Gene expression
Modeling gene regulation from DNA sequence
I study how sequence-to-function models can learn regulatory logic, predict expression across biological conditions, and reveal which parts of DNA shape molecular phenotypes.
What I work on
Research
I develop computational methods for reading, organizing, and comparing genomes — from models of gene regulation and RNA splicing to algorithms for annotation, assembly, and graph indexing.
Research areas
RNA splicing
Learning the rules of RNA splicing
I develop computational models of splice sites and junctions, with an emphasis on sequence context, cross-species transfer, variant effects, and reliable evidence for transcript reconstruction.
Genome annotation
Building accurate genome annotations
I develop LiftOn, a genome annotation lift-over algorithm that combines DNA and protein alignments to transfer accurate gene models across assemblies and species.
Genome assembly
Building complete and diverse reference genomes
I study how complete and diverse reference genomes become biologically useful, from assembling and annotating Han1 to annotating haplotype-resolved diploid genomes.
Pangenome indexing
Indexing genomic diversity with sequence graphs
I study graph representations and indexing algorithms that make collections of diverse genomes compact, searchable, and computationally practical.