Scott V. Nguyen
@scottnguyen.bsky.social
I study cells and love watching supercells. Senior biocurator at the ATCC.
Reposted by Scott V. Nguyen
BIOLOG question: is there a good pipeline or program to compare biolog results (either in terms of absorbance reads or carbon sources/antibiotics/etc) to KEGG outputs from whole genome sequencing? Right now our tech is doing am manual comparison but there has to be an easier way. 🦠🧬
November 10, 2025 at 7:49 PM
BIOLOG question: is there a good pipeline or program to compare biolog results (either in terms of absorbance reads or carbon sources/antibiotics/etc) to KEGG outputs from whole genome sequencing? Right now our tech is doing am manual comparison but there has to be an easier way. 🦠🧬
Reposted by Scott V. Nguyen
We are pleased to share the Schizosaccharomyces orthogroup web resource (fsnibs10.github.io/SOG/) with the pombe community.
August 5, 2025 at 10:36 AM
We are pleased to share the Schizosaccharomyces orthogroup web resource (fsnibs10.github.io/SOG/) with the pombe community.
Reposted by Scott V. Nguyen
Reposted by Scott V. Nguyen
Does anyone know if you can query RefSeq and parse the status codes w/o downloading ALL of it in genbank format first and then grep'ing those lines? Image from RefSeq docs, but AFAIK you can't directly query the "COMMENT" field with NCBI's esearch or RESTapi...
#bioinformatics #help
#bioinformatics #help
July 30, 2025 at 7:39 PM
Does anyone know if you can query RefSeq and parse the status codes w/o downloading ALL of it in genbank format first and then grep'ing those lines? Image from RefSeq docs, but AFAIK you can't directly query the "COMMENT" field with NCBI's esearch or RESTapi...
#bioinformatics #help
#bioinformatics #help
Reposted by Scott V. Nguyen
Hey all - check this post if you’re at #ASMicrobe this weekend.
Let’s have a meet up tomorrow for a photo op of microbiologists on @bsky.app who are at #ASMicrobe!
Be there at 3 PM at the main entrance giant ASM sign!
In person meetups are super fun - please be there!
And plz repost!
Let’s have a meet up tomorrow for a photo op of microbiologists on @bsky.app who are at #ASMicrobe!
Be there at 3 PM at the main entrance giant ASM sign!
In person meetups are super fun - please be there!
And plz repost!
Who is at #ASMicrobe?
Reply with a 👋 and let’s do a bsky meetup tomorrow for a group photo!
Please repost / share / like this post to extend its reach.
Let’s go! 🚀 🦠 🧬🖥️ 🧪
Reply with a 👋 and let’s do a bsky meetup tomorrow for a group photo!
Please repost / share / like this post to extend its reach.
Let’s go! 🚀 🦠 🧬🖥️ 🧪
June 22, 2025 at 1:57 AM
Hey all - check this post if you’re at #ASMicrobe this weekend.
Let’s have a meet up tomorrow for a photo op of microbiologists on @bsky.app who are at #ASMicrobe!
Be there at 3 PM at the main entrance giant ASM sign!
In person meetups are super fun - please be there!
And plz repost!
Let’s have a meet up tomorrow for a photo op of microbiologists on @bsky.app who are at #ASMicrobe!
Be there at 3 PM at the main entrance giant ASM sign!
In person meetups are super fun - please be there!
And plz repost!
Reposted by Scott V. Nguyen
Who is at #ASMicrobe?
Reply with a 👋 and let’s do a bsky meetup tomorrow for a group photo!
Please repost / share / like this post to extend its reach.
Let’s go! 🚀 🦠 🧬🖥️ 🧪
Reply with a 👋 and let’s do a bsky meetup tomorrow for a group photo!
Please repost / share / like this post to extend its reach.
Let’s go! 🚀 🦠 🧬🖥️ 🧪
June 21, 2025 at 4:50 PM
Who is at #ASMicrobe?
Reply with a 👋 and let’s do a bsky meetup tomorrow for a group photo!
Please repost / share / like this post to extend its reach.
Let’s go! 🚀 🦠 🧬🖥️ 🧪
Reply with a 👋 and let’s do a bsky meetup tomorrow for a group photo!
Please repost / share / like this post to extend its reach.
