Chung-Der Hsiao is Distinguished Professor of Chung Yuan Christian University for Department of Bioscience Technology. He completed the undergraduate and graduate education in National Taiwan University (majored in Fishery Science). By 2007, Chung-Der was recruited by Chung Yuan Christian University and established his own laboratory, where he used the cutting-edge methods to generate many zebrafish disease models like apoptosis, obesity, skin cancer and aging. From 2019, Chung-Der was promoted as full professor of CYCU; and from 2021, Chung-Der was promoted as director of Research Center for Aquatic Toxicology and Pharmacology. Recent studies in Chung-Der’s lab focus on using deep learning technology to study animal neuro behavior and cardiac physiology. Chung-Der (H-index 44) is author of over 250+ high impact journal articles, including Nature, Nature Physics, Biomedicine & Pharmacotherapy, Environmental pollution, Ecotoxicology and Environmental Safety etc. Heis frequently invited to talk at international and local conferences across a diverse range of fields, and has also spoken to school, students and public audiences. His research has strong application potentials and several patents have been issued regarding to use zebrafish as a human disease models like aging, obesity and cancer. (https://www.researchgate.net/profile/Chung_Der_Hsiao)
In our lab (http://cdhsiao.weebly.com/), we have setup several simple and cost-effective devices and deep learning-based methods to measure cardiac rhythm, blood flow, swimming activity and behavior in zebrafish. We believe those settings will benefit zebrafish community in the fields of cardiovascular physiology, excise physiology and behavior studies. Can visit our lab website for details.
Zebrafish genetic mutant screening and gene functional manipulation, High efficient plasmid construction by using Gateway recombination, High efficient transgenesis in Zebrafish by using Tol2 transposon, Conditionally gene expression by using Heat shock and Cre/LoxP system, Fluorescent double in situ hybridization and immunostaining, Confocal laser scan microscope and cell imaging, High resolution histology by using resin section, Image-based cytometry analysis of cell cycle deregulation, Transcriptomic analysis of gene expression by microarray and deep sequencing, TALEN/CRISPR-mediated gene knock out technology, Large-scale screening of suitable antibodies for serving Zebrafish community, Development of new small animal models suitable for performing drug screening, Animal behavioral assessment and new deep learning-based software development. Image analysis and locomotion tracking for experimental animals.
Awards/Honours:
2001 Chien-Tien Hsu’s Award Presentation,
The Chinese Society of Cell and Molecular Biology
2001/2002 Outstanding Students Conference Travel Grant,
Foundation for the Advancement of Outstanding Scholarship
2004 Distinguished Postdoctoral Fellowship, Academia Sinica
2004 Research Travel Grant, Max-Planck-Institute of Molecular Genetics, Germany
2004 Outstanding Post-Doctor Researchers Conference Travel Grant, Foundation for the Advancement of Outstanding Scholarship
2006 Visiting Scientist Research Grant, IMCB, A-Star, Singapore
2009 Visiting Scientist Research Grant, Genome Research Center, Academia Sinica
2020 Annual subsidies research rewards for colleges and universities
2021 Annual subsidies research rewards for colleges and universities
2022 Annual subsidies research rewards for colleges and universities
2023 Annual subsidies research rewards for colleges and universities
2025 Selecetd as Top 0.5% scholar in the Boiology field by ScholarGPS
B.Sc. (1991-1995) Department of Zoology, National Taiwan University
M.Sc. (1995-1998) Institute of Fisheries Science, National Taiwan University
Ph.D. (1998-2002) Institute of Fisheries Science, National Taiwan University
Postdoc (2003-2004) Institute of Molecular Biology, Academia Sinica
Distinguished Postdoc (2004-2006) Institute of Cellular and Organismic Biology, Academia Sinica
Visiting scientist (2006/3-2006/12) Institute of Molecular and Cellular Biology (IMCB), A-Star, Singapore
Visiting scientist (2009/7-2009/12) Genome Research Center, Academia Sinica
Assistant professor (2007/8-2013/7) Department of Bioscience Technology, Chung Yuan Christian University
Associate professor (2013/8-2019/7) Department of Bioscience Technology, Chung Yuan Christian University
Professor (2019/7-now) Department of Bioscience Technology, Chung Yuan Christian University; Department of Chemistry, Chung Yuan Christian University
Vice Director (2021/7-now), Center of Nanotechnology, Chung Yuan Christian University
Director (2021/7-now), Research Center for Aquatic Toxicology and Pharmacology, Chung Yuan Christian University
Distinguished Professor (2024/7-now)
Job Description
Current research topics in my lab: 1. Use cutting-edge computer vision technology like YOLO, SAM3 to do multiple animal behavior tracking. 2. Professional software development to conduct fully automatic data analysis for animal behaviors.
Preferred Intern Educational Level
Master and PhD students are welcome to join my lab to do collaboration.
Skill sets or Qualities
Need a strong foundation in your specific field (e.g., AI, Biotech). Experience with laboratory techniques or data analysis is highly valued. Good English proficiency is required.
Job Description
The RNA-Seq Analysis Pipeline: Interns are expected to understand the logic of the standard pipeline, even if they haven't mastered every tool: Quality Control (QC): Using tools like FastQC and MultiQC to assess raw FASTQ files. Preprocessing: Trimming adapters and low-quality bases (e.g., Trimmomatic, fastp). Alignment/Mapping: Aligning reads to a reference genome/transcriptome (e.g., STAR, HISAT2, Salmon, Kallisto). Quantification: Generating gene counts (e.g., FeatureCounts, HTSeq). Differential Expression (DE): Identifying genes that change across conditions (e.g., DESeq2, edgeR). Functional Annotation: Gene Ontology (GO) and Pathway Analysis (KEGG, Reactome) using packages like clusterProfiler.
Preferred Intern Educational Level
Undergraduate or graduate: specifically seek PhD or Master’s students.
Skill sets or Qualities
Core Technical Skill Set: The "Transcriptomics Stack" is fairly standardized across academia and industry.
| Category | Must-Have Skills | Preferred/Advanced Skills |
|---|---|---|
| Programming | R (Bioconductor) and Python (Pandas, NumPy, Biopython). | C++ (for algorithm development) or SQL. |
| Operating Systems | Linux/Unix Command Line (Bash scripting is essential for running tools). | High-Performance Computing (HPC) or Cloud (AWS/GCP). |
| Workflow Tools | Git/GitHub for version control. | Nextflow or Snakemake for reproducible pipelines. |
| Visualization | ggplot2, ComplexHeatmap, or Seurat (for single-cell). | R Shiny for creating interactive dashboards. |