Tzu-Ting, Cindy, Wei

Bioinformatician and Biologist based in Berlin, Germany

Email / LinkedIn / Twitter

Education

Doctor of Philosophy (PhD), Computational Methods for Oncology Program (07.2019-present)

Charité – Universitätsmedizin Berlin and Berlin Institute for Medical Systems Biology, Germany

• Established a Snakemake pipeline for statistical analysis and downstream visualisation of allele-specific gene expression (ASE)
• Investigated ASE as smoking injury proxy in CRUK lung cancer cohort (paper)
• Analysed allele-specific copy number in colorectal cancers in collaborations (paper)
• Applied regression methods to predict the functionality of somatic mutations in pan-cancer using WGS, RNA-seq, and epigenetic predictions from a deep leanring model in ICGC PCAWG working group
• Using single cell RNAseq data and somatic variants to uncover phenotypes of tumour-adjacent cells
• Developing an ML framework to identify informative somatic variants from WGS, WES, and single-cell RNAseq data from CRC patients

Master of Science, Translational Medical Research (09.2016-03.2018)

Major in Molecular Oncology, Heidelberg University, Germany

• Analysed differential gene expression to distinguish septic patients from other ICU patients
• Mathematical modelling of gene regulatory network (ODEs) in septic patients’ granulocytes

Bachelor of Science, Department of Life Science (09.2011-06.2015)

Cancer Research Center, National Tsing Hua University, Taiwan

• Investigated the role of PHF8 and PHF2 (histone lysine demethylase) in regulating Helicobacter pylori-induced Interleukin-8 inflammatory responses in gastric cancer
• Thesis won the Ministry of Science and Technology College Research Grant

Experience

Predoctoral Researcher (10.2018-05.2019)

Department of Medicine, University Freiburg Medical Centre, Germany

• Established an ATAC-seq analysis pipeline on Galaxy platform and analysed data from AML patients treated with hypomethylating agents
• Conducted RNA-seq analysis for a phase I clinical trial-TRANSATRA

Visiting Researcher (10.2018-12.2018)

Division of Applied Bioinformatics, DKFZ, Germany

• Built a random forest classifier to distinguish tissue of origin using GTEx RNAseq data

Research Assistant and Project Manager (08.2015-06.2016)

National Applied Research Laboratories, Taiwan

• Developed, published, and patented an image-based noninvasive blood glucose evaluation algorithm (paper)
• Managed a national pioneer grant, tasks including close monitoring of 17 laboratories developing Internet of Things devices in cooperation with various enterprises, annual demonstration event curation and execution, and performance evaluation

Activities

Industry Perspectives on Innovative Medicine - Best Presentation (08.2017)

EIT Health and University of Groningen and University Medical Centre

• Noninvasive intra-abdominal pressure monitoring device using impedance measurement (new medical application for ICU patient).

Life Science Meets IT Hackathon - 2nd Place and Best Business Case (05.2017)

EIT Health, Heidelberg University, and Heidelberg Startup Partners, Germany Prototyped a patient-centric blockchain solution (Ethereum) to reduce counterfeit medicine along the medicine supply chain, later published as a working paper

Skills

Programming and Systems tools

Python, R, Git, Jupyter Notebook, Bash Script, Linux, Mac OS, HPC (SGE and Slurm), Docker, Google Colab

Language

English (fluent/C1), Mandarin and Taiwanese (Native), German (intermediate/B1)

Publication and Poster

• Stella de Biase, Florian Massip, Tzu-Ting Wei, …, et al. Smoking-dependent expression alterations in nasal epithelium reveal immune impairment linked to germline variation and lung cancer risk, medRxiv, 2021

• Florian Uhlitz, Philip Bischoff, Stefan Peidli*, …Tzu-Ting Wei, …, et al. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer, EMBO Mol Med, 2021

• “Metabolism control and immune regulation via signal transduction in the pathophysiology of sepsis” 2017 17th Congress of European Shock Society (poster)
• “Identification of a sepsis-specific gene expression signature and signalling network in human granulocytes” 2017 17th Congress of European Shock Society (poster)
• T. Wei*, H. Tsai, C. Yang, W. Hsiao and K. Huang, Noninvasive glucose evaluation by human skin oxygen saturation level, IEEE International Instrumentation and Measurement Technology Conference Proceedings, 2016