Yun Yu
Carnegie Mellon University, PA·Computer Science
Comparing DNA sequences underlies much of biology. It is how genomes are assembled from short reads, how species are related, and how genes jumping between bacteria are spotted.
- Fields
Computer Science
Genetics
Mathematics & Statistics
- Topics
bioinformatics
computational biology
string algorithms
- Grants
- 2 known grants, through Aug 2030
What they work on
- Combine k-mer sketching theory with alphabet reductions to develop provable methods for fast similarity search between more distant sequences, such as those in protein databases.
- Extend the skani and skandiver approach to detect small and within-species mobile genetic elements in microbial genomes and annotate their boundaries.
- Prove average-case speed and accuracy bounds for the seed-chain-extend alignment algorithm under realistic error models that include insertions, deletions, duplications and subsampling.
- Use probabilistic subsampling to speed up RNA-seq quantification without mapping every read, and to filter candidate reads for more accurate discovery of novel RNA isoforms.
More about the research
Exact matches are easy to find, but real sequences differ through mutation and sequencing errors, and approximate matches are much harder. Fast software uses tricks that transform sequences, such as sketching (keeping a small sample of short subsequences called k-mers), but these tricks are often used without proof that they work. The lab's grants combine mathematical theory of these transformations with building practical bioinformatics software.
Why it matters
Microbial genome databases are growing faster than the software that analyzes them. Faster and more accurate tools could help researchers track mobile genetic elements that move between bacterial species and spot new protein-coding RNA isoforms. Proven guarantees let software developers build analysis tools they can trust.
Known grants
From NIH and NSF research grants. Labs often have other funding we can't see.
Closest labs
Todd Treangen
Rice University, TX·Computer Science·Early-career
Identify yet-unseen pathogens by linking taxonomy-based classification of sequences with genes whose functions are of concern, so that novel threats can be recognized in sequencing data.
Emile Gluck-Thaler
University of Wisconsin-Madison, WI·Genetics
Determine how rates of horizontal Starship transfer between fungi change in response to different environmental cues, using a newly developed laboratory transfer assay.
Lenore Pipes
University of Hawaii at Manoa, HI·Computer Science·Early-career
Replace arbitrary species-assignment cut-offs in the tronko phylogenetic placement software with local thresholds based on Bayesian estimates of effective population size across the tree.
The school
Carnegie Mellon University: 28 labs on PI Pages, $505M a year on research, 346 research doctorates a year.
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