Selected publications
Dirichlet Diffusion Score Model for Biological Sequence Generation
Introduces a diffusion model for discrete biological sequences, with applications to constrained sequence generation and human promoter design. Published at ICML (2023). Paper
A Complete Reference Genome Improves Analysis of Human Genetic Variation
Collaborative work showing how the T2T-CHM13 human reference improves mapping and variant analysis. Published in Science (2022). DOI
Comparative Genomics Meets Topology: a Novel View on Genome Median and Halving Problems
Uses topological ideas to formulate and study genome median and halving problems. Published in BMC Bioinformatics (2016). DOI
Recent software
Generative biology
DDSM
Dirichlet diffusion score models for generating discrete biological sequences under complex constraints.
3D genomics · Rust
rs-hicproj
Rust tools for working with Hi-C contact matrices and related genomic data.