Biography

I am a senior bioinformatician and research scientist with expertise in statistical methods, machine learning, modeling, and pipeline development. I have a proven track record of success in developing and applying bioinformatics to solve challenging problems in biology. My PhD thesis was selected as a case study for New Zealand eScience Infrastructure and published in eLife, receiving the Best Publication Award from my PhD institution. I have also developed various open-source bioinformatics software and workflows for biologists, downloaded by thousands. I am always eager to collaborate to solve challenging problems in biology, biostatistics, and bioinformatics.

The tools that I developed and published:

Tool	Download	Purpose
MirMachine		microRNA homology search tool using machine learning
Cellsnake		single-cell analysis tool for everyone

Research Interests

• Modelling and early prediction models in the context of personalized medicine
• Molecular oncology and cancer
• RNA biology, especially non-coding RNAs such as microRNAs, tRNA-derived molecules
• RNA-RNA interactions
• Biostatistics and molecular epidemiology
• NGS (DNA and RNA sequencing), transcriptomics from bulk RNA sequencing to spatial transcriptomics
• Reproducible bioinformatics pipelines, mostly using Snakemake, shell scripts, Python and R programming

Skills

• R, I am quite capable in tidyverse syntax (ggplot, caret, mlr3, Rmarkdown, shiny apps, functional programming, parallelization)
• Machine learning and data analysis in R
• Python (especially in bioinformatics context)
• Snakemake (I develop pipelines and also teach Snakemake)
• Biostatistics (basic modeling, survival models, and some newer machine learning algorithms)
• Linux (shell scripting and high-performance computing systems)
• Data Science and Machine learning (for predictive models, especially in R and Python, h2o, caret, Keras)