Research summaries and opinions from Kuan-Hao Chao.https://khchao.com/en-ushttps://khchao.com/posts/shorkie/https://khchao.com/posts/shorkie/Shorkie tests how fungal pretraining, evolutionary scale, and fine-tuning on yeast regulatory assays help a compact DNA model read expression and variant effects.Fri, 19 Sep 2025 00:00:00 GMTDNA language modelsGene expressionYeasthttps://khchao.com/posts/openspliceai/https://khchao.com/posts/openspliceai/OpenSpliceAI rebuilds SpliceAI as a faithful PyTorch implementation that researchers can retrain across species and use to study variant effects on splicing.Sun, 01 Jun 2025 00:00:00 GMTRNA splicingDeep learningOpen sourcehttps://khchao.com/posts/lifton/https://khchao.com/posts/lifton/LiftOn carries annotations onto new assemblies by joining Liftoff DNA alignments with miniprot protein evidence, using protein maximization to preserve accurate coding models.Sat, 01 Feb 2025 00:00:00 GMTGenome annotationComparative genomicsOpen sourcehttps://khchao.com/posts/splam/https://khchao.com/posts/splam/Splam grew from two needs: recognizing alternative splice junctions beyond one canonical transcript and filtering spurious RNA-seq junctions before transcript assembly.Thu, 15 Aug 2024 00:00:00 GMTRNA splicingDeep learningRNA-seqhttps://khchao.com/posts/wgt/https://khchao.com/posts/wgt/The Wheeler Graph Toolkit generates, recognizes, and visualizes Wheeler graphs, combining a fast heuristic with an SMT solver for graph structures behind pangenome indexes.Fri, 14 Jul 2023 00:00:00 GMTPangenomicsAlgorithmsOpen sourcehttps://khchao.com/posts/han1/https://khchao.com/posts/han1/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.Wed, 01 Mar 2023 00:00:00 GMTGenome assemblyHuman genomeComparative genomicshttps://khchao.com/posts/sangeranalyser/https://khchao.com/posts/sangeranalyser/sangeranalyseR turns ABIF or FASTA inputs into a reproducible R workflow for trimming reads, assembling consensus contigs, inspecting results, and exporting reports.Mon, 01 Mar 2021 00:00:00 GMTSanger sequencingR / BioconductorOpen source