu P, Soto MJ, Yoon BJ, Dougherty ER, Alexander FJ, Blaby I, Qian X. “TRIMER: Transcription regulation integrated with metabolic regulation.” iScience, 2021, 24(11):103218.

  • Ouyang, H., Hong, J., Malroy, J., Zhu, X. “An E. coli-Based Biosynthetic Platform Expands the Structural Diversity of Natural Benzoxazoles” ACS Synth. Biol., 2021, 10(9), 2151–2158.

  • Gao, B., and Sun, Q. Programming gene expression in multicellular organisms for physiology modulation through engineered bacteria. Nature Communications. 2021, 2(1):2689.