Data Scientist

• Oct 2023 - Present

- Maintaining in-house data mining and analysis pipeline (R packages, pthyon). - Processing, cleansing, and validating the integrity of experiment data to be used for analysis. - Maintaining and deploying LLM models. - Using machine learning tools to optimize in-house mammalian phenotype classifier models. - Data mining or extracting usable data from valuable data sources. - Collaborate with Business teams to prioritize business challenges and provide solutions. - Maintaining in-house data mining and analysis pipeline (R packages, pthyon). - Processing, cleansing, and validating the integrity of experiment data to be used for analysis. - Maintaining and deploying LLM models. - Using machine learning tools to optimize in-house mammalian phenotype classifier models. - Data mining or extracting usable data from valuable data sources. - Collaborate with Business teams to prioritize business challenges and provide solutions.

Data Analyst | Bioinformatician | Researcher

• Oct 2022 - Oct 2023

At Radboud University, I am working on several exciting projects where I am using data science and data engineering skills (using R and Python), as well as deploying machine learning models on cloud: #Research Project - Building a large dataset of DNA-DNA and DNA-protein interactions combining several types of high-throughput next generation sequencing (NGS) data in linux bash. The end goal is to Investigating the dynamic changes in 3D chromosome architectures of our interested region. #Support project - Cross validate the alternative transcripts identified in human PBMC under various stimulations (stimulation-dependent isoform switch). Currently Fantom5 is used for the cross validation. #Teaching assistant for Genomics and Big Data (NWI-BP031). Designing, teaching and grading students how R and R studio are used in genomics study. Focus on data processing and visualization, including basic R commands, dplyr, and ggplot. Show less

Data analyst | Bioinformatician | Researcher

• Dec 2021 - Sep 2022

At RIKEN, I collaborated with scientists, and collected, processed, visualized, and statistically analyzed data; and wrote my findings the results in a scientific journal. #Research Project - Identifying microbiota-dependent, aging-related biomarkers from various datasets, including RRBS, 16SrDNA, and RNA seq using R, python, and tableau. I Identified 3000+ microbiota-dependent, aging-related DNA methylation and 2600+ genes with R (feature extraction, k-means clustering, t-SNE, Pearson's correlation, time-series analysis). #Side Project1 - Identifying more than 210+ aging biomarker in large intestine from various public dataset using Python, R, scanpy, and pandas. Data were obtained from Amazon S3 or GEO database. I also delivered the dataset in an interactive platform using Tableau (https://public.tableau.com/app/profile/tsunghan.hsieh/viz/Tabula_muris_LargeIntestine/1#1). #Side Project2 - Global vaccination for Covid19 (SQL, docker, Azure Data Studio, Azure SQL Edge, Tableau) - Download data from public data source and clean data in SQL. - Build a SQL server running on docker for hosting global Covid19 data. - Run ETL process pipeline for extracting data by SQL (IDE: Azure Data studio). - Visualize data and provide useful insight by Tableau. - https://public.tableau.com/app/profile/tsunghan.hsieh/viz/covid19_16606524256070/1 Show less

Junior Research Fellow

• Nov 2021 - Dec 2021

PHD Candidate

• Sep 2015 - Oct 2021

In OIST, I was working as a PhD student to design and perform experiments using CRISPR-CAS9 genome editing, mouse model, ELISA. I was also designing, building, and maintaining the data process pipeline of various NGS data in HPC environment using Linux Shell, Linux Bash, Python, and R. The statistical method used in this project are: t-test, Wilcoxon signed rank, Pearson's correlation, F-test, linear regression, Analysis of Variance (ANOVA), and Principle component analysis (PCA).#Research Project: Identifying the role of AP-1 member JunB in T helper cell differentiation.- Publication: Hsieh T, Sasaki D, Taira N, Chien H, Sarkar S, Seto Y, Miyagi M and Ishikawa H (2022) JunB Is Critical for Survival of T Helper Cells. Front. Immunol. 13:901030. doi: 10.3389/fimmu.2022.901030- Publication: Koizumi, Shin-ichi, Daiki Sasaki, Tsung-Han Hsieh, Naoyuki Taira, Nana Arakaki, Shinichi Yamasaki, Ke Wang, et al. “JunB Regulates Homeostasis and Suppressive Functions of Effector Regulatory T Cells.” Nature Communications 9, no. 1 (December 2018): 5344. https://doi.org/10.1038/s41467-018-07735-4. Show less

Intern

• Jun 2017 - Jul 2017

- Examined the development and differentiation of human hematopoietic stem cells in humanized mouse model. - Prepared human hematopoietic stem cells from volunteer donors and inject into recipient mice. - Tracked the development and function of human DC, CD4 T, CD8 T, and B cells in recipient mouse organs by using flow cytometry. - Examined the development and differentiation of human hematopoietic stem cells in humanized mouse model. - Prepared human hematopoietic stem cells from volunteer donors and inject into recipient mice. - Tracked the development and function of human DC, CD4 T, CD8 T, and B cells in recipient mouse organs by using flow cytometry.

Project Manager

• Jan 2014 - Jul 2015

- Developed a IC-based, next generation DNA sequencer (NGS). - Designed and tested a new method for single-molecule DNA library preparation. - Collaborated with faculty from National Taiwan University to design a method of delivering single-molecule DNA into designated microwells. - Developed a IC-based, next generation DNA sequencer (NGS). - Designed and tested a new method for single-molecule DNA library preparation. - Collaborated with faculty from National Taiwan University to design a method of delivering single-molecule DNA into designated microwells.

Product manager

• Jun 2013 - Dec 2013

- Built prototype for an automated nucleic acid purification instrument within 6 months. - Designed and optimized chemical compositions in reagents of nucleic acid purification kits. - Built prototype for an automated nucleic acid purification instrument within 6 months. - Designed and optimized chemical compositions in reagents of nucleic acid purification kits.

Sales Representative

• Jun 2012 - Jun 2013

- Successfully sold six sets within one year under a fierce competition from Merck Millipore. - Successfully sold products to clients three months after entering the company. - Conducted cold call to develop new clients. - Made joint call with local distributors. - Successfully sold six sets within one year under a fierce competition from Merck Millipore. - Successfully sold products to clients three months after entering the company. - Conducted cold call to develop new clients. - Made joint call with local distributors.

Molecular Biologist

• Dec 2010 - Jun 2012

- Designed and tested nucleic acids purification toolkits and realtime PCR reagents. - Successfully launched new products within less than one year, including LabPrep (nucleic acids purification tool kits) and LabStar (realtime PCR reagents). - Wrote ISO 13485 Quality Manual for a new factory, which was built for production of IVD reagents. - Designed and tested nucleic acids purification toolkits and realtime PCR reagents. - Successfully launched new products within less than one year, including LabPrep (nucleic acids purification tool kits) and LabStar (realtime PCR reagents). - Wrote ISO 13485 Quality Manual for a new factory, which was built for production of IVD reagents.

R&D

• Feb 2010 - Dec 2010

- Designed and conducted proof-of-concept experiments for ccPCR in detection of Mycobacterium tuberculosis (TB). - ccPCR is a technique which allow the amplification of DNA/RNA under a fixed temperature. - Designed and conducted proof-of-concept experiments for ccPCR in detection of Mycobacterium tuberculosis (TB). - ccPCR is a technique which allow the amplification of DNA/RNA under a fixed temperature.

Teaching Assistant

• Sep 2008 - Feb 2010