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Erin Young

@erinyoung.bsky.social

Public Health #Bioinformatician. Wants to sequence ALL THE THINGS. Personal account with alternative spellings and grammar structures. She/her

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Erin Young@erinyoung.bsky.social · yesterday

Sequencing contamination is a total horror story… but at least Blobtools makes the disaster look aesthetic! 🎨🦠🧬🖥️ Spotting two clear coverage tiers (E. coli at ~25x and S. enterica at ~7x) in what was supposed to be a single sample. Beautiful chaos.

A Blobtools taxonomic blobplot showing high contamination in a non-isolate sample. The central scatter plot shows two distinct major clusters of contigs around 50–55% GC content: a higher-coverage cluster around 20–30x predominantly assigned to Escherichia coli (blue), and a lower-coverage cluster around 5–8x dominated by Salmonella enterica (orange), along with taxonomic hits to Shigella species and undefined contigs. Marginal histograms summarize total span (kb) across GC proportion and coverage.
Erin Young@erinyoung.bsky.social · 2w ago

I'm thrilled to be attending Nextflow/nf-core Data Carpentry In-Person Training (hosted by APHL) next week! That being said... I am also sweating a little bit knowing the backend who keeps our sequencing analysis running smoothly is also going. Wish our systems luck while we're out!

Erin Young@erinyoung.bsky.social · 2mo ago

I need a 3-stage pipeline or a trio-sequencing tool to build, solely so I can name it "The Three Sisters" and have a professional excuse to post my Goblin Valley photos.

The Three Sisters rock formation in Goblin Valley against a bright blue sky, featuring a partial view of a colorful Pokémon hat at the bottom.The shadowed side of the Three Sisters sandstone rock formation in Goblin Valley, showcasing three distinct pillars atop a large rock base against a bright blue sky.
Erin Young@erinyoung.bsky.social · 2mo ago

Setting new professional goals is always a great chance to reflect. This year, I’m continuing to evolve my previous objectives while channeling a lot of energy into leading the incredible AMD Mountain Region Bioinformatics Code Club! 💻🧬 Take a look at what we've been building:

GitHub - erinyoung/AMD-Mountain-Region-Bioinformatics-Code-Club: The AMD Mountain Region Bioinformatics Code Club is a 30-minute virtual session designed for public health professionals who want to st...

The AMD Mountain Region Bioinformatics Code Club is a 30-minute virtual session designed for public health professionals who want to strengthen their bioinformatics skills. Each session is hands-on...

github.com

Erin Young@erinyoung.bsky.social · 4mo ago

Finished the first week of MTN region code club, which was all about common Bioinformatic files: FASTQ, FASTA, SAM/BAM, BED, and VCF 🧬🖥️

AMD-Mountain-Region-Bioinformatics-Code-Club/2026-03-25 at main · erinyoung/AMD-Mountain-Region-Bioinformatics-Code-Club

The AMD Mountain Region Bioinformatics Code Club is a 30-minute virtual session designed for public health professionals who want to strengthen their bioinformatics skills. Each session is hands-on...

github.com

Erin Young@erinyoung.bsky.social · 5mo ago

I was recently reminded just how much I love geNomad's beautifully boxed summary information. It includes a clear file trees and built-in explanations for every output file in the stdout. 🧬🖥

Text box with white text and a black background with the output from geNomad with indications of the output files and what those files are.
Erin Young@erinyoung.bsky.social · 5mo ago

I had a fantastic morning connecting with some incredibly inspiring young scientists at our local STEM fair! Congratulations to all the students who showcased their curiosity, creativity, and hard work! (And their corresponding adults.) The future of science is bright! #sciencefair #STEM

A flier with instructions on judging the DAVIS SCHOOL DISTRICT STEM FAIR.
Sam Hobbs@hobbslabutah.bsky.social · 7mo ago

Hello world! I am excited to announce my lab is open at the University of Utah in the Department of Biochemistry. We are looking for scientists at all levels interested in studying host-virus interactions in both bacteria and animals. Come join us in beautiful Utah! (photo is 10 steps from lab)

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Erin Young@erinyoung.bsky.social · 8mo ago

Working from home with a sick-kid-that-feels-fine is such an adventure. Features: fever that reduces with acetaminophen random infrequent cough lots of energy and stir craziness

Erin Young@erinyoung.bsky.social · 9mo ago

I finally fleshed out one of my python scripts into a package: daisyblast Instead of pairwise blast results, this is intended to find blast hits that are shared by _n_ queries (like a daisy chain!). I can create dotplots of multiple samples

This combined alignment dot plot illustrates the syntenic relationships between the query sequence test_3.fasta___3 (x-axis) and four distinct subject sequences (y-axis), revealing a split between global collinearity and localized fragmentation. The subjects test_5.fasta___2 (dark blue) and test_4.fasta___3 (yellow) exhibit robust, nearly continuous diagonal alignments starting from the origin, indicating high homology and structural conservation with the query, though they diverge in coordinate space past the 100kb mark due to potential insertion/deletion events. Conversely, test_2.fasta___2 (light blue) and test_1.fasta___2 (orange) display discontinuous, "patchy" alignments clustered specifically around the 20,000 bp and 120,000 bp positions on the query; these high-coordinate matches (especially for the light blue sequence) are suggestive of translocated regions or shared repetitive motifs rather than continuous whole-sequence similarity.
Erin Young@erinyoung.bsky.social · 9mo ago

This is my first time working with NeighborNet (part of phangorn), and I think I'm going to need to do some reading so that 1) this makes sense to me, and 2) I can explain it to my collaborators

Phangorn's NeighborNet comparing 17 different phylogenetic trees. Tree tips are now web tips.