Hsuan-lin has a dream in integrating computational biology with medicine. After receiving M.D. in Taipei Medical University, she decided to pursue Ph.D. in Bioinformatics and Systems Biology in UCSD. Now she is a student in the Yeo Lab, aiming to decode post-transcriptional regulation using computational methods.
- M.D, Taipei Medical University (2013-2019)
- (Current) Ph.D. Student in UCSD Bioinformatics and Systems Biology
Practical Computational Skills
- Python, R, and Matlab
- Machine Learning and Statistical Modelling.
- 2020 Gene Yeo Lab: A New eCLIP pipeline
- Upgrade peak caller CLIPper to python 3
- Implement Metagene density for RNA-binding protein(RBP) function hypothesis
- Improving RBP binding site identification
- Collaborate with experimental biologist to investigate RBP role on metabolism and COVID.
- 2019 Winter Rotation: Trey Ideker Lab: Visible Neural Network(VNN) to Embed single cell RNA-seq in an interpretable latent space
- Formulate an information-theory-based criteria to prune Gene Ontology.
- Implemented Gene-Ontology based Neural Network and autoencoder.
- Sucessfully Embed neuronal subtypes in Gene ontology axes.
- 2019 Fall Rotation: Nathan Lewis Lab: Single Cell Secretome in Haematopoietic Stem Cells
- Analyze and combine several stromal and haematopoietic scRNA-seq
- Identify candidate cell-cell interaction that drive cell fate decision
- Collaborate with colleague to construct cell-cell functional enrichment pipeline and visualization.
- 2019 Summer Rotation: Hannah Carter Lab: Estimating KIR copy number from Whole Exome Sequencing data
- Resolved batch effect in Killer-Immunoglobuilin-like receptor(KIR) copy number variation with integrated NMF(iNMF).
- Corrected copy number matched populational allel frequency.
- 2016-now: Yu-Wei Wu’s lab: Pan-genomic View on Antibiotic Resistance
- 2016: Hung-Wen Chiu’s Lab: Using Time-Frequency Features To Recognize Abnormal Heart Sounds
- 2013-2015: Jui-Yu Wu’s Lab: Diagnostic PCR Primer Targeting Resistance Genes; Mechanisms of Beta-Lactamase Evolution.
- (In Prep)PangenomeNet: A pan-genome-based func-tional network approach for mining potential antibiotic-resistance hypothetical genes for Escherichia coli strains
- A pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains. HL Her, YW Wu. Bioinformatics 34 (13), i89-i95(2018)
- Using time-frequency features to recognize abnormal heart sounds. H Her, HW Chiu. Computing in Cardiology Conference (CinC), 2016, 1145-1147 (2016)
- 2016 President, TMU Medical Student Association
- 2017 TMU Programming competition 1st Place: RentBot; Backend design.
- 2018 Future finance and healthcare hackathon: Buver, a weight loss solution.
Honors and Grants
- 2017 and 2018 Ministry of Science and Technology, Student grant
- 2018 Foundation of the Advancment of Outstanding Scholarship Travel Grant
- 2013 Academic Excellence Award