Posts by Collection
about-us
contact
internship
news
My paper in Genome Biology and Evolution describes a new open source R package for processing Sanger sequencing data. See the paper here. It is available on Bioconductor.
sangeranalyseR is awarded the Best Poster at Bioc2021. Check out my sangeranalyseR poster!
I join Dr. Steven Salzberg’s and Dr. Mihaela Pertea’s lab as a CS Ph.D. student at the Johns Hopkins University.
sangeranalyseR and RNASeqR are released on Bioconductor 3.14
We are releasing Han1, the first gapless, fully annotated Chinese Han genome. Check it out on bioRxiv!
We are releasing WGT, the first Wheeler Graph suite with the fastest recognition algorithm. It’s on bioRxiv now!
I am presenting Han1 at 2022 Biological Data Science! Here is the link to the poster and the video to my 1-min lightening talk
My paper in G3: Genes, Genomes, Genetics describes the first gap-free assembly of a Han Chinese human, Han1. See the paper here
My paper WGT is accepted to RECOMB-Seq as a proceedings track paper and RECOMB as a poster. Great collaboration with langmead lab and Seshia lab. See you in İstanbul, Türkiye
Splam is accepted as a poster at MLCSB COSI, and Han1 is accepted as a highlight poster at HiTSeq COSI. Exciting to share our work at ISMB/ECCB 2023 in Lyon, France
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 and Jun-Yi Leu Lab! See the paper here
I am thrilled to release Splam v1.0.2, a splice site predictor that enhances spliced alignments. Check out the Splam GitHub, preprint and documentation!
My paper in iScience describes the fastest Wheeler graph recognition algorithm using renaming heuristics and SMT solver. See the WGT paper, check out GitHub and watch my RECOMB-Seq talk!
The paper I coauthored, CHESS 3, decribing a new human gene catalog, is now published in Genome Biology!
My co-authored paper introduces EASTR, a software tool designed to identify and eliminate inaccurately spliced alignment, has been published in Nature Communications!
I am presenting Splam at Genome Informatics. Check out v1.0.10 release. See you in Cold Spring Harbor, NY!
My research collaboration with Berkeley EECS is highlighted by JHU Whiting School of Enigneering and JHU CS Department. Explore our work on the Wheeler graph index with Pei-Wei Chen, Ben Langmead and and Sanjit Seshia.
LiftOn, my new genome lift-over tool, is selected as a talk at RECOMB-Seq 2024. Friends, see you in Boston, MA – preprint coming soon!
Excited to launch LiftOn v1.0.0! Explore my RECOMB-Seq talk slides, poster, GitHub repo and documentation.
LiftOn is selected for a 20-min talk at the ISMB 2024,General Computational COSI track. Preprint is available. See you in Montreal, Canada!
Check out my talk on “Predicting splice sites in DNA sequences with sequence models”. Video and slides are available now!
Excited to share that I’ll be joining the Kelley Lab at Calico for the 2024 summer internship! Connect with me in South San Francisco, CA!
Honored to receive the 2024 Mark O. Robbins Prize in High-Performance Computing. Huge thanks to my advisors, collaborators, and friends. Stay tuned for my talk at the 2025 ARCH Symposium!
Check out my talk on “Combining DNA and protein alignments to improve genome annotation with LiftOn”. Video and slides are available now!
Thrilled to be invited to share my research at Google Deep Dive! Watch my 1-hour presentation [Google internal only] and don’t miss the slides
Wrapping up my Calico internship with a 1-hour talk! Check out my slides. Thanks to all the great mentors, collaborators, and good friends in Kelley Lab!
JHU CS department wrote an article announcing my receipt of 2024 Mark O. Robbins Prize in High-Performance Computing 🎉
My splice site predictor, Splam, is published in the journal Genome Biology.
I am presenting my splice site predictor, Splam and OpenSpliceAI at Biological Data Science 2024. See you in Cold Spring Harbor, NY!
