Yu-Te Lin

Bioinformatics Scientist, PhD · Singapore

PhD bioinformatics scientist with 8+ years building production-ready pipelines and ML tools for NGS, RNA-seq, single-cell, and genome-scale metabolic modeling. I turn complex biological data into reproducible software — open-source Python packages, web platforms (Django/React), and ML inference apps used by labs and clinicians. Singapore PLOC holder, eligible to work immediately.

Work

  1. Sep 2017 – Aug 2025
    Graduate Researcher (PhD) · National Taiwan University
    Taipei, Taiwan
    • Built a diagnostic RNA-seq classification pipeline using a VAE to compress transcriptomes — AUROC 0.98 (vs. 0.75 baseline), AUPRC 0.88 (vs. 0.34), and ~40× faster inference for rare-disease prediction. Manuscript in preparation, to be submitted soon.
    • Developed pipeGEM, a Python framework integrating RNA-seq with genome-scale metabolic models; adopted by 8+ external research labs. → pipeGEM
    • Developed MitoTox, a web-based mitochondrial toxicity database (PostgreSQL + Django) with 100,000+ chemicals — cited 40+ times and used in predictive toxicology research. → MitoTOX
    • Shipped open-source bioinformatics tools with 35,000+ PyPI downloads; full CI/CD, unit tests, and Dockerized environments for reproducibility.
    • Built a PyQt6 desktop app wrapping the RNA-seq + ML inference pipeline so clinicians can run end-to-end transcriptomic analysis through a GUI. Manuscript in preparation, to be submitted soon.
    • Developed biodbs, a Python utility unifying programmatic access to 12+ biological repositories (KEGG, NCBI, ChEMBL), backing the MitoTox dataset. → biodbs
    • Built an image-based cell-counting pipeline (scikit-learn, cellpose, OpenCV) that beat commercial counters on non-spherical cells: +0.3 mean IoU, +0.4 mAP. → img_processor
    • Ported scTenifoldNet/Knk from MATLAB/R to Python for reproducible single-cell network analysis. → scTenifoldpy
    • Partnered with clinicians, wet-lab scientists, and engineers across 5+ projects; mentored 4 MSc students through to conference posters.
  2. Apr 2017 – Jul 2017
    Research Assistant (contract) · World Vegetable Center (AVRDC)
    Tainan, Taiwan
    • Ran high-throughput genotyping and PCR assays — wet-lab grounding that informs downstream computational modeling.

Repositories

scTenifoldpyPython

Python implementation of scTenifoldNet and scTenifoldKnk workflows for single-cell network analysis.

sctenifoldpy downloadsscTenifoldpy CIsctenifoldpy docs
★ 60
pipeGEMPython

Integrate omics data with genome-scale metabolic models and run comparative constraint-based analysis.

pipegem downloadspipeGEM CIpipegem docs
biodbsPython

Unified Python interface for fetching and structuring data from 12+ biological databases (KEGG, NCBI, ChEMBL, …).

biodbs downloadsbiodbs CIbiodbs docs
ppi_net_builderPython

Protein–protein interaction network construction and analysis in Python.

ppi-net-builder downloadsppi_net_builder CI
confocal_mito_analysisPython

Confocal image analysis pipeline for mitochondrial morphology — segmentation and quantification (NTU Mito Lab).

dox-ac16-omics-analysisPython

Multi-omics analysis pipeline for doxorubicin-treated AC16 cardiomyocytes — companion code for the npj Syst. Biol. Appl. paper.

MitoTOXDjango / PostgreSQL

Web-based mitochondrial toxicity database — 100,000+ chemicals, PostgreSQL + Django. Cited 40+ times in predictive toxicology research.

submission-navPython

Practical AI skill for academic submission workflows — turn manuscripts into ranked journal shortlists, compare author guidelines, plan revisions.

Selected publications

  • Temporal analysis of doxorubicin-induced cardiac toxicity and hypertrophy
    Lin Y-T, et al. · npj Systems Biology and Applications · 2025
  • Interpretable modeling of time-resolved single-cell gene–protein expression with CrossmodalNet
    Yang Y, Lin Y-T (2nd author), et al. · Briefings in Bioinformatics · 2023
  • MitoTox: a comprehensive mitochondrial toxicity database
    Lin Y-T, et al. · BMC Bioinformatics · 2021
  • Transcriptomic and metabolic network analysis of metabolic reprogramming and IGF-1 modulation in SCA3 transgenic mice
    Lin Y-T, et al. · International Journal of Molecular Sciences · 2021

Full publication list on Google Scholar →

Education

  • 2017 – 2025
    PhD, Biomedical Electronics and Bioinformatics
    National Taiwan University
    GPA 4.12/4.3. Thesis: Mechanistic and predictive models of mitochondrial dysfunction in toxicology and genetic disease. Awarded MOST Ph.D. Scholarship.
  • 2012 – 2017
    B.S., Life Sciences
    National Cheng Kung University