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.

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Ying Ge, PhD

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

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

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    News and Updates

  • August 2024, Dr. Timothy Aballo successfully defended his thesis and is now a member of the AbbVie team. Hold onto your hat in the windy city!
  • July 2024, Dr. Melissa Pergande has rolled over to a tenure-track position at Boston University. We'll miss you, big dog!
  • May 2024, longtime undergraduate research assistant Brad Li graduated and is headed to Vanderbilt University School of Medicine! Congratulations and good luck!
  • May 2024, Dr. Benjamin Wancewicz successfully defended his thesis. We're excited to see you fly high!
  • May 2024, Registration and Abstract submission is now open for the Wisconsin Human Proteomics Symposium to be held in Madison, WI, July 31 - Aug. 1, 2024. Register and submit your abstract here: [Link]
  • April 2024, Mallory Wilson was awarded the highly competitive NSF GRFP! Congratulations!
  • April 2024, Congratulations to Matthew Fischer and Andrew Perciaccante for being awarded highly competitive Honorable Mentions by the NSF GRFP!
  • March 2024, Congratulations to alumni Dr. David S. Roberts for winning an ASMS Postdoctoral Career Development Award, Emily Chapman for receiving an ASMS Graduate Student Award, and Brad Li for receiving an ASMS Undergraduate Student Award! A clean sweep for the Ge Group!
  • December 2023, Liam Bandura and Andrew Perciaccante joined our lab from the Chemistry program! Welcome to the Ge Group!
  • August 2023, Morgan Mann successfully defended his thesis and is starting a clinical fellowship in California. You da man(n)!
  • Aug. 2023, It is with heavy hearts and profound respect that we announce this Dr. Andrew J. Alpert memorial symposium on Sept. 13-15, 2023, to honor the life and legacy of the esteemed Dr. Andrew J. Alpert. Dr. Alpert was a brilliant scientist, a dedicated mentor, a devoted collaborator, and a legend in the field of chromatography. Dr. Alpert was a long-time collaborator and an honorary member of our group. The conference website is now available. [Link].
  • July 2023, Eli Larson successfully defended his thesis and is now moving on to bluer waters at Merck. We’re so grateful we had the oppor-tuna-ty to know you!
  • July 2023, Elizabeth Bayne successfully defended her thesis and headed back east to a position at Merck. We’ll miss our dancing queen!
  • May 2023, Jake's high sensitivity paper on single muscle cell heterogeneity in large proteoforms was published in PNAS! [Link]
  • May 2023, David S. Roberts successfully defended his thesis and is moving on to post-doc at Stanford. May the force be with you!
  • April 2023, Jake Melby successfully defended his thesis and is moving on to a position at AstraZeneca. We wish you all the best!
  • March 2023, Congratulations to ELI J LARSON on winning the Chemistry Department Gary Parr Award!
  • March 2023, Congratulations to DAVID S ROBERTS on winning the Chemistry Department Ivanisevic award!
  • March 2023, Elizabeth Bayne won an ASMS Graduate Student Travel Award. Congratulations!
