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32. Liang Chen ,Ziwei Zhang ,Yu Gao, “High throughput proteomics enabled by a fully automated dual-column liquid chromatography system coupled with mass spectrometry(submitted), chemRxiv, 10.26434/chemrxiv-2023-8lnlk

31. Xinghang Jiang; Olivia T. Ly; Hanna Chen; Ziwei Zhang; Beatriz A. Ibarra; Mahmud A Pavel; Grace E. Brown; Arvind Sridhar; David Tofovic; Abigail Swick; Richard Marszalek; Carlos G. Vanoye; Fritz Navales; Alfred L. George, Jr.; Salman R. Khetani; Jalees Rehman; Yu Gao; Dawood Darbar; Ankur Saxena, “Titin-dependent transient ventricular defects result in adult atrial arrhythmia and impaired contractility” (submitted)

30. Maldonado, Amanda; Haughan, Monica; Khin, Manead; Ekiert, Julia; Zhang, Ziwei; Lantvit, Daniel; Al Subeh, Zeinab ; Pierre, Herma; Salkovski, Maryna; Hirschhorn, Tal; Gao, Yu; Pearce, Cedric; Stockwell, Brent; Aldrich, Leslie; Oberlies, Nicholas; Burdette, Joanna,
“Probing the Cytotoxic Mechanism of Action of Eupenifeldin in Ovarian Cancer”, Journal of Natural Products, (submitted)

29. Shao, X.; Gomez, C.D.; Kapoor, N.; Considine, J.M.; Grams, C.; Naba, A.; Gao, Y.,
“MatrisomeDB 2.0: 2023 updates to the ECM protein knowledge database”, Nucleic Acids Research
Volume 51, Issue D1, Pages D1519–D1530, 2023, Try it here: MatrisomeDB 2.0

28. Cory Matsumoto, Xinhao Shao, Marko Bogosavljevic, Liang ChenYu Gao, “Automated container-less cell processing method for single-cell proteomics“, pre-print, 2022 See full story HERE.

27. Irina Laczkovich, Kyle Mangano, Xinhao Shao, Adam J. Hockenberry, Yu Gao, Alexander Mankin, Nora Vázquez-Laslop, Michael J. Federle, “Discovery of Unannotated Small Open Reading Frames in Streptococcus pneumoniae D39 Involved in Quorum Sensing and Virulence Using Ribosome Profiling“, mBio, 2022e0124722,

26. Zhang, Z.; Gao, Y.Evaluation of binding preference of different microtubes for nanoproteomics sample preparation“, J. Proteome Res. 2023, 22, 1, 279–284,, pre-print available at chemRxiv: http://10.26434/chemrxiv-2022-vtz66

25. Lee, F.; Shao, X.; Gao, Y.; Naba, A. “Time-lapsed proteomics reveals a role for the novel protein, SNED1, in modulating ECM composition and protein folding”, 2022, (submitted, under review), pre-print available at bioRxiv,

24. Shao, X.; Grams, C.; Gao, Y. “Sequence Coverage Visualizer: A web application for protein sequence coverage 3D visualization”, J. Proteome Res. 2023, 22, 2, 343–349,, pre-print available at bioRxiv, doi:

23. Guo, J.; Shen, S.; Liu, M.; Wang, C.; Low, B.; Chen, Y.; Hu, Y.; Xing, S.; Yu, H.; Gao, Y.; Fang, M.; Huan, T. “JPA: Joint Metabolic Feature Extraction Increases the Depth of Chemical Coverage for LC-MS-Based Metabolomics and Exposomics.” Metabolites 2022, 12, 212. 

22. Kyle Mangano, Tanja Florin, Xinhao Shao, Dorota Klepacki, Irina Chelysheva, Zoya Ignatova, Yu Gao, Alexander S Mankin, Nora Vázquez-Laslop, “Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria”, eLife, 2020.;

21. Shao, X.H.; Taha, I.N.; Clauser K.R.; Gao, Y.; Naba, A. “MatrisomeDB: the ECM-protein knowledge database”, Nucleic Acids Research, gkz849, 2020;


20. McClatchy, D.B.; Gao, Y.; Lavelle-Adam, M.; Yates, J.R. “Quantitative Analysis of Global Protein Stability Rates in Tissues”, Scientific Reports, 2020, 10, 15983.

