Papers, talks, releases, and milestones from Kuan-Hao Chao.https://khchao.com/en-ushttps://probgen2026.github.io/https://probgen2026.github.io/Excited to share that I’ll be giving a talk in the **Machine Learning in Genomics** session at the [Probabilistic Modeling in Genomics Conference 2026](https://probgen2026.github.io/) at [UC Berkeley](https://en.wikipedia.org/wiki/University_of_California,_Berkeley)! My talk is titled *“Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.”*Thu, 12 Feb 2026 00:00:00 GMTtalkhttps://doi.org/10.7554/eLife.107454.3https://doi.org/10.7554/eLife.107454.3Our OpenSpliceAI **Version of Record** is now published in [eLife](https://doi.org/10.7554/eLife.107454.3)—an open-source PyTorch framework for fast, modular splice-site prediction, transfer learning, and variant-effect scoring! Check out the [GitHub](https://github.com/Kuanhao-Chao/OpenSpliceAI) and [docs](https://ccb.jhu.edu/openspliceai/).Thu, 30 Oct 2025 00:00:00 GMTpublicationhttps://doi.org/10.1101/2025.09.19.677475https://doi.org/10.1101/2025.09.19.677475I’m excited to share our new [preprint](https://doi.org/10.1101/2025.09.19.677475) on **Shorkie**—a semi-supervised framework that predicts RNA-seq coverage from DNA sequence in *S. cerevisiae*.Mon, 01 Sep 2025 00:00:00 GMTpublicationhttps://khchao.com/thesis-defense/https://khchao.com/thesis-defense/Friends, I’m thrilled to invite you to my [public dissertation talk](https://khchao.com/thesis-defense/), \"*Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning*\" on August 25th. Hope to see you there!Fri, 01 Aug 2025 00:00:00 GMTtalkhttps://storage.googleapis.com/storage.khchao.com/K-H_Chao_dissertation.pdfhttps://storage.googleapis.com/storage.khchao.com/K-H_Chao_dissertation.pdfHeart full—I [defended my PhD](https://storage.googleapis.com/storage.khchao.com/K-H_Chao_dissertation.pdf) at Johns Hopkins on August 25, 2025. I’m deeply thankful to my advisors, Steven Salzberg & Mihaela Pertea; my committee—Ben Langmead, David Kelley, and Anqi Liu; labmates, friends, and family—for your unwavering support.Fri, 01 Aug 2025 00:00:00 GMTmischttps://www.illumina.com/https://www.illumina.com/Excited to announce I’ve joined [Illumina](https://www.illumina.com/) [Artificial Intelligence Lab](https://www.illumina.com/informatics/ai-in-genomics.html) as a Senior Deep Learning Scientist & Engineer.Fri, 01 Aug 2025 00:00:00 GMTjoinhttps://doi.org/10.7554/eLife.107454.1https://doi.org/10.7554/eLife.107454.1Our OpenSpliceAI paper is now live in [eLife](https://doi.org/10.7554/eLife.107454.1)—an open‑source PyTorch framework for fast, modular splice‑site prediction, transfer learning, and variant‑effect scoring! Check out the [GitHub](https://github.com/Kuanhao-Chao/OpenSpliceAI) and [docs](https://ccb.jhu.edu/openspliceai/).Tue, 01 Jul 2025 00:00:00 GMTpublicationhttps://www.cs.jhu.edu/news/solving-the-bottleneck-in-genome-biology/https://www.cs.jhu.edu/news/solving-the-bottleneck-in-genome-biology/Thrilled to share that the JHU Computer Science Department has spotlighted LiftOn—our new tool for accurate cross-species genome annotation transfer—in their news article: [Solving the Bottleneck in Genome Biology](https://www.cs.jhu.edu/news/solving-the-bottleneck-in-genome-biology/).Sun, 01 Jun 2025 00:00:00 GMTmischttps://github.com/Profluent-AI/OpenCRISPRhttps://github.com/Profluent-AI/OpenCRISPRExcited