Jason Fan

The paper introduces mehenDi, a tree-based differential testing method for RNA-Seq that accounts for inferential uncertainty, improving detection of differentially expressed transcripts and inner nodes.

The paper introduces lossless compression methods for colored de Bruijn graphs, reducing memory usage while maintaining query efficiency.

Fulgor is a compact k-mer index for efficient sequence matching and color queries, outperforming existing methods in space and speed.

The paper introduces a new data structure, Mac-dBG, that improves space efficiency for colored de Bruijn graphs by compressing color representations, while maintaining query efficiency.

The paper introduces a method to reduce the space required for reference indexing by using spectrum preserving tilings and sampling schemes, achieving significant space savings with minimal query slowdown.

This paper introduces a method to transfer knowledge across species by integrating sequence and network structure to create functional embeddings of proteins, showing improved cross-species functional similarity and phenolog prediction.