diff --git a/_pages/about.md b/_pages/about.md index 21f95c3336bff..9e22ad5f50921 100644 --- a/_pages/about.md +++ b/_pages/about.md @@ -9,22 +9,20 @@ redirect_from: --- {% include base_path %} -🎓 I'm a third-year Ph.D. Candidate in Computer Science at the Center for Computational Biology, Johns Hopkins University, working with Steven Salzberg and Mihaela Pertea. My academic journey started in Electrical Engineering at National Taiwan University (NTU), shifting towards computer science in my final year at the College of Engineering & Computer Science at Australian National University (ANU) 🦘🐨 +🎓 I'm a third-year Ph.D. Candidate in Computer Science at the Center for Computational Biology, Johns Hopkins University, working with Steven Salzberg and Mihaela Pertea. My academic journey started in Electrical Engineering at National Taiwan University (NTU), shifting towards computer science in my final year at the College of Engineering & Computer Science at Australian National University (ANU). +🧬 My research interest intersects deep learning with genomics and transcriptomics: -🧬 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://doi.org/10.1101/2024.05.16.593026)). +- In **transcriptional regulatory networks**,my work uses sequence models to decode DNA patterns, aiming to uncover insights into how cis-regulatory DNA sequences and trans-regulators interact. I am developing a yeast large language model (LLM) to better understand the mechanisms of yeast gene expression regulation. +- In **splice site predictiong**, I built a deep dilated residual convolutional neural network to decode the complexities of RNA splicing, alternative splicing, and the impact of genetic variants on cryptic splicing ([Learn more](https://www.biorxiv.org/content/10.1101/2023.07.27.550754v2)). +- In **genome assembly**, I assembled and annotated the first gapless Southern Chinese Han genome, [Han1](https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_024586135.1/), using PacBio HiFi and Oxford Nanopore long reads, with T2T-CHM13 as a guide ([Learn more](https://doi.org/10.1093/g3journal/jkac321)). +- For **pangenome indexing**, I applied new renaming heuristics and an SMT solver to make the Wheeler graph recognition problem computationally feasible ([Learn more](https://doi.org/10.1016/j.isci.2023.107402)). +- In **genome annotation**, I used 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)). -💻 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. +💻 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)**