Publications
After joining Texas A&M:
26. Min Feng and Qing Sun*. Bacterial diets’ effects on C. elegans early development. Under Preparation.
25. Min Feng and Qing Sun*. Bacterial metabolites essential for C. elegans post-embryonic development. Under Preparation.
24. Shujun He, Baizhen Gao, Rushant Sabnis, Qing Sun*, Nucleic Transformer: Classifying DNA sequences with Self-attention and Convolutions. Submitted.
23. Shujun He, Baizhen Gao, Rushant Sabnis, Qing Sun*, RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning, Briefings in Bioinformatics, 2023, 24(1): bbac581. https://doi.org/10.1093/bib/bbac581
22. Min Feng, Baizhen Gao, and Qing Sun*, Microbiota-derived metabolites in regulating the development and physiology of Caenorhabditis elegans. Frontiers in Microbiology, Under revision.
21. Shen-Long Tsai, Qing Sun, and Wilfred Chen, Advances in consolidated bioprocessing using synthetic cellulosomes, Current Opinion in Biotechnology, 2022, 17: 102840.
20. Bulten, W., Kartasalo, K., Chen, PH.C. et al. Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge. Nature Medicine, 2022, 28: 154–163. https://doi.org/10.1038/s41591-021-01620-2
19. Qing Sun, Maryam Raeeszadeh-Sarmazdeh, Shen-Long Tsai, and Wilfred Chen, Strategies for Multienzyme Assemblies, Methods in Molecular Biology, 2022, 2487: 113-131.
Programming gene expression in multicellular organisms for physiology modulation through engineered bacteria. Nature Communications. 2021, 2(1):2689. doi: 10.1038/s41467-021-22894-7. PubMed PMID: 33976154; PubMed Central PMCID: PMC8113242.
17. Shujun He, Baizhen Gao, Rushant Sabnis, and Qing Sun*. Nucleic Transformer: Deep Learning on Nucleic Acids with Self-attention and Convolutions. 2021. doi: https://doi.org/10.1101/2021.01.28.428629, Under minor revision.
16. Baizhen Gao, Rushant Sabnis, Tommaso Costantini, Robert Jinkerson, and Qing Sun*, A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community, Biochemical Society Transactions, 2020, 48: 399-409.
15. Qing Sun, Nicole M. Vega, Bernardo Cervantes, Christopher P. Mancuso, Ning Mao, Megan Taylor, James J. Collins, Ahmad S. Khalil, Jeff Gore, and Timothy K. Lu, Enhancing nutritional niche and host defenses by modifying the gut microbiome. Molecular Systems Biology, 2018, 10: 474-481.
14. Qing Sun, Shen-Long Tsai, and Wilfred Chen, Artificial scaffolds for enhanced biocatalysis, Methods in Enzymology, 2019, 617: 363-383.
13. Rebecca P. Chen, Daniel Blackstock, Qing Sun, and Wilfred Chen, Dynamic protein assembly by programmable DNA strand displacement, Nature Chemistry, 2018, 10: 474-481.
Before Texas A&M:
12. Qing Sun, Qi Chen, Daniel Blackstock and Wilfred Chen. Post-translational modification of bio-nanoparticles as a modular platform for biosensor assembly. ACS Nano, 2015, 9: 8554-8561.
11. Qing Sun, and Wilfred Chen. HaloTag mediated artificial cellulosome assembly on rolling circle amplification DNA template for efficient cellulose hydrolysis. Chemical Communications, 2016, 52: 6701-6704.
10. Qing Sun, Bhawna Madan, Shen-Long Tsai and Wilfred Chen. Creation of artificial cellulosome on DNA scaffolds by zinc finger protein-guided assembly for efficient cellulose hydrolysis. Chemical Communications, 2014, 50: 1423-1425.
9. Qi Chen, Qing Sun, Szu-Wen Wang, Eric T. Boder and Wilfred Chen. Thermally-responsive and biocatalytic protein nanocages by sortase-mediated stepwise modular display. Chemical Communications, 2015, 51: 12107-12110.
8. Daniel Blackstock, Qing Sun, and Wilfred Chen. Fluorescent protein-based molecular beacons by zinc finger protein-guided assembly. Biotechnology and Bioengineering. 2015, 112: 236-241.
7. Miso Park, Qing Sun and Wilfred Chen. Positional assembly of enzymes on bacterial outer membrane vesicles for cascade reactions. PLoS ONE 9(5): e97103. doi:10.1371/journal.pone.0097103.
6. Andrew R. Swartz, Qing Sun and Wilfred Chen, Ligand-induced crosslinking of Z-ELP-functionalized E2 protein nanoparticles for enhanced affinity precipitation of antibodies, Biomacromolecules., 18, 1654-1659, 2017.
5. Rebecca Chen*, Qi Chen*, Heejae Kim*, Ka-Hei Siu*, Qing Sun*, Shen-Long Tsai* and Wilfred Chen. Biomolecular Scaffolds for Enhanced Signaling and Catalytic Efficiency. Current Opinion in Biotechnology. 2014, 28:59–68. (*equal contribution)
4. Daniel Blackstock*, Miso Park*, Qing Sun*, Shen-Long Tsai* and Wilfred Chen. Engineering protein modules for diagnostic applications. Current Opinion in Chemical Engineering, 2013, 2: 416-424. (*equal contribution)
3. Heejae Kim*, Qing Sun, Fang Liu*, Shen-Long Tsai* and Wilfred Chen. Biologically assembled nanobiocatalysts. Topics in Catalysis, 2012, 55: 1138-1145. (*equal contribution)
2. Heejae Kim, Ka-Hei Siu, Maryam Raeeszadeh Sarmazdeh, Qing Sun, Qi Chen and Wilfred Chen. Bioengineering strategies to generate artificial protein complexes. Biotechnology and Bioengineering, 2015, 112: 1495-1505.
1. Ka-Hei Siu, Rebecca Chen, Qing Sun*, Long Chen, Shen-Long Tsai and Wilfred Chen. Synthetic scaffolds for pathway enhancement. Current Opinion in Biotechnology, 2015, 36, 98-106.
Qing Sun Lab 