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title: About
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# About me

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.

![My photo](/assets/img/her.jpg)


# Education
- M.D, Taipei Medical University (2013-2019)
- (Current) Ph.D. Student in UCSD Bioinformatics and Systems Biology

# Practical Computational Skills
- Python, R, and Matlab
- PostgreSQL
- Machine Learning and Statistical Modelling.

# Research Experience
- 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](https://drive.google.com/open?id=1vRWpueOYaxMQrsRBAlhqOxLFYbnNDAjC)
    + 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](https://drive.google.com/open?id=1WaI8buVv79Nqwmrgr63iH0zvlX6cMGJn)
    + 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](https://github.com/algaebrown/KIR_development/blob/batch_effect_correction/visualization/20190907_validate_by_ethnicity_allel_freq.ipynb)
    + 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](https://sites.google.com/site/yuwwubioinfo/): [Pan-genomic View on Antibiotic Resistance](https://algaebrown.github.io/research/)
- 2016: Hung-Wen Chiu's Lab: [Using Time-Frequency Features To Recognize Abnormal Heart Sounds](https://drive.google.com/file/d/17egLoQtNStUosdwfVd20eHIGdKoU8iW6/view)
- 2013-2015: Jui-Yu Wu's Lab: Diagnostic PCR Primer Targeting Resistance Genes; Mechanisms of Beta-Lactamase Evolution.

# Publications
[Google Scholar](https://scholar.google.com/citations?user=EQIcQpoAAAAJ&hl=enE); [Research Gate](https://www.researchgate.net/profile/Hsuan_Lin_Her)
- (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)

# Leadership Experience
- 2016 President, [TMU Medical Student Association](https://www.facebook.com/TMUMEDSA/)

# Other Experience
- 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

# Other
- Graphic Design and Visual Art [Portfolio](https://docs.google.com/presentation/d/12F5BlatxtLVkYQ48Kqy66fKiQwjRxkV47duFvHTSVqQ/edit?usp=sharing)
- [Algaebrown's Online Gallery](https://www.facebook.com/pg/AlgaeBrown)
- Cooking: "生資阿宅廚房日記"(translation: Kitchen of a geeky computational biologist)
 
