Erin Young
@erinyoung.bsky.social
Public Health #Bioinformatician. Wants to sequence ALL THE THINGS. Personal account with alternative spellings and grammar structures. She/her
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
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
November 21, 2025 at 11:41 PM
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
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 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
October 28, 2025 at 10:34 PM
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
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!
October 24, 2025 at 4:09 PM
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!
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.
October 17, 2025 at 5:35 PM
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.
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.
October 16, 2025 at 6:10 PM
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.
"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
I think that translates to ~1.5 million US dollars
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…
www.sciencedirect.com
October 14, 2025 at 9:04 PM
"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
I think that translates to ~1.5 million US dollars
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.
September 29, 2025 at 5:04 PM
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.
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.
/
/
September 23, 2025 at 6:01 PM
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.
/
/
Just finished updating my prokaryotic representative genome mash reference coinciding with refseq version 232
🧬🖥️🦠
🧬🖥️🦠
Mash Sketch of RefSeq Bacterial Reference Genomes
The mash reference that can be downloaded from the mash documentaion is for RefSeq version 70. I do not inherently have a problem with RefSeq version 70, but RefSeq is well past version 200 now. RefS...
zenodo.org
September 8, 2025 at 9:31 PM
Just finished updating my prokaryotic representative genome mash reference coinciding with refseq version 232
🧬🖥️🦠
🧬🖥️🦠
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. /
Since I helped someone install conda today, I'll share the process here. /
August 28, 2025 at 5:24 PM
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. /
Since I helped someone install conda today, I'll share the process here. /
Reposted by Erin Young
Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...
The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance
The 2024 WHO BPPL is a key tool for prioritising research and development investments
and informing global public health policies to combat AMR. Gram-negative bacteria
and rifampicin-resistant M tuber...
www.thelancet.com
August 27, 2025 at 4:13 PM
Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...
We have a new APHL fellow working with us!
@robbysainsbury.bsky.social is going to do some great things!
@robbysainsbury.bsky.social is going to do some great things!
August 19, 2025 at 7:49 PM
We have a new APHL fellow working with us!
@robbysainsbury.bsky.social is going to do some great things!
@robbysainsbury.bsky.social is going to do some great things!
We've successfully sequenced *6* Movbillivirus hominis (the virus that causes measles) found in local patients. The fastq and fasta files will eventually be found in BioProject PRJNA1293457. /
Morbillivirus hominis (ID 1293457) - BioProject - NCBI
A BioProject is a collection of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find l...
www.ncbi.nlm.nih.gov
August 8, 2025 at 9:03 PM
We've successfully sequenced *6* Movbillivirus hominis (the virus that causes measles) found in local patients. The fastq and fasta files will eventually be found in BioProject PRJNA1293457. /
Currently having an intern test how normalization impacts coverage for amplicon libraries. This one is normalized to 500X coverage.
August 7, 2025 at 5:16 PM
Currently having an intern test how normalization impacts coverage for amplicon libraries. This one is normalized to 500X coverage.
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.
GDC 2025 Main Stage: A Developer's Concert
YouTube video by Game Developers Conference
www.youtube.com
August 6, 2025 at 4:47 PM
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.
It's 8+1 day, so it's a day to feature Cecret (Lake)
Another 8+1 iconic outdoor spaces worth exploring on '801 Day'
It's Aug. 1, and why not celebrate
www.ksl.com
August 1, 2025 at 3:56 PM
It's 8+1 day, so it's a day to feature Cecret (Lake)
I finally have slurm up on both of my linux workstations! (please clap)
July 29, 2025 at 4:25 PM
I finally have slurm up on both of my linux workstations! (please clap)
Today's #soundtrack is from Abzu. This #ost is both orchestral and Choral. Tracks transition from tranquil, meditative tones to swelling, dramatic climaxes
#VideoGameMusic
#VideoGameMusic
July 18, 2025 at 4:04 PM
Today's #soundtrack is from Abzu. This #ost is both orchestral and Choral. Tracks transition from tranquil, meditative tones to swelling, dramatic climaxes
#VideoGameMusic
#VideoGameMusic
Just finished updating my prokaryotic representative genome mash reference coinciding with refseq version 231
🧬🖥️🦠
🧬🖥️🦠
Mash Sketch of RefSeq Bacterial Reference Genomes
The mash reference that can be downloaded from the mash documentaion is for RefSeq version 70. I do not inherently have a problem with RefSeq version 70, but RefSeq is well past version 200 now. RefS...
zenodo.org
July 15, 2025 at 9:55 PM
Just finished updating my prokaryotic representative genome mash reference coinciding with refseq version 231
🧬🖥️🦠
🧬🖥️🦠
Have I done primer design before? Yes.
Have I added in probe design before? Yes.
Has it been over a decade? Also, Yes.
Wish me luck!
Have I added in probe design before? Yes.
Has it been over a decade? Also, Yes.
Wish me luck!
July 15, 2025 at 3:42 PM
Have I done primer design before? Yes.
Have I added in probe design before? Yes.
Has it been over a decade? Also, Yes.
Wish me luck!
Have I added in probe design before? Yes.
Has it been over a decade? Also, Yes.
Wish me luck!
Today's #soundtrack is from Final Fantasy Crystal Chronicles. This #ost is mostly calm and whimsical instrumental pieces.
#VideoGameMusic
#VideoGameMusic
July 11, 2025 at 3:18 PM
Today's #soundtrack is from Final Fantasy Crystal Chronicles. This #ost is mostly calm and whimsical instrumental pieces.
#VideoGameMusic
#VideoGameMusic
Today's #soundtrack is from Drakengard 2. The Drakengard 2 #ost is dramatic and orchestral, which I think is great for creative or minimal-focus work. It also makes the day feel like a fantasy epic.
#VideoGameMusic
#VideoGameMusic
July 9, 2025 at 5:11 PM
Today's #soundtrack is from Drakengard 2. The Drakengard 2 #ost is dramatic and orchestral, which I think is great for creative or minimal-focus work. It also makes the day feel like a fantasy epic.
#VideoGameMusic
#VideoGameMusic
I kept my name because it comes with a theme song. I wish everyone everywhere the same privilege, even if their reasons are more valid.
Japan requires name change after marriage — with big effects on female scientists
Survey finds law requiring married couples to share the same family name causes havoc for researchers.
www.nature.com
July 7, 2025 at 3:58 PM
I kept my name because it comes with a theme song. I wish everyone everywhere the same privilege, even if their reasons are more valid.
I love being able to video conference in for friend's thesis defenses! Congratulations Amy Sawyer! (Not on bluesky... yet)
July 3, 2025 at 4:06 PM
I love being able to video conference in for friend's thesis defenses! Congratulations Amy Sawyer! (Not on bluesky... yet)
Today's #soundtrack is from Batman: Arkham Shadow. This #ost has a full orchestra and choir for dramatic and tense pieces.
#VideoGameMusic
#VideoGameMusic
July 2, 2025 at 5:21 PM
Today's #soundtrack is from Batman: Arkham Shadow. This #ost has a full orchestra and choir for dramatic and tense pieces.
#VideoGameMusic
#VideoGameMusic