Writing
Research summaries and opinions — notes on the work I do and the ideas behind it.
Research summary9 min read
The T2T Consortium finished both haplotypes of HG002 and released them as a benchmark. What the paper shows, how the two haplotypes were annotated, and the step of that annotation I contributed.
Research summary14 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.
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.
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.
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.
Research summary10 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.
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.
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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