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...

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...

Predicting dynamic expression patterns in budding yeast with a fungal DNA language model https://www.biorxiv.org/content/10.1101/2025.09.19.677475v1

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!

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...

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

🚀 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/

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!

@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

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...