CV

Education

• Ph.D in Computer Science, Johns Hopkins University, 08/2021 - present
• M.S. in Electronics Engineering, National Taiwan University, 09/2016 - 06/2019
• B.S. in Electrical Engineering, National Taiwan University, 09/2012 - 06/2016

Work experience

• Roche, Summer Intern, Computational Biology Molecular Lab Appplications, 06/2024 - 08/2024
  • Developed a structural variant calling pipeline to enhance recall and precision on a new sequencing platform.
• Apple, Product Design Intern, Input Device Team, 01/2018 - 07/2018
  • Developed circuit solutions and prototype software to a new MacBook keyboard design.
• Himax, Summer Intern, Video Image Processing Team, 07/2017 - 08/2017
  • Developed compression algorithms for 3D depth sensing solutions.

Skills

• Programming Languages: Python, R, C++, MATLAB
• Hardware Design: Verilog, FPGA, Arduino
• Tools: git, Latex, Bash, Snakemake

Selected Publications

IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads

Lin, Mao-Jan, Ben Langmead, and Yana Safonova. "IGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads." bioRxiv (2024).

Measuring, visualizing, and diagnosing reference bias with biastools

Lin, Mao-Jan, et al. "Measuring, visualizing, and diagnosing reference bias with biastools." Genome Biology 25.1 (2024): 101.

Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite

Lin, Mao-Jan, et al. "Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite." Frontiers in Immunology 13 (2022): 922513.

Hardware Accelerator Design for Dynamic-Programming-Based Protein Sequence Alignment with Affine Gap Tracebacks

Lin, Mao-Jan, Yu-Cheng Li, and Yi-Chang Lu. "Hardware accelerator design for dynamic-programming-based protein sequence alignment with affine gap tracebacks." 2019 IEEE Biomedical Circuits and Systems Conference (BioCAS). IEEE, 2019.

Teaching

• Teaching Assistant, Department of Computer Science, JHU 01/2025 – 05/2025
  • Sketching and Indexing for Sequences (EN.601.646) by Dr. Ben Langmead
• Teaching Assistant, Department of Computer Science, JHU 08/2022 – 12/2022
  • Introduction to Computational Immunogenomics (EN.601.451) by Dr. Yana Safonova
• Host of the Lab Programming Workshop, Lab of Dr. Pei-Lung Chen 09/2020 – 11/2020
  • Python training for clinical data processing
• Teaching Assistant, Department of Biomechanical Engineering, NTU 07/2020 – 08/2020
  • Bioinformatics Algorithms (BME5938) by Dr. Chien-Yu Chen