Thrilled to announce that I’ve co-founded the Deep Learning in Genomics Study Group at Hopkins with my friend Mahler Revsine! Dive into our study group repository for all meeting materials and my opening talk slides!
JHU has published a feature article about my splice site predictor, Splam, on the HUB, Computer Science, and Whiting School of Engineering websites 🎉
Excited 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, slides.
Excited to share that LiftOn is now published in Genome Research! Check it out on GitHub, Docs, Slides or my talk @ ISMB 2024
Thrilled to release OpenSpliceAI – my new open‐source Pytorch splice site prediction framework! Check out the preprint, GitHub, Docs Slides, or join the convo on bluesky.
Honored to deliver my recipient talk for the Mark O. Robbins Prize at HPC 2025. It was a privilege to connect with fellow computing experts. Check out my Slides.
OpenSpliceAI, SPLAM, and LiftOn are now featured on the JHU Open Source Programs Office (OSPO)! We’re excited that these projects have been added to the OSPO catalog.
Excited to present the overview of protein language models (PLM) and OpenCRISPR at Hopkins Deep Learning in Genomics Study Group! Check out my slides.
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.
Our OpenSpliceAI paper is now live in eLife—an open‑source PyTorch framework for fast, modular splice‑site prediction, transfer learning, and variant‑effect scoring! Check out the GitHub and docs.
Friends, I’m thrilled to invite you to my public dissertation talk, “Decoding the Language of Genomes: Bridging Sequences and Function through Deep Learning” on August 25th. Hope to see you there!
Heart full—I defended my PhD 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.
Excited to announce I’ve joined Illumina Artificial Intelligence Lab as a Senior Deep Learning Scientist & Engineer.
photos
portfolio
presentations
projects
publications
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Dec 2019
Kuan-Hao Chao, Y.W. Hsiao, Y.F. Lee, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, and E.Y. Chuang*
PDF Cite Code Documentation Slides sangeranalyseR: simple and interactive processing of Sanger sequencing data in R
Genome Biology and Evolution(GBE), Feb 2021
Kuan-Hao Chao*, Kirston Barton, Sarah Palmer, and Robert Lanfear*
PDF Cite Code Documentation Poster CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
Genome Biology, Dec 2022
Ales Varabyou, Markus J. Sommer, Beril Erdogdu, Ida Shinder, Ilia Minkin, Kuan-Hao Chao, Sukhwan Park, Jakob Heinz, Christopher Pockrandt, Alaina Shumate, Natalia Rincon, Daniela Puiu, Martin Steinegger, Steven L. Salzberg, Mihaela Pertea
PDF Cite Code DocumentationThe first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual
G3: Genes, Genomes, Genetics, Jan 2023
Kuan-Hao Chao*, A.V. Zimin, M. Pertea, S.L. Salzberg*
PDF Cite Code Documentation PosterEASTR: Correcting systematic alignment errors in multi-exon genes
Nature communications, May 2023
Ida Shinder*, Richard Hu, Hyun Joo Ji, Kuan-Hao Chao, Mihaela Pertea*
PDF Cite Code Documentation A feature extraction free approach for protein interactome inference from co-elution data
Briefings in Bioinformatics, Jun 2023
Yu-Hsin Chen†, Kuan-Hao Chao†, Jin Yung Wong, Chien-Fu Liu, Jun-Yi Leu*, Huai-Kuang Tsai*
PDF Cite Code Documentation WGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs
iScience, Jul 2023
Kuan-Hao Chao*†, Pei-Wei Chen†, Sanjit A. Seshia, Ben Langmead*
PDF Cite Code Documentation Poster Splam: a deep-learning-based splice site predictor that improves spliced alignments
bioRxiv, Aug 2023
Kuan-Hao Chao*, Alan Mao, Steven L Salzberg, Mihaela Pertea*
PDF Cite Code Documentation Poster Combining DNA and protein alignments to improve genome annotation with LiftOn
bioRxiv, May 2024
Kuan-Hao Chao*, Jakob M. Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea, and Steven L. Salzberg*
PDF Cite Code Documentation Poster