Senior Bioinformatics Scientist  •  Inti Labs, Taiwan

Sep. 2022 - Current

• As the chief bioinformatics scientist, facilitated the company's product development in genetic testing for reproductive medicine.
  • Utilized miRNA gene expression to predict the optimal timing for transferring fertilized embryos into the uterine endometrium. Developed a machine learning training pipeline using NVIDIA cuML and cuDF, resulting in a significant 4-fold reduction in the development time.
  • By utilizing AWS cloud computing services such as EC2, S3, and AWS Batch, the computational time of the bioinformatics pipeline was reduced by over 3 times. The integration of these services resulted in faster data processing and analysis, significantly enhancing the efficiency and performance of the bioinformatics workflow.
• As the planner for the company's server room, responsible for designing and implementing all hardware and network infrastructure for the new facility.
  
  • Successfully established an information server room from scratch, including user requirement analysis, network and hardware planning, access control system implementation, firewall configuration, and equipping meeting rooms while adhering to budget and timeline constraints.

Bioinfromatics Team Lead, Manager, Engineer   • ACT Genomics, Taiwan

Jun. 2014 - Aug. 2022

• Chief developer of the bioinformatics pipeline at the company to provide clinical cancer diagnostic services using next-generation sequencing platforms
  • Implemented NVIDIA Clara Parabricks to accelerate the analysis pipeline, reducing the processing time from two hours to just 20 minutes. Ensured the alignment process in Parabricks produced identical results compared to the traditional workflow through rigorous validation.
    
  • Organized a machine learning project to improve variant calling accuracy and reducing false-positives in Ion Torrent next generation sequencing data, reducing the manual analysis time by ~20%

  • Refactored the workflow of the bioinformatics analysis software using Nextflow, facilitating deployment of the software in both on-premises and cloud environments. Implemented scalable solutions to meet the demands of high-throughput analysis requirements.

  • Constructed a variant calling method from scratch for the detection of circulating tumor DNA for calling low frequency (~0.5%) variants with high specificity and sensitivity
  • Integrated the ion torrent variant caller into an in-house analysis pipeline, which enhanced the variant calling performance in several aspects, such as reducing the false-negative rate by ~10% during variant candidate generation.
  • Led the bioinformatics development for cancer panel analysis, encompassing products targeting 50 or 500 genes in cancer tissue samples (FFPE). Additionally, involved in the development of assays for blood-based testing, genetic cancer screening and cancer fusion gene detection.
    

• Agile development of bioinformatics for clinical sequencing services
  • Organized and led a bioinformatics team to conduct research and development of IVD products (ACTOncoIVD, USFDA)
  • Served as the person in charge of bioinformatics for assisting and obtaining the first certification of laboratory developed tests (LDTs) in Taiwan.
  • Implemented a quality assurance workflow for bioinformatics analysis under CAP & ISO-17025 regulations
  • Utilized JIRA to manage both internal and external user requirements, ensuring smooth communication and collaboration across teams.
  • Established Git flow process for software testing, version control, and release management, resulting in improved software development control and quality assurance.

Bioinformatics Engineer •  Cold Spring Biotech Corp., Taiwan

May 2014 - Jun. 2014

• Bioinformatics analysis support for the Pacific Biosciences sequencing services 

• Hardware and software maintenance of the Pacific Biosciences sequencers

Bioinformatics Engineer •  Genomics Biotech, Inc., Taiwan

Aug. 2012 - May 2014

• Provided bioinformatics solutions for viral genome assembly, variant calling/annotation, 4C-seq, RNA-seq analysis, viral DNA detection in liquid biopsy, antibody analysis and other customized analysis
• Established a real-time quality-control pipeline and a reporting system for the Illumina HiSeq, MiSeq, 454 Junior and Ion torrent sequencing platforms

Research Assistant •  Joint Genome Institute at Los Alamos National Laboratory, USA

Oct. 2008 - Jan. 2009

• Assisted in conducting research projects under the supervision of senior researchers at Gary Xie's lab.
  
• Performed a sequence comparison pipeline to classify subtypes of Clostridium botulinum