[1] From 2000 to 2003, he joined Sunney Xie's lab at Harvard University as a postdoc, where he and others worked on the development of coherent anti-Stokes Raman scattering (CARS) microscopy.

[21] From 2013 onward, Cheng and his research team devised methods that allow for the rapid acquisition of Raman spectra at microsecond time scale per pixel, facilitating vibrational spectroscopic imaging of live organisms.

Through vibrational spectroscopic imaging on human patient samples, Cheng and his collaborators identified cholesteryl ester as a pervasive metabolic indicator of highly malignant cancers.

[26] In collaboration with Professor Michael Sturek at the Indiana University School of Medicine, his team developed intravascular vibration-based photoacoustic catheters that can perform video rate imaging of lipids in an arterial wall.

[31] His recent invention, single pulse digitization,[32] has facilitated real-time super-resolution infrared chemical imaging of living organisms at video rate.

[39] His group also unveiled a metabolic shift in melanoma from pigment-rich to lipid-rich as it progresses from primary to metastatic stages, potentially advancing the detection and treatment of this aggressive skin cancer.

[41] His team further expanded on their work to create a non-invasive brain modulation technique using optically generated focused ultrasound with extremely precise spatial targeting.

Under a lab-built transient absorption microscope, Cheng and his student Pu-Ting Dong accidentally found fast photobleaching of staphyloxanthin, a chromophore in methicillin-resistant S. aureus (MRSA).

[44] Cheng, along with his coworkers, further discovered that certain wavelengths of light can deactivate natural light-absorbing molecules in a broad spectrum of bacteria and fungi, enabling the development of a therapy that sensitizes drug-resistant infections to low levels of hydrogen peroxide.

His 2005 paper in PNAS indicates that gold nanorods, when excited at 830 nm, exhibit strong two-photon luminescence with polarization dependence, plasmon-enhanced absorption, and higher signal intensity than traditional fluorescent probes, making them promising candidates for in vivo imaging applications.

[48] His 2009 work highlighted the versatility of gold nanorods in the biomedical field, emphasizing their unique optical properties, surface chemistry control, and potential for both imaging and therapeutic applications, particularly in the context of cancer treatment.