DNA language models
PreprintShorkie: reading yeast regulatory code with fungal DNA models
A compact fungal DNA language model for predicting budding-yeast RNA-seq coverage and regulatory variant effects.
Connected work
Projects
A project-level map of the papers, software, technical posts, talks, and reports behind my research.
Each project below collects the related outputs in one place: paper, code, docs, research summary, and technical notes where available.
Splice prediction
PublishedOpenSpliceAI: retrainable splice-site prediction in PyTorch
A modular PyTorch implementation of SpliceAI that can be retrained across species and used for genome-wide variant rescoring.
Genome annotation
PublishedLiftOn: combining DNA and protein evidence for genome annotation
A genome-annotation lift-over tool that combines DNA alignments with protein evidence to preserve accurate coding models.
Genomic databases
ReleasedGFFBase: high-performance genomic annotation engine
A high-performance genomic-annotation engine combining a SIMD Rust parser, DuckDB columnar backend, and zero-copy PyArrow interface.
RNA splicing
PublishedSplam: splice-junction recognition for cleaner RNA-seq alignments
A splice-junction recognizer designed to filter spurious RNA-seq junctions and improve downstream transcriptome assembly.
Genome assembly
PublishedHan1: a gapless Southern Han Chinese reference genome
A complete, reference-quality, fully annotated genome assembled from a Southern Han Chinese individual.
Pangenomics
PublishedWheeler Graph Toolkit: algorithms for pangenome indexing
A toolkit for recognizing, visualizing, generating, and repairing Wheeler graphs used in pangenome indexing.
Sequencing software
PublishedsangeranalyseR: reproducible Sanger sequencing workflows in R
An R/Bioconductor workflow and Shiny interface for trimming, assembling, inspecting, and reporting Sanger sequencing data.
RNA-seq analysis
PublishedRNASeqR: automated two-group RNA-Seq analysis workflow
An R package providing an end-to-end automated pipeline for two-group RNA-Seq analysis and visualization.
Diploid genomics
PublishedHG002: a complete diploid human genome benchmark
A complete diploid HG002 reference and benchmark with haplotype-resolved sequence and gene annotation.