Let’s go! 🚀 🦠 🧬🖥️ 🧪
Reposted by Scott V. Nguyen
Need bacterial DNA methylation data? Well, we’ve been re-basecalling all ONT data for the ATCC Genome Portal to get it. A huge effort, but as of today we have Mthyl data for ~1,500 bacterial strains. Attending #ASMicrobe? happy to chat IRL about it too. i.e. > genomes.atcc.org/genomes/67e8...
ATCC® 9945a™ | Bacillus paralicheniformis | ATCC Genome Portal
Bacillus paralicheniformis is a strain of bacteria in the Bacillus genus. This genome was published to the ATCC Genome Portal on 2022-04-02
genomes.atcc.org
June 19, 2025 at 8:39 PM
Need bacterial DNA methylation data? Well, we’ve been re-basecalling all ONT data for the ATCC Genome Portal to get it. A huge effort, but as of today we have Mthyl data for ~1,500 bacterial strains. Attending #ASMicrobe? happy to chat IRL about it too. i.e. > genomes.atcc.org/genomes/67e8...
Reposted by Scott V. Nguyen
Advice needed: A former student now in industry is asking about pros/cons of doing an industry-sponsored PhD, given the current climate and not getting in anywhere this cycle. I remember there was chatter about this a couple years ago but it's a good time to revive this chat. Please RT.
May 27, 2025 at 6:14 PM
Advice needed: A former student now in industry is asking about pros/cons of doing an industry-sponsored PhD, given the current climate and not getting in anywhere this cycle. I remember there was chatter about this a couple years ago but it's a good time to revive this chat. Please RT.
Reposted by Scott V. Nguyen
🥰 New publication out from @scottnguyen.bsky.social and my team @officialatcc.bsky.social stemming from genomics work done for the ATCC Genome Portal.
Reclassification of atypical Moraxella catarrhalis ATCC 23246 as Moraxella veridica sp. nov
www.microbiologyresearch.org/content/jour... 🧪 🧬🖥 🦠
Reclassification of atypical Moraxella catarrhalis ATCC 23246 as Moraxella veridica sp. nov
www.microbiologyresearch.org/content/jour... 🧪 🧬🖥 🦠
Reclassification of atypical Moraxella catarrhalis ATCC 23246 as Moraxella veridica sp. nov.
Whole-genome sequencing of cultures at the American Type Culture Collection (ATCC®) is ongoing, with reference-quality genome sequences for our microbial strains added to the ATCC® Genome Portal on a ...
www.microbiologyresearch.org
May 21, 2025 at 5:42 PM
🥰 New publication out from @scottnguyen.bsky.social and my team @officialatcc.bsky.social stemming from genomics work done for the ATCC Genome Portal.
Reclassification of atypical Moraxella catarrhalis ATCC 23246 as Moraxella veridica sp. nov
www.microbiologyresearch.org/content/jour... 🧪 🧬🖥 🦠
Reclassification of atypical Moraxella catarrhalis ATCC 23246 as Moraxella veridica sp. nov
www.microbiologyresearch.org/content/jour... 🧪 🧬🖥 🦠
Reposted by Scott V. Nguyen
It's finally out! 🧪🧬🖥️
My 50th paper is about a new bacterial species! 🧫🦠
Everybody, welcome Janthinobacterium aestuarii sp. nov.!!!
👉 doi.org/10.1099/ijse...
My 50th paper is about a new bacterial species! 🧫🦠
Everybody, welcome Janthinobacterium aestuarii sp. nov.!!!
👉 doi.org/10.1099/ijse...
May 2, 2025 at 11:27 AM
It's finally out! 🧪🧬🖥️
My 50th paper is about a new bacterial species! 🧫🦠
Everybody, welcome Janthinobacterium aestuarii sp. nov.!!!
👉 doi.org/10.1099/ijse...
My 50th paper is about a new bacterial species! 🧫🦠
Everybody, welcome Janthinobacterium aestuarii sp. nov.!!!
👉 doi.org/10.1099/ijse...
Reposted by Scott V. Nguyen
Every now again it’s useful to repeat advice about accessing papers that are behind a paywall that excludes you. Email the author. My estimate is that 90% of academics are so thrilled that a living, breathing, possibly even reading, person shows interest that they will swiftly send you a copy.
May 3, 2025 at 1:44 PM
Every now again it’s useful to repeat advice about accessing papers that are behind a paywall that excludes you. Email the author. My estimate is that 90% of academics are so thrilled that a living, breathing, possibly even reading, person shows interest that they will swiftly send you a copy.