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Most Recent Publications

  1. Roberts, D. S.; Loo, J. A.; Tsybin, Y. O.; Liu, X.; Wu, S.; Chamot-Rooke, J.; Agar, J. N.; Paša-Tolić, L.; Smith, L. M.; Ge, Y., Top-down proteomics. Nature Reviews Methods Primers 2024, 4 (1), 38. Article
  2. Wang, Y.; Zhao, M.; Liu, X.; Xu, B.; Reddy, G. R.; Jovanovic, A.; Wang, Q.; Zhu, C.; Xu, H.; Bayne, E. F.; Xiang, W.; Tilley, D. G.; Ge, Y.; Tate, C. G.; Feil, R.; Chiu, J. C.; Bers, D. M.; Xiang, Y. K., Carvedilol Activates a Myofilament Signaling Circuitry to Restore Cardiac Contractility in Heart Failure. JACC: Basic to Translational Science 2024. Article
  3. Habeck, T.; Brown, K. A.; Des Soye, B.; Lantz, C.; Zhou, M.; Alam, N.; Hossain, M. A.; Jung, W.; Keener, J. E.; Volny, M.; Wilson, J. W.; Ying, Y.; Agar, J. N.; Danis, P. O.; Ge, Y.; Kelleher, N. L.; Li, H.; Loo, J. A.; Marty, M. T.; Paša-Tolić, L.; Sandoval, W.; Lermyte, F., Top-down mass spectrometry of native proteoforms and their complexes: a community study. Nature Methods 2024. Article
  4. Stroik, D.; Gregorich, Z. R.; Raza, F.; Ge, Y.; Guo, W., Titin: roles in cardiac function and diseases. Front Physiol 2024, 15, 1385821. Article
  5. Anderson, C. L.; Brown, K. A.; North, R. J.; Walters, J. K.; Kaska, S. T.; Wolff, M. R.; Kamp, T. J.; Ge, Y.; Eckhardt, L. L., Global Proteomic Analysis Reveals Alterations in Differentially Expressed Proteins between Cardiopathic Lamin A/C Mutations. Journal of Proteome Research 2024,23 (6), 1970-1982. Article
  6. Wancewicz, B.; Pergande, M. R.; Zhu, Y.; Gao, Z.; Shi, Z.; Plouff, K.; Ge, Y., Comprehensive Metabolomic Analysis of Human Heart Tissue Enabled by Parallel Metabolite Extraction and High-Resolution Mass Spectrometry. Anal Chem 2024,96 (15), 5781-5789. Article
  7. Rossler, K. J.; de Lange, W. J.; Mann, M. W.; Aballo, T. J.; Melby, J. A.; Zhang, J.; Kim, G.; Bayne, E. F.; Zhu, Y.; Farrell, E. T.; Kamp, T. J.; Ralphe, J. C.; Ge, Y., Lactate- and immunomagnetic-purified hiPSC-derived cardiomyocytes generate comparable engineered cardiac tissue constructs. JCI Insight, 2024, Article
  8. Chapman, E. A.; Li, B. H.; Krichel, B.; Chan, H.-J.; Buck, K. M.; Roberts, D. S.; Ge, Y. Native Top-Down Mass Spectrometry for Characterizing Sarcomeric Proteins Directly from Cardiac Tissue Lysate. J. Am. Soc. Spectr. 2024, Article
  9. Bayne, E. F.; Buck, K. M.; Tower, A. G.; Zhu, Y.; Pergande, M. R.; Zhou, T.; Price, S.; Rossler, K. J.; Morales-Tirado, V.; Lloyd, S.; Wang, F.; He, Y.; Tian, Y.; Ge, Y. High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF. J Proteome Res 2024, Article
  10. Paltzer, W. G.; Aballo, T. J.; Bae, J.; Flynn, C. G. K.; Wanless, K. N.; Hubert, K. A.; Nuttall, D. J.; Perry, C.; Malawi, R.; Ge, Y.; Mahmoud, A. I., mTORC1 regulates the metabolic switch of postnatal cardiomyocytes during regeneration. J. Mol. Cell. Cardiol. 2024 Article
  11. Rogers, H. T.; Melby, J. A.; Ehlers, L. E.; Fischer, M. S.; Larson, E. J.; Gao, Z.; Rossler, K. J.; Wang, D.; Alpert, A. J.; Ge, Y. Small-Scale Serial Size Exclusion Chromatography (s3SEC) for High Sensitivity Top-Down Proteomics of Large Proteoforms. Anal. Chem. 2024 Article
