Research summaries and opinions from Kuan-Hao Chao.https://khchao.com/en-ushttps://khchao.com/posts/shorkie/https://khchao.com/posts/shorkie/The story behind Shorkie — a fungal DNA language model that learns the regulatory grammar of budding yeast and predicts how its genes turn on and off over time.Fri, 19 Sep 2025 00:00:00 GMTDNA language modelsGene expressionYeasthttps://khchao.com/posts/openspliceai/https://khchao.com/posts/openspliceai/The story behind OpenSpliceAI — a faithful, fast PyTorch reimplementation of SpliceAI that anyone can retrain on any species, and use to read the splicing impact of genetic variants.Sun, 01 Jun 2025 00:00:00 GMTRNA splicingDeep learningOpen sourcehttps://khchao.com/posts/lifton/https://khchao.com/posts/lifton/The story behind LiftOn — a genome-annotation tool that fuses DNA alignment (Liftoff) and protein alignment (miniprot) so you can carry accurate gene annotations onto a new assembly, even across species.Sat, 01 Feb 2025 00:00:00 GMTGenome annotationComparative genomicsOpen sourcehttps://khchao.com/posts/splam/https://khchao.com/posts/splam/The story behind Splam — a compact deep-learning model that scores a splice junction from its local sequence, more accurately than SpliceAI, and uses it to strip spurious alignments out of RNA-seq.Thu, 15 Aug 2024 00:00:00 GMTRNA splicingDeep learningRNA-seqhttps://khchao.com/posts/wgt/https://khchao.com/posts/wgt/The story behind the Wheeler Graph Toolkit — software to generate, recognize, and visualize Wheeler graphs, the elegant class of graphs that can be indexed and searched like a BWT, using a fast heuristic and an SMT solver.Fri, 14 Jul 2023 00:00:00 GMTPangenomicsAlgorithmsOpen sourcehttps://khchao.com/posts/han1/https://khchao.com/posts/han1/The story behind Han1 — the first gapless, reference-quality, fully annotated human genome from a Han Chinese individual, and what comparing two finished human genomes revealed.Wed, 01 Mar 2023 00:00:00 GMTGenome assemblyHuman genomeComparative genomicshttps://khchao.com/posts/sangeranalyser/https://khchao.com/posts/sangeranalyser/The story behind sangeranalyseR — a free, open-source R/Bioconductor package that takes you from raw .ab1 chromatograms to aligned consensus sequences in about four lines of code, with an interactive Shiny GUI.Mon, 01 Mar 2021 00:00:00 GMTSanger sequencingR / BioconductorOpen source