My name is Jiri Novotny, I come from the Czech Republic, and I am a bioinformatician. Currently I am doing a Ph.D. at the Institute of Molecular Genetics of the Czech Academy of Sciences in the Laboratory of Genomics and Bioinformatics.
Recently I have joined Immunai as a single-cell data curator / computational biologist.
I am usually analyzing transcriptomic data: bulk and single-cell RNA-seq, and qPCR. But I also have some proficiency in general bioinformatics (all those formats, command line tools, etc.) and other methods, e.g. variant calling, chromatin accessibility (ATAC-seq), TCR sequencing, etc.
I like to help biologists to interpret their data in form of reports and visualizations, as well as public services and databases. I am interested in cancer biology, mainly in the tumor microenvironment, extracellular matrix remodeling, and cancer-associated fibroblasts.
- scdrake - a pipeline for droplet-based single-cell RNA-seq data.
I am fluent in R and Python and have experience in making pipelines, general data wrangling and visualization, web development (Python/Django, R/Shiny, HTML5/CSS3, JavaScript), UNIX scripting (bash) and system administration, Git versioning and continuous integration (GitHub Actions). I like to write clean code and documentation (and really appreciate if others also do so 😊). Occasionally, I contribute to open-source projects, or at least open constructive issue tickets.
- AmtDB - database of ancient human mitochondrial DNA (private code, full-stack developer role).
I am also teaching practicals in the Analysis of Gene Expression at the University of Chemistry and Technology in Prague.
To grab the chance to promote my study programme, here is the link: http://studuj.bioinformatiku.cz/
I would say, it's not an easy, but interesting and satisfying field and the future is bright as more people are needed to analyze the neverending, large bunch of biological data or to develop tools that make this task easier for others.
Several times I was also participating as a lecturer at Prague Autumn School - RNASeq Data Analysis Workshop organized by SeqMe company.