  12. Chapman, E. A.; Roberts, D. S.; Tiambeng, T. N.; Andrews, J.; Wang, M.-D.; Reasoner, E. A.; Melby, J. A.; Li, B. H.; Kim, D.; Alpert, A. J.; Jin, S.; Ge, Y. Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics. Nature Communications 2023, 14, 8400. Article
  13. Brown, K. A.; Morris, R. K.; Eckhardt, S. J.; Ge, Y.; Gellman, S. H. Phosphorylation Sites of the Gastric Inhibitory Polypeptide Receptor (GIPR) Revealed by Trapped-Ion-Mobility Spectrometry Coupled to Time-of-Flight Mass Spectrometry (TIMS-TOF MS). J. Am. Chem. Soc. 2023, Epub ahead of Print Article
  14. West, K. H. J.; Ma, S. V.; Pensinger, D. A.; Tucholski, T.; Tiambeng, T. N.; Eisenbraun, E. L.; Yehuda, A.; Hayouka, Z.; Ge, Y.; Sauer, J.; Blackwell, H. E. Characterization of an Autoinducing Peptide Signal Reveals Highly Efficacious Synthetic Inhibitors and Activators of Quorum Sensing and Biofilm Formation in Listeria monocytogenes. Biochemistry. 2023. Article
  15. Lermyte, F.; Habeck, T.; Brown, K.; Des Soye, B.; Lantz, C.; Zhou, M.; Alam, N.; Hossain, M.A.; Jung, W.; Keener, J.; Volny, M.; Wilson, J.; Ying, Y.; Agar, J.; Danis, P.; Ge, Y.; Kelleher, N.; Li, H.; Loo, J.; Marty, M.; Pasa-Tolic, L.; Sandoval, W. Top-down mass spectrometry of native proteoforms and their complexes: A community study. Under review at Nature Portfolio. 2023. PREPRINT
  16. Wancewicz, B.; Zhu, Y.; Fenske, R.J.; Weeks, A.M.; Wenger, K.; Pabich, S.; Daniels, M.; Punt, M.; Nall, R.; Peter, D.C.; Brasier, A.; Cox, E.D.; Davis, D.B.; Ge, Y.; Kimple, M.E. Metformin monotherapy alters the human plasma lipidome independent of clinical markers of glycemic control and cardiovascular disease risk in a type 2 diabetes clinical cohort. Journal of Pharmacology and Experimental Therapeutics. 2023. Article
  17. Yan, J.; Wu, Q.; Maity, M.; Braun, D.R.; Alas, I.; Wang, X.; Ying, X.; Zhu, Y.; Bell, B.A.; Rajski, S.R.; Ge, Y.; Richardson, D.D.; Zhong, W.; Bugni, T.S. Rapid Unambiguous Structure Elucidation of Streptnatamide A, a New Cyclic Peptide Isolated from A Marine-derived Streptomyces sp. Chemistry -A European Journal. 2023. Article
  18. Pergande, M. R.; Osterbauer, K. J.; Buck, K. M.; Roberts, D. S.; Wood, N. N.; Balasubramanian, P.; Mann, M. W.; Rossler, K. J.; Diffee, G. M.; Colman, R. J.; Anderson, R. M.; Ge, Y. Mass Spectrometry-Based Multiomics Identifies Metabolic Signatures of Sarcopenia in Rhesus Monkey Skeletal Muscle. Journal of Proteome Research 2023.Article
  19. Melby, J.A.; Brown, K.A.; Gregorich, Z.R.; Roberts, D.S.; Chapman, E.A.; Ehlers, L.E.; Gao, Z.; Larson, E.J.; Jin, Y.; Lopez, J.R.; Hartung, J.; Zhu, Y.; McIlwain, S.J.; Wang, D.; Guo, W.; Diffee, G.M.; Ge, Y. High sensitivity top-down proteomics captures single muscle cell heterogeneity in large proteoforms. PNAS. 2023, 120(19), e2222081120. Article
  20. Rossler, K.J.; de Lange, W.; Mann, M.W.; Aballo, T.J.; Melby, J.A.; Zhang, J.; Kim, G.; Bayne, E.F.; Zhu, Y.; Farrell, E.T.; Kamp, T.J.; Ralphe, J.C.; Ge, Y. Lactate and Immunomagnetic-purified iPSC-derived Cardiomyocytes Generate Comparable Engineered Cardiac Tissue Constructs. JCI Insight. 2023. Article
  21. Rogers, H.T.; Roberts, D.S.; Larson, E.J.; Melby, J.A.; Rossler, K.J.; Carr, A.V.; Brown, K.A.; Ge, Y. Comprehensive Characterization of Endogenous Phospholamban Proteoforms Enabled by Photocleavable Surfactant and Top-down Proteomics. Anal. Chem. 2023. Article
