From 8ebab3773304da6dad44dfe701079c6f827bcc33 Mon Sep 17 00:00:00 2001 From: Kuan-Hao Chao Date: Wed, 19 Jun 2024 11:11:56 -0700 Subject: [PATCH] Update _pages/about.md --- _pages/about.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/_pages/about.md b/_pages/about.md index c0b75d96fd675..21f95c3336bff 100644 --- a/_pages/about.md +++ b/_pages/about.md @@ -13,14 +13,18 @@ redirect_from: + 🧬 My research interest intersects **"graphs"** with genomics and transcriptomics: + +- In **deep learning in genomics**, my work focuses on utilizing sequence models to decode patterns in DNA sequences, aiming to uncover insights into the transcriptional regulatory networks that integrate cis-regulatory DNA sequences with the activity of trans-regulators. I am developing a yeast large language model (LLM) to better understand the mechanisms of yeast gene expression regulation. +- In **splice site prediction**, I built a deep dilated residual convolutional neural network to decode the complexities of RNA splicing and understand the impact of genetic variants on cryptic splicing ([Learn more](https://www.biorxiv.org/content/10.1101/2023.07.27.550754v2)). - In **genome assembly**, De Bruijn graphs are widely used. For an example of its application, check out my [Han1 assembly](https://doi.org/10.1093/g3journal/jkac321), the first gapless Southern Chinese Han genome. - For **pangenome indexing**, I've contributed to making the Wheeler graph recognition problem computationally feasible through innovative heuristic methods combined with an SMT solver ([Learn more](https://doi.org/10.1016/j.isci.2023.107402)). -- In **genome annotation**, I have utilized graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. ([Learn more](https://ccb.jhu.edu/lifton/)). -- My **transcriptome assembly** work focuses on modeling RNA-Seq data using directed acyclic splice graphs, with ongoing research into graph neural networks to decode the complexities of RNA splicing. ([Learn more](https://www.biorxiv.org/content/10.1101/2023.07.27.550754v2)). +- In **genome annotation**, I have utilized graph-based methods to stitch together fragmented DNA and protein alignments, thereby assembling them into more accurate annotations. ([Learn more](https://doi.org/10.1101/2024.05.16.593026)). + -💻 As a staunch advocate for open-source software, I invite you to explore my **[NEWS](https://khchao.com/news/)** page for the latest updates on my projects. +💻 I am an advocate for open-source software, embracing the philosophy of "build what you need, use what you build". I invite you to explore my **[NEWS](https://khchao.com/news/)** page for the latest updates on my projects. 💬 Feel free to reach out to me for collaborations, discussions, or just to say hi! **[Coffee chat! ☕️](https://calendly.com/kuanhao-chao/30min)**