Reposted by Scott V. Nguyen
As you drive up Clifton Road towards CDC’s Roybal campus, there are often signs by the side of the road.
This past month, they have been focused on the importance of public health and the commitment of its staff.
I thought I would share a few of them here. #publichealth
This past month, they have been focused on the importance of public health and the commitment of its staff.
I thought I would share a few of them here. #publichealth
February 19, 2025 at 1:41 AM
As you drive up Clifton Road towards CDC’s Roybal campus, there are often signs by the side of the road.
This past month, they have been focused on the importance of public health and the commitment of its staff.
I thought I would share a few of them here. #publichealth
This past month, they have been focused on the importance of public health and the commitment of its staff.
I thought I would share a few of them here. #publichealth
My new favorite virus species, Kayvirus kay.
January 31, 2025 at 4:28 PM
My new favorite virus species, Kayvirus kay.
Reposted by Scott V. Nguyen
🚨 New paper alert! 🚨
Say hello to Kalamari 🦑—your new go-to resource for genomic epidemiology & pathogen surveillance. 🌍
✅ Representative genomes
✅ Common contaminants
✅ Custom taxonomy
✅ Open-source tools for easy data access
Read it here: journals.asm.org/eprint/JUUNS...
Say hello to Kalamari 🦑—your new go-to resource for genomic epidemiology & pathogen surveillance. 🌍
✅ Representative genomes
✅ Common contaminants
✅ Custom taxonomy
✅ Open-source tools for easy data access
Read it here: journals.asm.org/eprint/JUUNS...
Kalamari: a representative set of genomes of public health concern | Microbiology Resource Announcements
Public health laboratories sequence microbial pathogens daily for many applications,
including genomic epidemiology (1), species identification (2), and metagenomic analysis (3). Relevant databases ex...
journals.asm.org
January 24, 2025 at 2:44 PM
🚨 New paper alert! 🚨
Say hello to Kalamari 🦑—your new go-to resource for genomic epidemiology & pathogen surveillance. 🌍
✅ Representative genomes
✅ Common contaminants
✅ Custom taxonomy
✅ Open-source tools for easy data access
Read it here: journals.asm.org/eprint/JUUNS...
Say hello to Kalamari 🦑—your new go-to resource for genomic epidemiology & pathogen surveillance. 🌍
✅ Representative genomes
✅ Common contaminants
✅ Custom taxonomy
✅ Open-source tools for easy data access
Read it here: journals.asm.org/eprint/JUUNS...
Reposted by Scott V. Nguyen
500 classrooms have signed up for Skype a Scientist 2025!
@skypeascientist.bsky.social matches scientists with classrooms, scout troops, libraries, & other groups for Q&A sessions. It's FREE!
We have an advertising budget of $0. So tell an educator in your life that we exist
SkypeAScientist.com
@skypeascientist.bsky.social matches scientists with classrooms, scout troops, libraries, & other groups for Q&A sessions. It's FREE!
We have an advertising budget of $0. So tell an educator in your life that we exist
SkypeAScientist.com
January 23, 2025 at 10:58 PM
500 classrooms have signed up for Skype a Scientist 2025!
@skypeascientist.bsky.social matches scientists with classrooms, scout troops, libraries, & other groups for Q&A sessions. It's FREE!
We have an advertising budget of $0. So tell an educator in your life that we exist
SkypeAScientist.com
@skypeascientist.bsky.social matches scientists with classrooms, scout troops, libraries, & other groups for Q&A sessions. It's FREE!
We have an advertising budget of $0. So tell an educator in your life that we exist
SkypeAScientist.com
Reposted by Scott V. Nguyen
We created a publications page for ATCC R&D scientists who have published peer reviewed work recently www.atcc.org/resources/pu... It's a pretty broad range - virology, cell bio, bacteriology, genomics, bioinformatics - but still fun for me to look through.
Publications
Read our recent publications to learn about our innovative research and explore exciting applications of our products.
www.atcc.org
January 9, 2025 at 5:01 PM
We created a publications page for ATCC R&D scientists who have published peer reviewed work recently www.atcc.org/resources/pu... It's a pretty broad range - virology, cell bio, bacteriology, genomics, bioinformatics - but still fun for me to look through.