to present the overview of protein language models (PLM) and [OpenCRISPR](https://github.com/Profluent-AI/OpenCRISPR) at [Hopkins Deep Learning in Genomics Study Group](https://drive.google.com/drive/folders/15yCXZd5sCuCwPULc3b7p8X5OK8XqbdNp?usp=drive_link)! Check out my [slides](https://drive.google.com/file/d/1hg6cVl6dahL5GJBgwszxuZwrayGIKihT/view?usp=sharing).Tue, 01 Apr 2025 00:00:00 GMTtalkhttps://www.arch.jhu.edu/announcing-recipients-of-the-2024-mark-o-robbins-prize/https://www.arch.jhu.edu/announcing-recipients-of-the-2024-mark-o-robbins-prize/Honored to deliver my recipient talk for the [Mark O. Robbins Prize](https://www.arch.jhu.edu/announcing-recipients-of-the-2024-mark-o-robbins-prize/) at [HPC 2025](https://www.arch.jhu.edu/arch-symposium/). It was a privilege to connect with fellow computing experts. Check out my [Slides](https://storage.googleapis.com/storage.khchao.com/slides/HPC_symposium_2025.pdf).Tue, 01 Apr 2025 00:00:00 GMTawardhttps://ospo.library.jhu.edu/services/open-source-project-catalog/entry/169/https://ospo.library.jhu.edu/services/open-source-project-catalog/entry/169/[OpenSpliceAI](https://ospo.library.jhu.edu/services/open-source-project-catalog/entry/169/), [SPLAM](https://ospo.library.jhu.edu/services/open-source-project-catalog/entry/170/), and [LiftOn](https://ospo.library.jhu.edu/services/open-source-project-catalog/entry/171/) are now featured on the [JHU Open Source Programs Office (OSPO)](https://ospo.library.jhu.edu/)! We’re excited that these projects have been added to the [OSPO catalog](https://ospo.library.jhu.edu/services/open-source-project-catalog/).Tue, 01 Apr 2025 00:00:00 GMTmischttps://doi.org/10.1101/2025.03.20.644351https://doi.org/10.1101/2025.03.20.644351Thrilled to release **OpenSpliceAI** – my new open‐source Pytorch splice site prediction framework! Check out the [preprint](https://doi.org/10.1101/2025.03.20.644351), [ GitHub](https://github.com/Kuanhao-Chao/OpenSpliceAI), [Docs](https://ccb.jhu.edu/openspliceai/) [Slides](https://storage.googleapis.com/storage.khchao.com/slides/JHU_joint_lab_meeting_2024.pdf), or join the convo on [bluesky](https://bsky.app/profile/kuanhaochao.bsky.social/post/3ll4vnhpkuk2d).Sat, 01 Mar 2025 00:00:00 GMTpublicationhttps://doi.org/10.1101/gr.279620.124https://doi.org/10.1101/gr.279620.124Excited to share that LiftOn is now published in [Genome Research](https://doi.org/10.1101/gr.279620.124)! Check it out on [ GitHub](https://github.com/Kuanhao-Chao/LiftOn), [Docs](https://ccb.jhu.edu/lifton/), [Slides](https://storage.googleapis.com/storage.khchao.com/slides/ISMB_talk_2024.pdf) or [my talk @ ISMB 2024](https://youtu.be/1zSz67rxQtA?si=3D_aNxR_OpYe3Fm9)Sat, 01 Feb 2025 00:00:00 GMTpublicationhttps://youtu.be/MvpYQYQvZ0Uhttps://youtu.be/MvpYQYQvZ0UExcited to share my work on a Multi-Species Fungal Language Model that improves ChIP-exo and RNA-Seq coverage predictions in JHU joint lab meeting. Check my [video](https://youtu.be/MvpYQYQvZ0U), [slides](https://storage.googleapis.com/storage.khchao.com/slides/JHU_joint_lab_meeting_2025.pdf).Wed, 01 Jan 2025 00:00:00 GMTjoinhttps://doi.org/10.1186/s13059-024-03379-4https://doi.org/10.1186/s13059-024-03379-4JHU has published a feature article about my splice site predictor, [Splam](https://doi.org/10.1186/s13059-024-03379-4), on