Kuan-Hao Chao


Computer Science PhD Student in Computational Biology Group
@ Johns Hopkins University

Advisor: Steven Salzberg & Mihaela Pertea

More Info

🧑🏻‍💻   About me

I am a second-year computer science Ph.D. student supervised by Dr. Steven Salzberg and Dr. Mihaela Pertea at Center for Computational Biology, Johns Hopkins University. I received my Bachelor of Science in Electrical Engineering from National Taiwan University (NTU). In my senior year of college, I went on exchange to study at the College of Engineering & Computer Science, Australian National University (ANU).

My area of interest lies in the creation of innovative algorithms that can be applied to computational genomics, with a particular emphasis on transcriptome (RNA sequencing) and genome assembly. I have a particular passion for developing highly efficient algorithms and ultra-fast tools that improve gene annotation precision and the quality of genome. I am also a big fan of open source software. Two of my R packages on Bioconductor are sangeranalyseR and RNASeqR. Visit my research page 🔬 for more information.

Salzberg & Pertea Lab, Center for Computational Biology, JHU
Ph.D. student

  • Building a multi-sample assembler upon StringTie aming to construct a more precise gene catalog. C++ |
  • Improving Liftoff to achieve higher cross-species lift-over accuracy.
  • Assembled Han1, the first gapless Southern Han Chinese individual genome | Han1
  • Conducted the first-ever gene content comparison between two fully annotated individuals, Han1 and T2T-CHM13.
  • Han1 paper (Chao et.al.)

Langmead Lab, Department of Computer Science, JHU
collab with
Seshia Lab, Department of Electrical Engineering and Computer Sciences, UC Berkeley
Research student

  • Developing algorithms to improve the graph-based sequence indexing aiming to apply them to the pan-genome graph.
  • Developed the first Wheeler graph toolkit, WGT, to generate, recognize, and visualize Wheeler graph. C++
  • Proposed a fast algorithm, Wheelie , making the NP-complete Wheeler Graph recognition problem solvable in practice.
  • WGT paper (Chao et.al.)

HK Tsai Lab, Institute of Information Science, Academia Sinica
Research assistant

  • Developed SPIFFED by applying a convolutional neural network to improve current tools on predicting protein-protein interactions using protein co-elution profiles.

Lanfear Lab, Division of Ecology and Evolution, Research School of Biology, ANU
Research assistant

  • Developed a bioconductor R package, sangeranalyseR, to democratize sanger sequencing data analysis in R.
  • Implemented Bandelt tree encoding/decoding algorithm published in 1985.
  • sangeranalyseR paper (Chao et.al.)

Bioinformatics Core Lab, Centers of Genomic and Precision Medicine, NTU
Research assistant

  • Conducted differential gene expression analysis and pathway enrichment analysis using RNA-Seq data.
  • Developed a bioconductor R package to provide a robust pipeline to automate the standard two-group RNA-Seq analysis in R.
  • RNASeqR paper (Chao et.al.)

  • Processed and visualized PC login and logoff history to help the team build a system to find insiders in the company.