iiinova — where your digital self keeps evolving

Erin Young @erinyoung.bsky.social · 24/09/2026

Today at the AMD Mountain Region Bioinformatics Code Club, we tackled package and environment management with Conda! In public health bioinfo, being able to download bioinformatic tools and dependencies separate and without root (or IT) just makes life easier. 💻🧬

github.com

AMD-Mountain-Region-Bioinformatics-Code-Club/2026-09-23 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...

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Erin Young @erinyoung.bsky.social · 08/09/2026

Just finished updating my prokaryotic representative genome mash reference coinciding with RefSeq version 237 zenodo.org/records/2266... 🧬🖥️🦠

zenodo.org

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Erin Young @erinyoung.bsky.social · 06/08/2026

Blocked off focus time to finally update a few things today. The universe: Here’s a GitHub Actions outage instead. Going to get a diet soda instead, I guess.

Screenshot of the GitHub Status page for GitHub Actions. It displays a title "Actions" with an orange exclamation icon on the right and the status label "Degraded" below. A 90-day history bar shows mostly green uptime bars (99.77% uptime overall), but includes several scattered red and yellow lines, concluding with an orange status bar on "Today".

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Erin Young @erinyoung.bsky.social · 04/08/2026

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.

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Erin Young @erinyoung.bsky.social · 29/07/2026

I'm ready to "-resume" the Nextflow / nf-core Data Carpentry training today! (Is this too cheesy?)

A screen above a table with a challenge involving nextflow's resume option. The table below has an electrical outlet with two chords and a whiteboard cleaner. White boards surround the screen on either side and above.

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Erin Young @erinyoung.bsky.social · 28/07/2026

Safely landed in Madison for the Nextflow / nf-core Data Carpentry training!

A large-scale textile art installation suspended in a modern, multi-story building atrium. Long, sheer sheer fabric panels hang vertically from the ceiling, featuring intricate green, pink, and white embroidered or lace-like patterns depicting large, cascading fern fronds, leaves, and botanical flora. Large floor-to-ceiling windows line the background, looking out onto a green urban landscape.

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Erin Young @erinyoung.bsky.social · 22/07/2026

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!

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Erin Young @erinyoung.bsky.social · 09/07/2026

I love it when things finally work after dealing with bugs for the past few days.

A pygenomeviz synteny plot comparing nine genomic sequences (labeled 4051906_2 through 4051902_2) stacked vertically. Black arrows along each horizontal track indicate genes and their orientations. Broad, dark grey shaded blocks link homologous regions between adjacent sequences, covering nearly the entire length of all tracks. This indicates exceptionally high sequence conservation and identical gene order across all nine samples, with only a few minor inversions or localized variations visible on the far-left side. A sequence identity legend on the bottom right scales from 30% to 100%, with the dominant dark grey color signifying near-perfect identity.

Key Takeaways for Plasmid Similarity & HGT
Looking at this alignment, a few things stand out immediately regarding your search for plasmid similarity or HGT:

Near-Perfect Global Synteny: The massive, unbroken blocks of dark grey connecting the tracks from top to bottom show that these sequences are almost entirely homologous. The gene order (synteny) and content are nearly identical across all nine replicons.

Evidence of Recent HGT: Because these sequences are so highly conserved across multiple distinct IDs, this is a textbook signature of recent Horizontal Gene Transfer of an entire mobile genetic element (like a conjugative plasmid). There has been very little time for mutational drift, insertions, or deletions to differentiate them.

Minor Structural Hotspot (Far Left): The only notable variations are the crossing lines (inversions) and slightly different colored bands on the left side of the plot. This region likely contains a hotspot for recombination, a transposable element, or an integron cassette where small-scale rearrangements or gene swapping events have occurred.

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Erin Young @erinyoung.bsky.social · 25/06/2026

One of the best things about working on the top floor is hearing rain hit the roof.

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Erin Young @erinyoung.bsky.social · 05/06/2026

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.

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Erin Young @erinyoung.bsky.social · 21/05/2026

Dear @vscode.dev , I want to thank your devs for adding Mermaid diagrams to preview in 1.121

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Erin Young @erinyoung.bsky.social · 13/05/2026

The new work logo just dropped. Here's hoping it makes all my routine emails look incredibly smart and official.

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Erin Young @erinyoung.bsky.social · 12/05/2026

Nothing brings me more joy than announcing a "necessary reboot" of the shared workstation just to immediately monopolize 100% of the CPU.

A screenshot of a Linux terminal running htop. It shows dozens of CPU cores arranged in columns, numbered up to 84. Nearly every single core is completely maxed out with solid green bars reading 100.0% usage. The visual representation of pure, unadulterated resource hoarding.

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Erin Young @erinyoung.bsky.social · 11/05/2026

FYI, Nancy Drew: Ghost Dogs of Moon Lake has a great cozy-spooky #OST. The game also has some great information about how to avoid getting Hantavirus from animal droppings. #VideoGameMusic

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Erin Young @erinyoung.bsky.social · 04/05/2026

I have the personal engagement skills of an Excel spreadsheet, but I do understand the rationality of more engagement in social media in the space of public health. Notes from Dr. Sharfstein #APHL #APHL2026

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Erin Young @erinyoung.bsky.social · 04/05/2026

I'm feeling very welcomed to Baltimore for the 75th APHL annual conference. #APHL #APHL2026

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Erin Young @erinyoung.bsky.social · 20/04/2026