the [HUB](https://hub.jhu.edu/2024/12/11/splam-pinpoints-gene-splicing/), [Computer Science](https://www.cs.jhu.edu/news/new-ai-tool-pinpoints-gene-splicing-with-unmatched-precision/), and [Whiting School of Engineering](https://engineering.jhu.edu/news/new-ai-tool-pinpoints-gene-splicing-with-unmatched-precision/) websites 🎉Sun, 01 Dec 2024 00:00:00 GMTpublicationhttps://doi.org/10.1186/s13059-024-03379-4https://doi.org/10.1186/s13059-024-03379-4I am presenting my splice site predictor, [Splam](https://doi.org/10.1186/s13059-024-03379-4) and OpenSpliceAI at [Biological Data Science 2024](https://meetings.cshl.edu/meetings.aspx?meet=DATA). See you in Cold Spring Harbor, NY!Tue, 01 Oct 2024 00:00:00 GMTtalkhttps://scholar.google.com/citations?user=2B51EUIAAAAJ&hl=enhttps://scholar.google.com/citations?user=2B51EUIAAAAJ&hl=enThrilled to announce that I’ve co-founded the Deep Learning in Genomics Study Group at Hopkins with my friend [Mahler Revsine](https://scholar.google.com/citations?user=2B51EUIAAAAJ&hl=en)! Dive into our [study group repository](https://drive.google.com/drive/folders/15yCXZd5sCuCwPULc3b7p8X5OK8XqbdNp?usp=drive_link) for all meeting materials and my [opening talk slides](https://drive.google.com/file/d/1TWSMVFt0FdWuR1GITrUb__AEALJ0Ar7_/view?usp=sharing)!Tue, 01 Oct 2024 00:00:00 GMTtalkhttps://www.cs.jhu.edu/news/phd-student-kuan-hao-chao-wins-mark-o-robbins-prize-in-high-performance-computing/https://www.cs.jhu.edu/news/phd-student-kuan-hao-chao-wins-mark-o-robbins-prize-in-high-performance-computing/JHU CS department wrote an [article](https://www.cs.jhu.edu/news/phd-student-kuan-hao-chao-wins-mark-o-robbins-prize-in-high-performance-computing/) announcing my receipt of 2024 Mark O. Robbins Prize in High-Performance Computing 🎉Sun, 01 Sep 2024 00:00:00 GMTawardhttps://github.com/Kuanhao-Chao/splamhttps://github.com/Kuanhao-Chao/splamMy splice site predictor, [Splam](https://github.com/Kuanhao-Chao/splam), is published in the journal [Genome Biology](https://doi.org/10.1186/s13059-024-03379-4).Sun, 01 Sep 2024 00:00:00 GMTpublicationhttps://drive.google.com/file/d/1xA0ln9r1xWXX8gYLqVgowaPpthOb6eGo/view?usp=drive_linkhttps://drive.google.com/file/d/1xA0ln9r1xWXX8gYLqVgowaPpthOb6eGo/view?usp=drive_linkThrilled to be invited to share my research at Google Deep Dive! Watch my 1-hour [presentation [Google internal only]](https://drive.google.com/file/d/1xA0ln9r1xWXX8gYLqVgowaPpthOb6eGo/view?usp=drive_link) and don't miss the [slides](https://storage.googleapis.com/storage.khchao.com/slides/Google_Deep_Dive_2024_0806.pdf)Thu, 01 Aug 2024 00:00:00 GMTtalkhttps://storage.googleapis.com/storage.khchao.com/slides/Calico_project_showcase_2024_0821.pdfhttps://storage.googleapis.com/storage.khchao.com/slides/Calico_project_showcase_2024_0821.pdfWrapping up my Calico internship with a 1-hour talk! Check out my [slides](https://storage.googleapis.com/storage.khchao.com/slides/Calico_project_showcase_2024_0821.pdf). Thanks to all the great mentors, collaborators, and good friends in [Kelley Lab](https://www.calicolabs.com/people/david-kelley-ph-d/)!Thu, 01 Aug 2024 00:00:00 GMTtalkhttps://youtu.be/1zSz67rxQtA?si=3D_aNxR_OpYe3Fm9https://youtu.be/1zSz67rxQtA?si=3D_aNxR_OpYe3Fm9Check out my talk on \"Combining DNA and protein alignments to improve genome annotation