Welcome to Ge Research Group!

The Ge lab at UW-Madison aims to understand the molecular and cellular mechanisms underlying cardiovascular diseases via systems biology approaches featuring cutting-edge high-resolution mass spectrometry (MS)-based comparative proteomics and metabolomics in conjunction with biochemical/biological/physiological functional studies.


Ying Ge, PhD

Associate Professor, Department of Cell and Regenerative Biology
Associate Professor, Department of Chemistry
Director of Mass Spectrometry
Human Proteomics Program
School of Medicine and Public Health
University of Wisconsin-Madison
Biographical Sketch

Faculty trainer, Translational Cardiovascular Science Training Program
Faculty trainer, Chemistry-Biology Interface Training Program
Faculty trainer, UW Graduate Program in Cellular and Molecular Biology
Faculty trainer, UW Graduate Program in Molecular and Cellular Pharmacology
Faculty trainer, UW Graduate Program in Cellular and Molecular Pathology
Faculty trainer, UW Molecular and Environmental Toxicology Training Program
Faculty trainer, UW Physiology Training Program

    News and Updates

  • Dec. 2017, Wenxuan (Vege) Cai won UW-Madison Cardiovascular Research Center (CVRC) poster award. Congratulations!
  • Dec. 2017, Stanford Mitchell, first year Molecular and Cellular Pharmacology student joined the group. Welcome!
  • Nov. 2017, Bifan Chen won CPSA USA 2017 Steven A. Hofstadler Graduate Student award. Congratulations!
  • August 22, 2017, Zachery Gregorich passed his doctoral defense. Congratulations to Dr. Gregorich! [Photos]
  • August 19, 2017, the Ge Group enjoyed the summer picnic in Devil's Lake State Park. [Photos]
  • August 6, 2017, the Ge Group enjoyed the summer group party in Ying's house. [Photos]
  • June 2017, the Ge Group attended the 65th ASMS conference in Indianapolis, IN. [Photos]
  • June 2017, Wenxuan (Vege) Cai, a 3rd year Molecular and Cellular Pharmacology (MCP) graduate student, was awarded a highly competitive American Heart Association Pre-doctoral fellowship. Congrats Vege!
  • April 13, 2017, Hannah Karp has received the Hilldale research fellowship. Congrats Hannah!
  • March 30, 2017, Hannah Karp has received the Mary Shine Peterson Undergraduate Award. Congrats Hannah!
  • March 17, 2017, Samantha Knott (first year Chembio student) is awarded NSF graduate student fellowship! Congrats to Sam!
  • Mar. 2017, Bifan Chen is awarded with the 2017 ASMS (American Society for Mass Spectrometry) Graduate Student Award. Congratulations!
  • Feb. 1, 2017, Trisha Tucholski is awarded a National Institutes of Health (NIH) Chemistry-Biology Interface Training Program (CBI) Traineeship. Congrats Trisha!

  • Dec 17 2016, the Ge group enjoyed the winter group party in WIMR. [Photos]
  • Nov. 2016, 1st year graduate students, Tim Tiambeng, Samantha Knott, and Stephanie Werner have joined our group. Welcome!
  • Oct. 2016, the Ge group enjoyed the fall picnic in the picnic point. [Photos]
  • Oct. 2016, Dr. Beini Lyu has joined our group as an honorary fellow. Welcome!
  • Oct. 2016, Prof. Ruixiang Liu, Dr. Fang Guo and Dr. Ya Liu have joined our group as visiting scholars. Welcome!
  • Anouncement: Professor Ying Ge and Professor Joe Loo (UCLA) are organizing a Uppcon2017 at Cornell. Check the conference website here! [ Uppcon 2017]
  • Aug. 2016, the Ge group enjoyed the summer's outing at the Devils Lake. [Photos]
  • Jun. 2016, the Ge Group attended the 64th ASMS conference in San Antonio. [Photos]
  • Apr. 2016, congratulations to Cyrus Colah on winning the Hilldale Undergraduate Fellowship! Thanks to Tania Guardado for being an excellent mentor!
  • Apr. 2016, Zach Gregorich is awarded with the 2016 ASMS (American Society for Mass Spectrometry) Graduate Student Award. Congratulations!
  • Mar. 2016, congratulations to our undergraduate student Rachel Heuer on receiving the Theodore Herfurth Sophomore Scholarship from the College of Letters and Science!
  • Jan. 2016, Yiwen Gu has joined the Ge Group. Welcome!