  22. Wancewicz, B.; Zhu, Y.; Fenske, R.K.; Weeks, A.M.; Wenger, K.; Pabich, S.; Daniels, M.; Punt, M.; Nall, R.; Peter, D.C.; Brasier, A.; Cox, E.D.; Davis, D.B.; Ge, Y.; Kimple, M. Metformin Monotherapy Alters the Human Plasma Lipidome Independent of Clinical Markers of Glycemic Control and Cardiovascular Disease Risk in a Type 2 Diabetes Clinical Cohort. J. of Pharmacology and Exp. Therapeutics. 2023. Article
  23. Aballo, T. J.; Roberts, D.S.; Bayne, E. F.; Zhu, W.; Walcott, G.; Mahmoud, A. I.; Zhang, J.; Ge, Y. Integrated Proteomics Reveals Alterations in Sarcomere Composition and Developmental Processes during Postnatal Swine Heart Development, J. Mol. Cell. Cardiol. 2023, 176, 33-40 Article
  24. Larson, E.J. ; Pergande, M. R; Moss, M. E.; Rossler, K. J.; Wenger, R. K.; Krichel, B.; Josyer, H.; Melby, J. A.; Roberts, D. S.; Pike, K.; Shi, Z.; Chan, H.; Knight, B.; Rogers, H. T.; Brown, K. A.; Ong, I. M.; Kyowon Jeong, K.; Marty, M.; McIlwain, S. J.; Ge, Y. MASH Native: A Unified Solution for Native Top-Down Proteomics Data Processing bioRxiv 2023, doi: 10.1101/2023.01.02.522513 Article
  25. Mann, M.; Fu, Y.; Xu, X.; Roberts, D.S.; Li, Y.; Zhou, J., Ge, Y.; Brasier, A.R. Bromodomain-containing Protein 4 Regulates Innate Inflammation in Airway Epithelial Cells via Modulation of Alternative Splicing. Front. Immunol., 2023, 14, Article
  26. Chapman, E.; Aballo, J. J.; Melby, J.A.; Zhou, T.; Price, S. J.; Rossler, K. J.; Lei, I.; Tang, P. C.; Ge, Y. Defining the Sarcomeric Proteoform Landscape in Ischemic Cardiomyopathy by Top-down Proteomics, J. Proteome Res. 2023, 22, 931-941 Article
  27. Bayne, E.F.; Rossler, K. J.; Gregorich, Z. R.; Aballo, T. J.; Roberts, D.S.; Chapman, E. A.;Guo, W.; Ralphe, J.C.; Kamp, T.J.; Ge, Y. Top-down Proteomics of Myosin Light Chain Isoforms Define Chamber-Specific Expression in the Human Heart, J Mol Cell Cardiol 2023, 181, 89-97. Article
  28. Brown, K. A.; Gugger, M. K.; Roberts, D. S.; Moreno, M.; Chae, P. S.; Ge, Y.; Jin, S. Synthesis, Self-Assembly Properties, and Degradation Characterization of a Nonionic Photocleavable Azo-Sulfide Surfactant Family, Langmuir, 2023, DOI: 10.1021/acs.langmuir.2c02820 Article
  29. Wu, Q.; Bell, B.A.; Yan, J.; Chevrette, M.G.; Brittin, N.J.; Zhu, Y.; Chanana, S.; Maity, M.; Braun, D.R.; Wheaton, A.M.; Guzei, I.A.; Ge, Y.; Rajski, S.R.; Thomas, M.G.; Bugni, T.S.; SR Metabolomics and Genomics Enable the Discovery of a New Class of Nonribosomal Peptidic Metallophores from a Marine Micromonospora. J. Am. Chem. Soc. 2023, 145, 58–69. Article
  30. Brown, K.A.; Gugger, M.; Yu, Z.; Moreno, D.; Jin, S.; Ge, Y. A Nonionic, Cleavable Surfactant for Native Mass Spectrometry and Top-down Proteomics, Anal. Chem. 2023, 95, 1801–1804 Article
  31. Wu, Q.; Bell, B.A.; Yan, J.; Chevrette, M.G.; Brittin, N.J.; Zhu, Y.; Chanana, S.; Maity, M.; Braun, D.R.; Wheaton, A.M.; Guzei, I.A.; Ge, Y.; Rajski, S.R.; Thomas, M.G.; Bugni, T.S.; SR Metabolomics and Genomics Enable the Discovery of a New Class of Nonribosomal Peptidic Metallophores from a Marine Micromonospora. J. Am. Chem. Soc., 2022, Online ahead of print. Article
  32.  Sun M.; Jin Y.; Zhang Y.; Gregorich Z.R.; Ren J.; Ge Y.; Guo W.; SR Protein Kinases Regulate the Splicing of Cardiomyopathy-Relevant Genes via Phosphorylation of the RSRSP Stretch in RBM20. Genes, 2022, 13(9), 1526. Article.