Reposted by Scott V. Nguyen
It’s official: The Microbiology Society is on Bluesky!
January 8, 2025 at 12:03 PM
It’s official: The Microbiology Society is on Bluesky!
Comparative analysis shows that the 'Gulf of America' is a later heterotypic synonym of 'Gulf of Mexico'.
January 7, 2025 at 7:25 PM
Comparative analysis shows that the 'Gulf of America' is a later heterotypic synonym of 'Gulf of Mexico'.
Reposted by Scott V. Nguyen
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
December 11, 2024 at 4:29 PM
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
This work took a long time, from receiving the samples back when I was still at the DC PHL in early 2020 to finally getting published in IJSEM now.
Check out a novel Stenotrophomonas species that was isolated from contaminated viral transport media: www.microbiologyresearch.org/content/jour...
Check out a novel Stenotrophomonas species that was isolated from contaminated viral transport media: www.microbiologyresearch.org/content/jour...
Expanding the Stenotrophomonas maltophilia complex: phylogenomic insights, proposal of Stenotrophomonas forensis sp. nov. and reclassification of two Pseudomonas species
A novel Stenotrophomonas species was isolated as a contaminant in viral transport media at the District of Columbia Department of Forensic Sciences Public Health Laboratory. Phylogenomic and biochemic...
www.microbiologyresearch.org
December 5, 2024 at 2:23 PM
This work took a long time, from receiving the samples back when I was still at the DC PHL in early 2020 to finally getting published in IJSEM now.
Check out a novel Stenotrophomonas species that was isolated from contaminated viral transport media: www.microbiologyresearch.org/content/jour...
Check out a novel Stenotrophomonas species that was isolated from contaminated viral transport media: www.microbiologyresearch.org/content/jour...
Reposted by Scott V. Nguyen
If you find yourself reading a paper from my team in the near future and think:
A/ FFS there’s a lot of backstory in this Introduction!
or B/ references to papers before 1920? 1906!!? WTH?
I’m to blame. Well… me and way way too much coffee and a deep dive down the citations rabbit hole… 😆
A/ FFS there’s a lot of backstory in this Introduction!
or B/ references to papers before 1920? 1906!!? WTH?
I’m to blame. Well… me and way way too much coffee and a deep dive down the citations rabbit hole… 😆
November 19, 2024 at 8:12 PM
If you find yourself reading a paper from my team in the near future and think:
A/ FFS there’s a lot of backstory in this Introduction!
or B/ references to papers before 1920? 1906!!? WTH?
I’m to blame. Well… me and way way too much coffee and a deep dive down the citations rabbit hole… 😆
A/ FFS there’s a lot of backstory in this Introduction!
or B/ references to papers before 1920? 1906!!? WTH?
I’m to blame. Well… me and way way too much coffee and a deep dive down the citations rabbit hole… 😆
Reposted by Scott V. Nguyen
OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes academic.oup.com/nar/advance-... #jcampubs
OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes
Abstract. OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, proka
academic.oup.com
November 13, 2024 at 2:25 PM
Reposted by Scott V. Nguyen
5,048 genomes! 4,224 bacteria, 451 viruses, 359 fungi, and 4 protists. 1,649 type-strains.
This is an important milestone at the ATCC Genome Portal. When I joined ATCC we set a goal of 5,000 microbial genomes by 2025: we’ve passed that mark early! 🤗🧬 🦠#genomics #bioinformatics
This is an important milestone at the ATCC Genome Portal. When I joined ATCC we set a goal of 5,000 microbial genomes by 2025: we’ve passed that mark early! 🤗🧬 🦠#genomics #bioinformatics
Home | ATCC Genome Portal
The ATCC Genome Portal is a repository of high-quality, authenticated microbial reference genomes.
buff.ly
November 6, 2024 at 4:51 PM
5,048 genomes! 4,224 bacteria, 451 viruses, 359 fungi, and 4 protists. 1,649 type-strains.
This is an important milestone at the ATCC Genome Portal. When I joined ATCC we set a goal of 5,000 microbial genomes by 2025: we’ve passed that mark early! 🤗🧬 🦠#genomics #bioinformatics
This is an important milestone at the ATCC Genome Portal. When I joined ATCC we set a goal of 5,000 microbial genomes by 2025: we’ve passed that mark early! 🤗🧬 🦠#genomics #bioinformatics
January 31, 2024 at 5:32 PM