Most Recent Publications

  1. Gao, L.; Gregorich, Z. R.; Zhu, W.; Mattapally, S.; Lou, X.; Borovjagin, A. V.; Walcott, G. P.; Pollard, A. E.; Fast, V. G.; Ge, Y.; Zhang, J. Large cardiac-muscle patches engineered from human induced-pluripotent stem-cell–derived cardiac cells improve recovery from myocardial infarction in swine., Circulation, 2017, Epub ahead of print, DOI:10.1161/CIRCULATIONAHA.117.030785
  2. Chen, B.; Brown, K.A.; Lin, Z.; Ge, Y. Top-down proteomics: ready for prime time? Anal. Chem. 2017 Epub ahead of print, DOI: 10.1021/acs.analchem.7b04747. (Ge, Y. Corresponding author)
  3. Wei, L.; Gregorich, Z. R.; Lin, Z.; Cai, W.; Jin, Y.; McKiernan, S. H.; Mcilwain, S.; Aiken, J. M.; Moss, R. L.; Diffee, G. M.; Ge, Y. Novel sarcopenia-related alterations in sarcomeric protein post-translational modifications in skeletal muscles identified by top-down proteomics, Mol. Cell. Proteomics, Epub ahead of print, DOI: 10.1074/mcp.RA117.000124 (Ge, Y. Corresponding author)
  4. Hu, C.; Worth, M.; Fan, D.; Li, B.; Li, H.; Lu, L. Zhong, X.; Lin, Z.; Wei, L.; Ge, Y.; Li, L.; Jiang, J. Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase, Nat. Chem. Biol. Epub ahead of print. DOI: 10.1038/nchembio.2494.
  5. Rana, A. S. J. B.; Ge, Y.; Strieter, E. R. Ubiquitin chain enrichment middle-down mass spectrometry (ubichem-ms) reveals cell-cycle dependent formation of lys11/lys48 branched ubiquitin chains. J. Proteome Res.. 2017, 16 , 3363-3369. DOI: 10.1021/acs.jproteome.7b00381.
  6. Chen, B.; Guo, X.; Tucholski, T.; Lin, Z.; Mcilwain, S.; Ge, Y. The impact of phosphorylation on electron capture dissociation of proteins: a top-down perspective. J. Am. Soc. Mass Spectrom., 2017, 28, 1805–1814. DOI: 10.1007/s13361-017-1710-3 (Ge, Y. Corresponding author)
  7. Wu, C.-G., Chen, H., Guo, F., Yadav, V. K., McIlwain, S. J., Rowse, M., Choudhary, A., Lin, Z., Li, Y., Gu, T., Zheng, A., Xu, Q., Lee, W., Resch, E., Johnson, B., Day, J., Ge, Y., Ong, I. M., Burkard, M. E., Ivarsson, Y., Xing, Y. PP2A-B′ holoenzyme substrate recognition, regulation and role in cytokinesis. Cell Disc. 2017, 3, 17027. DOI:10.1038/celldisc.2017.27
  8. Gregorich Z. R.; Cai, W.; Lin, Z.; Chen, A. J.; Peng, Y.; Kohmoto, T.; Ge, Y. Distinct sequences and post-translational modifications in cardiac atrial and ventricular myosin light chains revealed by top-down mass spectrometry. J. Mol. Cell. Cardiol., 2017, 107, 13-21. DOI: 10.1016/j.yjmcc.2017.04.002. (Ge, Y. Corresponding author)
  9. Cai, W.; Tucholski, T.; Chen, B.; Alpert, A. J.; McIlwain, S.; Kohmoto, T.; Jin, S.; Ge, Y. Top–down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Anal Chem., 2017, 89, 5467-5475. DOI: 10.1021/acs.analchem.7b00380. (Ge, Y. Corresponding author)
  10. Jin, Y.; Wei, L.; Cai, W.; Lin, Z.; Wu, Z.; Peng, Y.; Kohmoto, T.; Moss, R. M.; Ge, Y. Complete Characterization of Cardiac Myosin Heavy Chain (223 kDa) Enabled by Size-Exclusion Chromatography and Middle-down Mass Spectrometry. Anal Chem., 2017, 89, 4922-4930. DOI: 10.1021/acs.analchem.7b00113. (Ge, Y. Corresponding author)
  11. Chen, B.; Hwang, L.; Ochowicz, W.; Lin, Z.; Guardado-Alvarez, T. M.; Cai, W.; Xiu, L.; Dani, K.; Colah, C.; Jin, S.; Ge, Y. Coupling Functionalized Cobalt Ferrite Nanoparticle Enrichment with Online LC/MS/MS for Top-down Phosphoproteomics. Chem. Sci., 2017, DOI: 10.1039/C6SC05435H. (Ge, Y. Corresponding author)
  12. Yang, L; Gregorich Z. R.; Cai, W.; Zhang, P; Young, B; Gu, Y; Zhang, J; Ge, Y. Quantitative Proteomics and Immunohistochemistry Reveal Insights into Cellular and Molecular Processes in the Infarct Border Zone One Month after Myocardial Infarction. J. Proteome Res., 2017, 16, 2101-2112. DOI: 10.1021/acs.jproteome.7b00107. (Ge, Y. Corresponding author)
  13. Crowe, S. O.; Rana, A. S.; Deol, K. K.; Ge, Y.; Strieter, E. R. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains in Cellulo. Anal Chem., 2017, 89, 4428-4434. DOI: 10.1021/acs.analchem.6b03675.
