Computational biologist (PhD). Geneticist by training, bioinformatician by trade.
I work on microbial genomics, mostly genome mining: finding and characterizin biosynthetic gene clusters across genomes and metagenomes. I build the pipelines and tools that make that work reproducible, and I do the wet-lab side myself.
Currently doing postdoc at Wageningen University (Medema group).
Stack: R · Python · bash · Nextflow
Work: metagenomics · metatranscriptomics · phylogenetics · functional annotation · machine learning
- BGCViz — Shiny app that cross-references BGC predictions from different tools using genomic coordinates, so you can see where they agree and where they don't
- rRNADif — quantifies intragenomic 16S rRNA variation and places copies on a tree (docs)
- ashelper — helper methods for antiSMASH and BiG-SCAPE output; standardizes BGC visualization for metagenomic data
- hrmR — high-resolution melt (HRM) analysis for qPCR data
- Mag_cleaning_pipeline — automated cleaning and QC of metagenome-assembled genomes
- bigscape_pfam_explorer — explore BiG-SCAPE gene cluster families alongside their Pfam domain content
- pfam_tools — utilities for Pfam-based functional annotation
BGCViz and rRNADif I wrote from scratch during my time in the Ostash group, which is why they live under that org.
Also contributed to metaWRAP (my commits).