Seanome on the Nextflow Podcast

Why Seanome, origin story, and marine genomics pipelines with Nextflow

I was on the Nextflow Podcast! It was great to reconnect with Phil Ewels, who I last talked to in ~2019 (6 years ago?!?) at the “Nextflow Camp” in 2019.

I talked about my 15+ year journey from a double-major in Biological Engineering and Mathematics at MIT (since they didn’t have a computational biology major yet! I had to invent my own), being lucky enough to work in Sean Eddy’s lab as a summer intern at Janelia Farm Research Campus, working in Jill Mesirov’s lab at the Broad Institute, doing a Bioinformatics Master’s degree at UCSC, then a Bioinformatics PhD at UCSD, getting to be part of the early data science team at Chan Zuckerberg Biohub, a stint consulting for Arcadia Science, then learning about drug development at BridgeBio, and finally starting Seanome last year.

A big reason WHY I started Seanome is Botryllus schlosseri, the coolest organism you’ve never heard of. My collaborator, Prof. Ayelet Voskoboynik (also on Seanome’s scientific advisory board!) introduced me to Botryllus Histocompatibility Factor (BHF), a gene that is very similar to our acute organ transplant rejection genes aka histocompatibility genes. AND YET, this gene has no sequence similarity to any human genes! I became obsessed with this and wanted to figure out a flexible way to find similarities between really different genes, and lead to writing the prototype (see an example run here!)

I’m also really excited to reconnect with the nf-core open-source community, which is a lovely group of people helping each other out by making best-practices pipelines in genomics and beyond. I’ve contributed to nf-core/rnaseq, nf-core/scrnaseq, wrote my own nf-core/kmermaid, and am now leading development for nf-core/proteinannotator. We made a bunch of progress on proteinannotator at the May 2025 nf-core Hackathon in Boston at the Nextflow Summit — stay tuned for progress!

🎧 Listen here: Episode 49 — Olga Botvinnik on marine genomics, open science & Seanome