  14. Gregorich Z. R.; Cai, W.; Jin, Y.; Wei, L.; Chen, A. J.; McKiernane, S. H.; Aiken, J. M.; Moss, R. L.; Diffee, G. M.; Ge, Y. Top-down targeted proteomics reveals decrease in myosin regulatory light chain phosphorylation that contributes to sarcopenic muscle dysfunction. J. Proteome Res., 2016, 15 (8), pp 2706–2716. DOI: 10.1021/acs.jproteome.6b00244. (Ge, Y. Corresponding author)
  15. Crowe, S.O.; Pham, G.H.; Ziegler, J.C.; Deol, K.K.; Guenette, R.G.; Ge, Y.; Strieter, E.R. Subunit-specific labeling of ubiquitin chains by using sortase: insights into the selectivity of deubiquitinases. ChemBioChem., 2016, 17(16):1525-31. DOI: 10.1002/cbic.201600276.
  16. Cai, W.; Tucholski, T. M.; Gregorich Z. R.; Ge, Y. Top-down proteomics: technology advancements and application to heart diseases. Expert Rev. Proteomics., 2016, 13, 717-730. DOI: 10.1080/14789450.2016.1209414 (Ge, Y. Corresponding author)
  17. Jin, Y.; Peng, Y.; Lin, Z.; Chen, Y. C.; Wei, L.; Hacker, T. A.; Larsson, L.; Ge, Y. Comprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics. J Muscle Res Cell Motil., 2016, 37(1-2):41-52. DOI: 10.1007/s10974-016-9443-7. (Ge, Y. Corresponding author)
  18. Hwang, L.; Guardado-Alvarez†, T.; Ayaz-Gunner, S.; Ge, Y.; Jin S. A Family of Photolabile Nitroveratryl-Based Surfactants That Self-Assemble into Photodegradable Supramolecular Structures. Langmuir, 2016, 32 (16): pp 3963–3969. (Ge, Y. Corresponding author)
  19. Chen, B.; Peng, Y.; Valeja, S. G.; Xiu, L.; Alpert, A. J.; Ge, Y. Online Hydrophobic Interaction Chromatography-Mass spectrometry for Top-down Proteomics. Anal. Chem. 2016, 88(3):1885-91. (Ge, Y. Corresponding author)
  20. Cai, W.; Guner, H.; Gregorich, Z. R.; Chen, A. J.; Ayaz-Guner, S.; Peng, Y.; Valeja, S. G.; Liu, X.; Ge, Y. MASH Suite Pro: A Comprehensive Software Tool for Top-down Proteomics. Mol. Cell. Proteomics. 2016, 15(2):703-14. (Ge, Y. Corresponding author)
  21. Yu, D.; Peng, Y.; Ayaz-Guner, S.; Gregorich Z. R.; Ge, Y. Comprehensive characterization of AMP-activated protein kinase catalytic domain by top-down mass spectrometry. J. Am. Soc. Mass Spectrom. 2016, 27(2): 220-232 (Ge, Y. Corresponding author)
  22. Gregorich Z. R.; Peng, Y.; Wolff, J. J.; Guo, W.; Guner, H.; Doop, J.; Hacker, T. A.; Ge, Y. Comprehensive assessment of regional and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. J. Mol. Cell. Cardiol. 2015, 87, 103-112. (Ge, Y. Corresponding author)
  23. Chen, Y.-C.; Ayaz-Guner, S.; Peng, Y.; Lane, M. L.; Locher, M.; Larsson, L.; Kohmoto, T.; Moss, R. L.; Ge, Y. A top-down LC/MS+ method for assessing actin isoforms as a potential cardiac disease marker. Anal Chem. 2015, 87(16): 8399-406. (Ge, Y. Corresponding author)
  24. Chang, Y. H.; Ye, L.; Cai, W.; Lee, Y.; Guner, H.; Lee, Y.; Kamp, T. J.; Zhang, J.; Ge, Y. Quantitative Proteomics Reveals Differential Regulation of Protein Expression in Recipient Myocardium after Trilineage Cardiovascular Cell Transplantation. Proteomics. 2015, 15, 2560-2567 DOI: 10.1002/pmic.201500131. (Ge, Y. Corresponding author)
  25. Valeja, S. G.; Xiu, L.; Gregorich, Z. R.; Guner, H.; Jin, S.; Ge, Y. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal Chem. 2015, 87(10), 5363-71. (Ge, Y. Corresponding author)
  26. Hwang, L.; Ayaz-Guner, S.; Cai, W.; Gregorich Z. R.; Jin, S.; Ge, Y. Specific enrichment of phosphoproteins using functionalized multivalent nanoparticles. J. Am. Chem. Soc., 2015, 87, 5363-5371. (Ge, Y. Corresponding author)
  27. Chang, Y.; Gregorich Z. R.; Chen, A. J.; Hwang L.; Guner, H.; Yu, D.; Zhang, J.; Ge, Y. New mass spectrometry-compatible degradable surfactant for tissue proteomics. J. Proteome Res., 2015, 14, 1587-1599. (Ge, Y. Corresponding author)
  28. Chen, Y.; Sumandea, M. P.; Larsson, L.; Moss, R. L.; Ge, Y. Dissecting human skeletal muscle troponin proteoforms by top-down mass spectrometry. J. Muscle Res. Cell Motil., 2015, 36, 168-181. (Ge, Y. Corresponding author)

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