with LiftOn\". [Video](https://youtu.be/1zSz67rxQtA?si=3D_aNxR_OpYe3Fm9) and [slides](https://storage.googleapis.com/storage.khchao.com/slides/ISMB_talk_2024.pdf) are available now!Mon, 01 Jul 2024 00:00:00 GMTreleasehttps://www.arch.jhu.edu/news-events/all/robbins-award/https://www.arch.jhu.edu/news-events/all/robbins-award/Honored to receive the 2024 [Mark O. Robbins Prize](https://www.arch.jhu.edu/news-events/all/robbins-award/) in High-Performance Computing. Huge thanks to my advisors, collaborators, and friends. Stay tuned for my talk at the 2025 ARCH Symposium!Sat, 01 Jun 2024 00:00:00 GMTawardhttps://www.youtube.com/watch?v=MyWwUzjIBVk&feature=youtu.behttps://www.youtube.com/watch?v=MyWwUzjIBVk&feature=youtu.beCheck out my talk on \"Predicting splice sites in DNA sequences with sequence models\". [Video](https://www.youtube.com/watch?v=MyWwUzjIBVk&feature=youtu.be) and [slides](https://storage.googleapis.com/storage.khchao.com/slides/joint_lab_meeting_slides.pdf) are available now!Wed, 01 May 2024 00:00:00 GMTreleasehttps://www.calicolabs.com/people/david-kelley-ph-d/https://www.calicolabs.com/people/david-kelley-ph-d/Excited to share that I'll be joining the [Kelley Lab](https://www.calicolabs.com/people/david-kelley-ph-d/) at [Calico](https://www.calicolabs.com/) for the 2024 summer internship! Connect with me in South San Francisco, CA!Wed, 01 May 2024 00:00:00 GMTjoinhttps://github.com/Kuanhao-Chao/LiftOnhttps://github.com/Kuanhao-Chao/LiftOn[LiftOn](https://github.com/Kuanhao-Chao/LiftOn) is selected for a 20-min talk at the ISMB 2024, General Computational COSI track. [Preprint](https://doi.org/10.1101/2024.05.16.593026) is available. See you in Montreal, Canada!Wed, 01 May 2024 00:00:00 GMTpublicationhttps://github.com/Kuanhao-Chao/LiftOnhttps://github.com/Kuanhao-Chao/LiftOnExcited to launch [LiftOn v1.0.0](https://github.com/Kuanhao-Chao/LiftOn)! Explore my RECOMB-Seq [talk slides](https://storage.googleapis.com/storage.khchao.com/slides/RECOMB-Seq_talk_2024.pdf), [poster](https://storage.googleapis.com/storage.khchao.com/poster/RECOMB_LiftOn.pdf), [GitHub repo](https://github.com/Kuanhao-Chao/LiftOn) and [documentation](https://ccb.jhu.edu/lifton/).Mon, 01 Apr 2024 00:00:00 GMTreleasehttps://ccb.jhu.edu/lifton/https://ccb.jhu.edu/lifton/[LiftOn](https://ccb.jhu.edu/lifton/), my new genome lift-over tool, is selected as a talk at [RECOMB-Seq 2024](https://recomb-seq.github.io/). Friends, see you in Boston, MA – preprint coming soon!Fri, 01 Mar 2024 00:00:00 GMTpublicationhttps://engineering.jhu.edu/news/the-human-genome-is-biased-but-rearranging-it-can-help/https://engineering.jhu.edu/news/the-human-genome-is-biased-but-rearranging-it-can-help/My research collaboration with Berkeley EECS is highlighted by [JHU Whiting School of Enigneering](https://engineering.jhu.edu/news/the-human-genome-is-biased-but-rearranging-it-can-help/) and [JHU CS Department](https://www.cs.jhu.edu/news/the-human-genome-is-biased-but-rearranging-it-can-help/). Explore our work on the Wheeler graph index with Pei-Wei Chen, Ben Langmead and and Sanjit Seshia.Mon, 01 Jan 2024 00:00:00 GMTawardhttps://doi.org/10.1101/2023.07.27.550754https://doi.org/10.1101/2023.07.27.550754I am presenting [Splam](https://doi.org/10.1101/2023.07.27.550754) at [Genome Informatics](https://meetings.cshl.edu/meetings.aspx?meet=info&year=23). Check