19. Gao, Y.; Dasgupta, C.; Huang, L.; Song, R.; Zhang, Z.W.; Zhang, L. “Multi-omics integration reveals short and long-term effects of gestational hypoxia on the heart development”, Cells 2019, 8(12), 1608;


18. Gao, Y.; Yates, J.R. “Protein Analysis by Shotgun Proteomics”, book chapter in “Mass Spectrometry‐Based Chemical Proteomics”, 2019;



Before UIC

17. Gao, Y.; López-Aguilar, A.; Hou, X; Yates, J.R.; and Wu, P. “A Chemoenzymatic Study Of O-Glcnac-Modified Proteins in Effector and Memory CD8+ T Cells in a Listeria Monocytogenes Infection Model.”, ACS Chemical Biology, 2017, 12, 3031.;


16. Yu Gao, Jiao Ma,  Alan Saghatelian, John R. Yates III, “Targeted Searches for Novel Peptides in Big Mass Spectrometry Data Sets”, bioRxiv, 2017;


15. Xu, T.; Park, S.K.; Venable, J.D.; Wohlschlegel, J.A.; Diedrich, J.K.; Cociorva, D.; Lu, B.; Liao, L.; Hewel, J.; Han, X.; Wong, C.C.L.; Fonslow, B.; Delahunty, C.; Gao, Y.; Shah, H.; Yates, J.R. “ProLuCID: An improved SEQUEST-like Algorithm with Enhanced Sensitivity and Specificity.”, Journal of Proteomics, 2015, 129, 16-24.;


14. Doran, T.; Gao, Y. Simanski, S.; McEnaney, P.; Kodadek, T.J. “High Affinity Binding of Conformationally Constrained Synthetic Oligomers to An Antigen-Specific Antibody: Discovery of a Diagnostically Useful Synthetic Ligand for Murine Type 1 Diabetes Autoantibodies”, Bioorganic & Medicinal Chemistry Letters, 2015, 25(21), 4910-4917.; 

13. Gao, Y.; Kodadek, T.J. “Direct Comparison of Linear and Macrocyclic Compound Libraries as a Source of Protein Ligands”, ACS Combinatorial Sciences, 2015, 17 (3), 190–195. *ACS Editors’ Choice, Top 10 most downloaded paper in first half 2015.; 

12. Gao, Y.; Amar, S.; Pahwa, S.; Fields, G.; Kodadek, T.J. “Rapid Lead Discovery Through Iterative Screening of One Bead One Compound Libraries”, ACS Combinatorial Sciences, 2015, 17 (1), 49–59. *Top 10 most downloaded paper in first half 2015. ; 


11. Sarma, B.K.; Liu, X.; Gao, Y.; Kodadek, T.J. “Solid Phase Synthesis of 1,3,4-oxadiazin-5 (6R)-one and 1,3,4-oxadiazol-2-one Scaffolds from Acyl Hydrazides”, Organic & Biomolecular Chemistry, 2015, 13, 59.;



10. Doran, T.; Gao, Y.; Mendes, K.; Dean, S.; Kodadek, T.J. “The Utility of Redundant Combinatorial Libraries in Distinguishing High and Low Quality Screening Hits”, ACS Combinatorial Sciences, 2014, 16 (6), 259–270.  *ACS Editors’ Choice;



9. Gao, Y.; Kodadek, T.J. “Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library”, Journal of Visualized Experiments, (88), e51299.; 2014


8. Rzuczek, S.G.; Gao, Y.; Tang, Z.; Thornton, C.; Kodadek, T.J.; Disney, M.D. “Features of Modularly Assembled Compounds That Impart Bioactivity Against an RNA Target”, ACS Chemical Biology, 2013, 8(10) 2312–2321.;


7. Gao, Y.; Kodadek, T.J. “Synthesis and Screening of Stereochemically Diverse Combinatorial Libraries of Peptide Tertiary Amides”, Chemistry & Biology (now Cell Chemical Biology), Volume 20, Issue 3, 360-369, 2013.;



6. Wang, X.; Gao, Y.; Xu, Y.; Liu, J. “An efficient preparation of a photolabile agent MNI-glu by regioselective nitration of 4-methoxyindoline derivative”, Synthetic Communications, 41(2009), 15, 4030-4038.;



5. Gao, Y.; He, R.; He, Y.; Liu, T.; Qi, R.; Liu, G. “PEG-conjugated PAMAM dendrimers mediate efficient intramuscular gene expression”, The AAPS Journal, 11 (2009), 3, 395-405;



4. Gao, Y.; He, Y.; Liu, T.; Qi, R. “Recent Advances of Dendrimers in Delivery of Genes & Drugs”, Mini-Reviews in Medicinal Chemistry, 8 (2008), 889-900.; DOI:

3. Zhang, Q.; Gao, Y.; Zhai, Y.; Liu, F.; Gao, G. “Synthesis of sesbania gum supported dithiocarbamate chelating resin and studies on its adsorption performance for metal ions”, Carbonhydrate Polymers, 73(2), 2008, 359–363.;



2. Sun, H.; Gao, Y.; Zhai, Y.; Zhang, Q.; Liu, F.; Gao, G. “Recent Advances in Synthesis of Chiral Ionic Liquids”, Progress in Chemistry, 20 (2008), 698-712.


1. Zhai, Y.; Gao, Y.; Liu, F.; Zhang, Q.; Gao, G. “Synthesis of nanostructured TiO2 particles in room temperature ionic liquid and its photocatalytic performance”, Materials Letters, 61 (2007), 5056–5058;