Fangyuan Ding
University of California-Irvine, CA·Biophysics·Early-career
A single gene can make several different proteins. This happens through RNA splicing, in which the cell cuts and rejoins the RNA copy of a gene in different ways.
- Fields
Biophysics
Biomedical Engineering
Mathematics & Statistics
- Topics
RNA splicing
alternative splicing
RNA isoforms
- Grants
- 2 known grants, through Jul 2028
What they work on
- Develop SMOOTHY-FISH, a fluorescence in situ hybridization method that maps short RNA species such as splice isoforms, microRNAs and edited RNAs inside single cells with single-base specificity.
- Use magnetic tweezers to measure how fast and stably SMOOTHY-FISH probes bind and fold, and build a mechanistic model and platform that suggests reliable probe sets for any RNA target.
- Apply SMOOTHY-FISH to study how circular RNAs are produced alongside their linear isoforms, and explore whether circular RNA levels can be adjusted quantitatively.
- Build spatial stochastic reaction-diffusion models and inference pipelines that estimate rates of splicing and RNA degradation from static FISH images of RNA isoforms, testing competing splicing mechanisms.
More about the research
Healthy development depends on this flexibility, and splicing errors are linked to cancer and neurodegenerative diseases. Yet many important RNA forms are hard to see inside cells. These include alternative splice versions (isoforms), tiny microRNAs, edited RNAs and circular RNAs. They differ from related molecules by only short stretches of sequence, sometimes a single base. Watching splicing in living cells also tends to disturb the process itself. The research combines new imaging tools with mathematical models to map and time these RNA events in single cells.
Why it matters
RNA-based medicines have shown promise for hard-to-treat chronic and rare diseases. A low-cost tool that maps any RNA at single-base resolution, together with measured rules of splicing, could clarify how RNA regulation goes wrong in diseases such as cancer and neurodegeneration. Learning how circular RNA production can be tuned could lay groundwork for future therapies.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Closest labs
Jianyuan Zhang
Rutgers University-New Brunswick, NJ·Chemistry·Early-career
Build MRI contrast agents from metallobuckytrios, two gadolinium-filled carbon cages bonded to one C60, carrying biochemical ligands that bind cancer cells at multiple points, and test their image brightness, structural precision and metal safety.
Jie Xiao
Johns Hopkins University, MD·Biophysics
Measure how DNA supercoiling changes transcription speed and coupling between neighboring RNA polymerase molecules, using single-molecule imaging of purified RNA polymerase and DNA constructs.
Yufei Huang
University of Pittsburgh, PA·Computer Science
Develop a contrastive learning-based geometric graph attention model that learns gene expression patterns aware of tissue shape from single-cell spatial transcriptomics data, so that the patterns match the tissue structure seen in histology.
The school
University of California-Irvine: 46 labs on PI Pages, $645M a year on research, 524 research doctorates a year.
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