My favorite quote from this is "I just hope the bioinformatics community could collaboratively come up with guidelines and common practices on tool rewriting to advance this field in a friendly manner. After all, ... Empathy matters more than technical benefit or legal correctness."

lh3.github.io

The AI Rewrite Dilemma

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Erin Young @erinyoung.bsky.social · 16/04/2026

This seems like I should implement this

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Erin Young @erinyoung.bsky.social · 18/03/2026

Today’s #soundtrack is from Final Fantasy IX. This #ost blends medieval folk, whimsical orchestration, and melancholic piano. #VideoGameMusic

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Erin Young @erinyoung.bsky.social · 16/03/2026

Today's #soundtrack is from Factorio. This #ost is industrial ambient and minimalist. Tracks layer mechanical drones and distant synth textures, shifting from sparse atmospheric hums to steady, hypnotic rhythms that mirror the quiet expansion of a sprawling automated factory. #VideoGameMusic

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Erin Young @erinyoung.bsky.social · 10/03/2026

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.

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Erin Young @erinyoung.bsky.social · 05/03/2026

Today's #soundtrack is from Hearthstone. This #ost is whimsical and orchestral. Tracks blend playful tavern melodies with subtle magical fanfares, shifting from lighthearted jingles to adventurous, epic motifs. #VideoGameMusic

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Erin Young @erinyoung.bsky.social · 23/02/2026

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.

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Reposted by Erin Young

Sam Hobbs @hobbslabutah.bsky.social · 22/01/2026

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 · 13/01/2026

It's great being able to connect with my fellow public health bioinformaticians at the AMD Leads Meeting in Atlanta!

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Erin Young @erinyoung.bsky.social · 10/12/2025

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

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Erin Young @erinyoung.bsky.social · 21/11/2025

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.

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Erin Young @erinyoung.bsky.social · 28/10/2025

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.

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Erin Young @erinyoung.bsky.social · 24/10/2025

I have finally done it! I finished a rough draft for a manuscript and sent to to co-authors for editing. I may have it submitted by the end of this year!

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Erin Young @erinyoung.bsky.social · 17/10/2025

I had an EPI contact me to see if any isolates were clustering with 2024CK-00004 and 2024CK-00250 for EPI reasons. Pathogen Detection has these two isolates in the same cluster, making this question relatively easy to answer.

A phylogenetic tree of pathogen detection cluster PDS000161821.27, which contains both isolates that initiated the investigation in red with additional isolates.

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Erin Young @erinyoung.bsky.social · 16/10/2025

I probably need some different colors, but I've made a graph detailing the number of AMR genes we've seen in organisms that we've sequenced for the last few months.

Stacked bargraph where the x-axis the year-month and the values are the number of bla*{NDM,OXA,VIM,GES,IMP,KPC}* genes identified in sequencing efforts that month. The legend is to the right in order for general matching of AMR gene to value.

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Erin Young @erinyoung.bsky.social · 14/10/2025

"WGS-informed prevention could hypothetically generate net savings of €1.35 million annually if transmission was stopped once a clonal isolate was detected in a second patient." I think that translates to ~1.5 million US dollars

sciencedirect.com

Estimating the potential economic and health impact of integrated genomic surveillance in a hospital setting

Integrated genomic surveillance, combining whole genome sequencing (WGS) of bacterial isolates with patient movement data, promises improved detection…

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Erin Young @erinyoung.bsky.social · 29/09/2025

And today's (useless) figure is that the mean depth observed in a bam file is linearly associated with the number of reads in the corresponding fastq files.

A scatter plot comparing the number of reads and the overall mean depth observed in a bam file, which appears to have a linear relationship.

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Erin Young @erinyoung.bsky.social · 23/09/2025

I had 18 samples (33 million+ reads) of SARS-CoV-2 amplicon-based sequencing that would not create a decent consensus fasta after aligning with `bbmap` and trimming/consensus generation with `ivar`, but would if I tweaked the pipeline a bit. /

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Erin Young @erinyoung.bsky.social · 28/08/2025

Conda is an open-source command-line system for package and environment management. It's free, and generally does not need admin privileges. Since I helped someone install conda today, I'll share the process here. /

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Erin Young @erinyoung.bsky.social · 19/08/2025

We have a new APHL fellow working with us! @robbysainsbury.bsky.social is going to do some great things!

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Erin Young @erinyoung.bsky.social · 07/08/2025

Currently having an intern test how normalization impacts coverage for amplicon libraries. This one is normalized to 500X coverage.

Samtools plot ampliconstats image of a SARS-CoV-2 sample sequenced using Artic V5.3.2 primers after normalization. Each bar represents one amplicon (x-axis), and the y-axis (log scale) indicates the number of reads. Three types of read counts are shown:
Purple bars: Total number of reads per amplicon (#reads)
Yellow bars: All aligned read depth, regardless of quality (all depth)
Blue bars: Reads meeting quality and alignment criteria (usable depth)

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Erin Young @erinyoung.bsky.social · 06/08/2025

I watched this video of a concert that was part of Game Developers Conference (GDC), and the back of my mind won't stop trying to find a Public Health or Bioinformatics Conference equivalent.

youtube.com

GDC 2025 Main Stage: A Developer's Concert

YouTube video by Game Developers Conference

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Erin Young @erinyoung.bsky.social · 29/07/2025

I finally have slurm up on both of my linux workstations! (please clap)

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Erin Young @erinyoung.bsky.social · 18/07/2025

Today's #soundtrack is from Abzu. This #ost is both orchestral and Choral. Tracks transition from tranquil, meditative tones to swelling, dramatic climaxes #VideoGameMusic

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