Kuan-Hao Chao
@kuanhaochao.bsky.social
Senior Deep Learning Scientist Illumina | CS PhD candidate at CS PhD student at @jhu.edu @jhucompsci.bsky.social
Teaching machines to learn biology 🧬💻
https://khchao.com/
Teaching machines to learn biology 🧬💻
https://khchao.com/
Pinned
Kuan-Hao Chao
@kuanhaochao.bsky.social
· Mar 24
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species https://www.biorxiv.org/content/10.1101/2025.03.20.644351v1
Friends, I’m excited to release OpenSpliceAI, an open‐source, efficient, and modular framework for splice site prediction. It reimplements and extends SpliceAI (Jaganathan et al., 2019) using the modern PyTorch framework. 1/
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Reposted by Kuan-Hao Chao
In @elife.bsky.social, our OpenSpliceAI paper, led by @kuanhaochao.bsky.social, is now 'official' though it's been online since July. If you want to enjoy the reviewers' comments and our responses, check it out at: doi.org/10.7554/eLif...
OpenSpliceAI provides an efficient modular implementation of SpliceAI enabling easy retraining across nonhuman species
OpenSpliceAI is an open, retrainable framework for splice site prediction that enables rapid, memory-efficient, cross-species analyses at scale with accuracy comparable to SpliceAI.
doi.org
October 31, 2025 at 11:44 AM
In @elife.bsky.social, our OpenSpliceAI paper, led by @kuanhaochao.bsky.social, is now 'official' though it's been online since July. If you want to enjoy the reviewers' comments and our responses, check it out at: doi.org/10.7554/eLif...
Reposted by Kuan-Hao Chao
Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA.
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Predicting dynamic expression patterns in budding yeast with a fungal DNA language model
Predicting gene expression from DNA sequence remains challenging due to complex regulatory codes. We introduce a masked DNA language model pretrained on 165 fungal genomes closely related to budding y...
www.biorxiv.org
October 13, 2025 at 11:06 PM
Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA.
Preprint: www.biorxiv.org/content/10.1...
Preprint: www.biorxiv.org/content/10.1...
Reposted by Kuan-Hao Chao
Predicting dynamic expression patterns in budding yeast with a fungal DNA language model https://www.biorxiv.org/content/10.1101/2025.09.19.677475v1
September 21, 2025 at 5:34 PM
Predicting dynamic expression patterns in budding yeast with a fungal DNA language model https://www.biorxiv.org/content/10.1101/2025.09.19.677475v1
Reposted by Kuan-Hao Chao
Congratulations, @kuanhaochao.bsky.social!
September 4, 2025 at 1:22 PM
Congratulations, @kuanhaochao.bsky.social!
Heart full—I defended my PhD in @jhucompsci.bsky.social @jhu.edu(Aug 25). Thanks to my advisors @stevensalzberg.bsky.social and Mihaela Pertea; my committee— @benlangmead.bsky.social, David Kelley & Anqi Liu; and all labmates, collaborators, and mentors. You made me who I am today. Deeply grateful!
August 26, 2025 at 1:28 PM
Heart full—I defended my PhD in @jhucompsci.bsky.social @jhu.edu(Aug 25). Thanks to my advisors @stevensalzberg.bsky.social and Mihaela Pertea; my committee— @benlangmead.bsky.social, David Kelley & Anqi Liu; and all labmates, collaborators, and mentors. You made me who I am today. Deeply grateful!
Friends I’m defending my PhD!
🗓 Mon, Aug 25 • 2:30 PM–4:30 PM ET
📍 JHU Homewood — Clark Hall 110
💻 Zoom: jhubluejays.zoom.us/j/9385611117...
If you’re into genomics or deep learning (or just curious how AI reads DNA), I’d love to have you there—friends welcome!
Details: khchao.com/thesis-defen...
🗓 Mon, Aug 25 • 2:30 PM–4:30 PM ET
📍 JHU Homewood — Clark Hall 110
💻 Zoom: jhubluejays.zoom.us/j/9385611117...
If you’re into genomics or deep learning (or just curious how AI reads DNA), I’d love to have you there—friends welcome!
Details: khchao.com/thesis-defen...
Join our Cloud HD Video Meeting
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jhubluejays.zoom.us
August 21, 2025 at 5:37 PM
Friends I’m defending my PhD!
🗓 Mon, Aug 25 • 2:30 PM–4:30 PM ET
📍 JHU Homewood — Clark Hall 110
💻 Zoom: jhubluejays.zoom.us/j/9385611117...
If you’re into genomics or deep learning (or just curious how AI reads DNA), I’d love to have you there—friends welcome!
Details: khchao.com/thesis-defen...
🗓 Mon, Aug 25 • 2:30 PM–4:30 PM ET
📍 JHU Homewood — Clark Hall 110
💻 Zoom: jhubluejays.zoom.us/j/9385611117...
