Shorkie: learning yeast regulatory code from related fungi
Research summary13 min read
Shorkie tests how fungal pretraining, evolutionary scale, and fine-tuning on yeast regulatory assays help a compact DNA model read expression and variant effects.
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Research summaries and opinions — notes on the work I do and the ideas behind it.
OpenSpliceAI: retrainable splice-site prediction in PyTorch
Research summary7 min read
OpenSpliceAI rebuilds SpliceAI as a faithful PyTorch implementation that researchers can retrain across species and use to study variant effects on splicing.
LiftOn: combining DNA and protein evidence for genome annotation
Research summary12 min read
LiftOn carries annotations onto new assemblies by joining Liftoff DNA alignments with miniprot protein evidence, using protein maximization to preserve accurate coding models.
Splam: a splice-junction recognizer for cleaner RNA-seq alignments
Research summary9 min read
Splam grew from two needs: recognizing alternative splice junctions beyond one canonical transcript and filtering spurious RNA-seq junctions before transcript assembly.
WGT: algorithms for Wheeler graphs and pangenome indexing
Research summary9 min read
The Wheeler Graph Toolkit generates, recognizes, and visualizes Wheeler graphs, combining a fast heuristic with an SMT solver for graph structures behind pangenome indexes.
Han1: an algorithmic path to a complete annotated genome
Research summary9 min read
Han1 shows how long-read assembly, reference-guided gap closing, polishing, and annotation lift-over produced a gap-free Southern Han Chinese genome ready for gene-level comparison.
sangeranalyseR: making Sanger workflows reproducible in R
Research summary7 min read
sangeranalyseR turns ABIF or FASTA inputs into a reproducible R workflow for trimming reads, assembling consensus contigs, inspecting results, and exporting reports.
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