Ge joined the University of Wisconsin–Madison as an assistant scientist, where she oversaw the mass spectrometry programme. She became an Associate Professor in 2015, and full Professor in 2019.
Ge develops high-resolution mass spectrometry proteomics to better understand cardiac disease.  To image the very large proteins of human heart tissue, Ge combines fourier-transform ion cyclotron resonance (FT–ICR) mass spectrometry with electron-capture dissociation. She has worked to create a top-down disease proteomic platform that allows for the separation, detection and characterisation of the biomarkers of heart damage.
Nanoproteomics, a technique developed by Ge and co-workers, makes use of nanoparticles and high resolution mass spectrometry to capture and characterise cardiac troponins, including troponin I. Being able to test for and characterise troponin I would help with the early detection and diagnosis of heart disease. The peptide-functionalised superparamagnetic nanoparticles are combined with top-down mass spectrometry to identify the molecular fingerprints of troponins. Rather than just detecting cardiac troponins, which is possible using ELISA-based antibody testing, this higher level of characterisation will allow Ge to identify various forms of modified troponins, allowing a personalised understanding of cardiac disease.
Ge served on the board of the Top-Down Proteomics Consortium, on the editorial board of the Journal of Muscle Research and Cell Motility, as treasurer for the American Society for Mass Spectrometry (2016-2018).
[https://scholar.google.com/citations?user=Ymgpd5QAAAAJ&hl=en&oi=sra Ying Ge] publications indexed by Google Scholar.