If you’re into genomics or deep learning (or just curious how AI reads DNA), I’d love to have you there—friends welcome!
Details: khchao.com/thesis-defen...
Thrilled to join Illumina AI Lab as Senior Deep Learning Engineer! Huge thanks to my mentors & friends at @jhu.edu and Calico, and a special shout-out to Kyle, Kishore, and Tracie for the warm welcome. Excited to build AI-driven genomics solutions together! #AI #Genomics
I’m thrilled to announce that I’ve joined the Illumina Artificial Intelligence Lab as a Senior Deep Learning Scientist & Engineer! | Kuan-Hao Chao
I’m thrilled to announce that I’ve joined the Illumina Artificial Intelligence Lab as a Senior Deep Learning Scientist & Engineer! 🎉
It’s been an absolute privilege to collaborate with the talented ...
www.linkedin.com
August 5, 2025 at 2:45 PM
🚀 Thrilled to share our OpenSpliceAI paper is out in @elife.bsky.social
Open‑source, PyTorch extension of SpliceAI—fast, modular splice‑site prediction, transfer learning, and variant‑effect scoring.
🔗 Paper doi.org/10.7554/eLif...
🔗 Code github.com/Kuanhao-Chao...
🔗 Docs ccb.jhu.edu/openspliceai/
Open‑source, PyTorch extension of SpliceAI—fast, modular splice‑site prediction, transfer learning, and variant‑effect scoring.
🔗 Paper doi.org/10.7554/eLif...
🔗 Code github.com/Kuanhao-Chao...
🔗 Docs ccb.jhu.edu/openspliceai/
July 23, 2025 at 2:02 PM
🚀 Thrilled to share our OpenSpliceAI paper is out in @elife.bsky.social
Open‑source, PyTorch extension of SpliceAI—fast, modular splice‑site prediction, transfer learning, and variant‑effect scoring.
🔗 Paper doi.org/10.7554/eLif...
🔗 Code github.com/Kuanhao-Chao...
🔗 Docs ccb.jhu.edu/openspliceai/
Open‑source, PyTorch extension of SpliceAI—fast, modular splice‑site prediction, transfer learning, and variant‑effect scoring.
🔗 Paper doi.org/10.7554/eLif...
🔗 Code github.com/Kuanhao-Chao...
🔗 Docs ccb.jhu.edu/openspliceai/
Excited to introduce LiftOn – an open-source tool for accurate, scalable liftover of genome annotations (GFF) across assemblies. 🚀
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
June 17, 2025 at 2:21 PM
Excited to introduce LiftOn – an open-source tool for accurate, scalable liftover of genome annotations (GFF) across assemblies. 🚀
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
👉 Code & community: github.com/Kuanhao-Chao...
It’s been incredibly rewarding building this for the genomics community. Can’t wait for your feedback and contributions!
Reposted by Kuan-Hao Chao
@kuanhaochao.bsky.social and Alan Mao built an open-source version of SpliceAI, a deep learning model for predicting human splice sites, and it turned into quite a project! Many new features including training modules, check out the whole thread below
Friends, I’m excited to release OpenSpliceAI, an open‐source, efficient, and modular framework for splice site prediction. It reimplements and extends SpliceAI (Jaganathan et al., 2019) using the modern PyTorch framework. 1/
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species https://www.biorxiv.org/content/10.1101/2025.03.20.644351v1
March 24, 2025 at 2:48 PM
@kuanhaochao.bsky.social and Alan Mao built an open-source version of SpliceAI, a deep learning model for predicting human splice sites, and it turned into quite a project! Many new features including training modules, check out the whole thread below
Friends, I’m excited to release OpenSpliceAI, an open‐source, efficient, and modular framework for splice site prediction. It reimplements and extends SpliceAI (Jaganathan et al., 2019) using the modern PyTorch framework. 1/
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species https://www.biorxiv.org/content/10.1101/2025.03.20.644351v1
March 24, 2025 at 1:51 PM
Friends, I’m excited to release OpenSpliceAI, an open‐source, efficient, and modular framework for splice site prediction. It reimplements and extends SpliceAI (Jaganathan et al., 2019) using the modern PyTorch framework. 1/
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Mihaela Pertea, @stevensalzberg.bsky.social, Anqi Liu, Alan Mao
Friends, LiftOn is now published in @genomeresearch.bsky.social! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments
@stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao
doi.org/10.1101/gr.2...
@stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao
doi.org/10.1101/gr.2...
Combining DNA and protein alignments to improve genome annotation with LiftOn
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
doi.org
March 3, 2025 at 2:24 PM
Friends, LiftOn is now published in @genomeresearch.bsky.social! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments
@stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao
doi.org/10.1101/gr.2...
@stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao
doi.org/10.1101/gr.2...