  33.  Roberts, D.S.; Mann, M.; Li, B.H.; Kim, D.; Brasier, A.R.; Jin, S. Ge, Y. Distinct Core Glycan and O-Glycoform Utilization of SARS-CoV-2 Omicron Variant Spike Protein RBD Revealed by Top-Down Mass Spectrometry. Chem. Sci. 2022, Epub ahead of print. Article.
  34.  Larson, E.J.; Gregorich, Z.R.; Zhang, Y.; Li, B.H.; Aballo, T.J.; Melby, J.A.; Ge, Y.; Guo, W. RBM20 Ablation is Associated With Changes in The Expression of Titin-Interacting and Metabolic Proteins. Molecular Omics, 2022. Article.
  35. Gupta, K.; Brown, K.A.; Hsieh, M.L.; Hoover, B.; Wang, J.; Khoury, M.K.; Pilli, V.S.S.; Beyer, R.S.; Voruganti, N.R.; Chaudhary, S.; Roberts, D.S.; Murphy, R.M.; Hong, S.; Ge, Y.; Liu, B. Necroptosis is associated with Rab27-independent expulsion of extracellular vesicles containing RIPK3 and MLKL. Journal of Extracellular Vesicles, 2022, 11, e12261. Article.
  36. Zhu, Y.; Esnault, S.; Ge, Y.; Jarjour, N.N; Brasier, A.R. Airway fibrin formation cascade in allergic asthma exacerbation: implications for inflammation and remodeling. Clin Proteomics. 2022, 19(1), 15. Article.
  37. Zhu, Y.; Esnault, S.; Ge, Y.; Jarjour, N.N.; Brasier, A.R. Segmental Bronchial Allergen Challenge Elicits Distinct Metabolic Phenotypes in Allergic Asthma. Metabolites, 2022, 12(5), 381. Article.
  38. Tiambeng, T.N.; Wu, Z.; Melby, J.A.; Ge, Y. Size Exclusion Chromatography Strategies and MASH Explorer for Large Proteoform Characterization. Methods Mol Biol. 2022, 2500, 15-30. Article.
  39. Zhang, Y.; Wang, C.; Sun, M.; Jin, Y.; Braz, C.U.; Khatib, H.; Hacker, T.A.; Liss, M.; Gotthardt, M.; Granzier, H.; Ge, Y.; Guo, W. RBM20 phosphorylation and its role in nucleocytoplasmic transport and cardiac pathogenesis. FASEB Journal, 2022, Epub ahead of print. Article.
  40. Buck, K.M.; Roberts, D.S.; Aballo, T.J.; Inman, D.R.; Jin, S.; Ponik, S.; Brown, K.A.; Ge, Y. One-Pot Exosome Proteomics Enabled by a Photocleavable Surfactant. Anal. Chem., 2022, 94, 7164-7168. Article.
  41. Li, A.; Campbell, K.; Lal, S.; Ge, Y.; Keogh, A.; Macdonald, P.S.; Lau, P.; Linke, W.A.; Van der Velden, J.; Field, A.; Martinac, B.; Grosser, M.; dos Remedios, C. Peripartum cardiomyopathy: a global effort to find the cause and cure for the rare and little understood disease Biophysical Reviews. 2022, 14, 369-379. Article.

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