out [v1.0.10 release](https://github.com/Kuanhao-Chao/splam/releases/tag/v1.0.10). See you in Cold Spring Harbor, NY!Fri, 01 Dec 2023 00:00:00 GMTreleasehttps://github.com/ishinder/EASTRhttps://github.com/ishinder/EASTRMy co-authored paper introduces *[EASTR](https://github.com/ishinder/EASTR)*, a software tool designed to identify and eliminate inaccurately spliced alignment, has been published in [Nature Communications](https://doi.org/10.1038/s41467-023-43017-4)!Wed, 01 Nov 2023 00:00:00 GMTpublicationhttps://khchao.com/news/#2023-11-01-thrilled-to-announce-i-ve-passed-my-gradhttps://khchao.com/news/#2023-11-01-thrilled-to-announce-i-ve-passed-my-gradThrilled to announce I've passed my Graduate Board Oral Exam! Huge thanks to Steven Salzberg, Mihaela Pertea, Ben Langmead, Liliana Florea, and Winston Timp for their invaluable service on my GBO committee.Wed, 01 Nov 2023 00:00:00 GMTmischttps://ccb.jhu.edu/chess/https://ccb.jhu.edu/chess/The paper I coauthored, [*CHESS 3*](https://ccb.jhu.edu/chess/), decribing a new human gene catalog, is now published in [Genome Biology](https://doi.org/10.1186/s13059-023-03088-4)!Sun, 01 Oct 2023 00:00:00 GMTpublicationhttps://doi.org/10.1016/j.isci.2023.107402https://doi.org/10.1016/j.isci.2023.107402My paper in *iScience* describes the fastest Wheeler graph recognition algorithm using renaming heuristics and SMT solver. See the [WGT paper](https://doi.org/10.1016/j.isci.2023.107402), check out [GitHub](https://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit) and watch my [RECOMB-Seq talk](https://www.youtube.com/watch?v=TkX9S024Dk8)!Tue, 01 Aug 2023 00:00:00 GMTpublicationhttps://github.com/Kuanhao-Chao/splamhttps://github.com/Kuanhao-Chao/splamI am thrilled to release Splam **v1.0.2**, a splice site predictor that enhances spliced alignments. Check out the Splam [GitHub](https://github.com/Kuanhao-Chao/splam), [preprint](https://doi.org/10.1101/2023.07.27.550754) and [documentation](https://ccb.jhu.edu/splam/)!Sat, 01 Jul 2023 00:00:00 GMTpublicationhttps://bits.iis.sinica.edu.tw/https://bits.iis.sinica.edu.tw/My co-first author paper on analyzing protein interactome using co-elution data is published in *Briefing in Bioinformatics*. Great collaboration with [HK Tsai Lab](https://bits.iis.sinica.edu.tw/) and [Jun-Yi Leu Lab](https://www.imb.sinica.edu.tw/~jleu/)! See the paper [here](https://doi.org/10.1093/bib/bbad229)Thu, 01 Jun 2023 00:00:00 GMTpublicationhttps://cosi.iscb.org/wiki/MLCSB:Homehttps://cosi.iscb.org/wiki/MLCSB:HomeSplam is accepted as a poster at [MLCSB COSI](https://cosi.iscb.org/wiki/MLCSB:Home), and [Han1](https://doi.org/10.1093/g3journal/jkac321) is accepted as a highlight poster at [HiTSeq COSI](https://hitseq.org/). Exciting to share our work at [ISMB/ECCB 2023](https://www.iscb.org/ismbeccb2023) in Lyon, FranceMon, 01 May 2023 00:00:00 GMTawardhttps://doi.org/10.1101/2022.10.15.512390https://doi.org/10.1101/2022.10.15.512390My paper [WGT](https://doi.org/10.1101/2022.10.15.512390) is accepted to [RECOMB-Seq](https://recomb-seq.github.io/) as a proceedings track paper and [RECOMB](http://recomb2023.bilkent.edu.tr/) as a poster. Great collaboration with [langmead lab](https://langmead-lab.org/) and [Seshia lab](https://people.eecs.berkeley.edu/~sseshia/). See you in İstanbul, TürkiyeWed, 