May, 15th 2018

Hi!

I'm Federico Marini, Virchow Fellow @CTH Mainz/IMBEI

PhD in Biostatistics/Bioinformatics @IMBEI:
Development of applications for interactive and reproducible data analysis

\(\rightarrow\) Methods and tools to maximize information extraction and knowledge transfer, strengthen translational interactions




You can find this presentation here: https://federicomarini.github.io/erum2018/
@FedeBioinfo

Background

  • large amounts of complex datasets - everywhere!
  • lack of analytical skills: data understanding << data generation

Wishlist for accessible and robust data analyses:

  • Comprehensiveness
  • Interactivity (empowers the domain expert \(\rightarrow\) better insights)
  • Reproducibility (re-performing the same analysis with the same code)

Enabling transparency, independent verification, standing on the shoulder of giants

Particularly true in the field of Bioinformatics!

RNA-seq

High-dimensional snapshot of the transcriptomic activity

RNA-seq: genes \(\times\) samples tables
Aim: identification of differentially expressed genes, gene signatures, many more

Platelets transcriptomics

Exploratory Data Analysis (EDA) + Differential Expression (DE) analysis \(\rightarrow\) analyze, visualize, integrate

  • thrombocytes: anucleated, yet carrying a vast repertoire of transcripts
  • scenarios: alteration of thrombin signaling, crosstalk with tumor development

🙏 The Bioconductor project makes these task possible for many researchers!

My contributions:

\(\rightarrow\) Web-based applications enabling interactivity and reproducibility

Under the hood