01 Mar 2023 00:00:00 GMTpublicationhttps://www.ncbi.nlm.nih.gov/assembly/GCA_024586135.1/https://www.ncbi.nlm.nih.gov/assembly/GCA_024586135.1/My paper in *G3: Genes, Genomes, Genetics* describes the first gap-free assembly of a [Han Chinese human, Han1](https://www.ncbi.nlm.nih.gov/assembly/GCA_024586135.1/). See the paper [here](https://doi.org/10.1093/g3journal/jkac321)Sun, 01 Jan 2023 00:00:00 GMTpublicationhttps://meetings.cshl.edu/meetings.aspx?meet=data&year=22https://meetings.cshl.edu/meetings.aspx?meet=data&year=22I am presenting Han1 at [2022 Biological Data Science](https://meetings.cshl.edu/meetings.aspx?meet=data&year=22)! Here is the link to the [poster](https://storage.googleapis.com/storage.khchao.com/JHU%20PhD/Han1/Han1_poster.pdf) and the video to my [1-min lightening talk](https://youtu.be/2m5wrqqsn4E)Tue, 01 Nov 2022 00:00:00 GMTtalkhttps://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkithttps://github.com/Kuanhao-Chao/Wheeler_Graph_ToolkitWe are releasing [WGT](https://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit), the first Wheeler Graph suite with the fastest recognition algorithm. It's on [bioRxiv](https://doi.org/10.1101/2022.10.15.512390) now!Sat, 01 Oct 2022 00:00:00 GMTpublicationhttps://www.ncbi.nlm.nih.gov/assembly/GCA_024586135.1/https://www.ncbi.nlm.nih.gov/assembly/GCA_024586135.1/We are releasing [Han1](https://www.ncbi.nlm.nih.gov/assembly/GCA_024586135.1/), the first gapless, fully annotated Chinese Han genome. Check it out on [bioRxiv](https://doi.org/10.1101/2022.08.08.503226)!Mon, 01 Aug 2022 00:00:00 GMTpublicationhttps://bioconductor.org/packages/release/bioc/html/sangeranalyseR.htmlhttps://bioconductor.org/packages/release/bioc/html/sangeranalyseR.html[sangeranalyseR](https://bioconductor.org/packages/release/bioc/html/sangeranalyseR.html) and [RNASeqR](https://github.com/Kuanhao-Chao/RNASeqR) are released on *Bioconductor 3.14*Fri, 01 Oct 2021 00:00:00 GMTreleasehttps://salzberg-lab.org/https://salzberg-lab.org/I join Dr. [Steven Salzberg](https://salzberg-lab.org/)'s and Dr. [Mihaela Pertea](https://ccb.jhu.edu/people/mpertea/)'s lab as a CS Ph.D. student at the Johns Hopkins University.Wed, 01 Sep 2021 00:00:00 GMTjoinhttps://bioc2021.bioconductor.org/https://bioc2021.bioconductor.org/sangeranalyseR is awarded the **Best Poster** at [Bioc2021](https://bioc2021.bioconductor.org/). Check out my sangeranalyseR [poster](https://f1000research.com/posters/10-888)!Sun, 01 Aug 2021 00:00:00 GMTawardhttps://storage.googleapis.com/storage.khchao.com/biobaby/index.htmlhttps://storage.googleapis.com/storage.khchao.com/biobaby/index.htmlPlay my Unity games! [biobaby](https://storage.googleapis.com/storage.khchao.com/biobaby/index.html), [flappy penguin](https://storage.googleapis.com/storage.khchao.com/flappy_penguin/index.html) and [more](https://storage.googleapis.com/storage.khchao.com/tanks_fire/index.html).Tue, 01 Jun 2021 00:00:00 GMTmischttps://doi.org/10.1093/gbe/evab028https://doi.org/10.1093/gbe/evab028My paper in *Genome Biology and Evolution* describes a new open source R package for processing Sanger sequencing data. See the paper [here](https://doi.org/10.1093/gbe/evab028). It is available on [Bioconductor](https://bioconductor.org/packages/release/bioc/html/sangeranalyseR.html).Mon, 01 Mar 2021 00:00:00 GMTpublication