I just started a Substack! If you're into #genomics #bioinformatics and #AIxBio topics - please subscribe. Especially if you want to follow topics around data quality, authenticity and traceability - which are my jam. 😊 bioinformer.substack.com?r=3xrm83&utm...

Jonathan Jacobs | Substack

Authenticity and data provenance in #genomics & #bioinformatics. Also #scicom, #gaming #DnD #EDM #punk @ Home 🧘🏼‍♂️🐕🏕️🏃♟👾🎮 🎸he/him. Click to read Jonathan Jacobs on Substack. Launched 2 days ago.

bioinformer.substack.com

What if waste could become a resource? Join Dr. Ryan Bing as he explores how engineered microbes can transform waste feedstocks into valuable compounds. Looking forward to moderating this session! #ASMMicrobe @bioinformer.bsky.social

@elisabethbik.bsky.social reminds us that public-good curation is also understanding the relationship between integrity, curiosity and truth. Our new guide with @sagepub.com champions the role of information curators. #PublicGoodCuration Download the guide bit.ly/3Kemcqn

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. 🦠🧬

We are pleased to share the Schizosaccharomyces orthogroup web resource (fsnibs10.github.io/SOG/) with the pombe community.

How many #plasmids can #bacteria carry? royalsocietypublishing.org/doi/10.1098/...

How many plasmids can bacteria carry? A synthetic biology perspective | Open Biology

Plasmids are pinnacle tools in synthetic biology and other biotechnological applications. They serve as the simplest approach to introduce recombinant DNA, which is then transcribed into RNA that func...

royalsocietypublishing.org

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

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!

Jonathan Jacobs@bioinformer.bsky.social · last yr.

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! 🚀 🦠 🧬🖥️ 🧪

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! 🚀 🦠 🧬🖥️ 🧪

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...

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.

🥰 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.

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 ...

microbiologyresearch.org

It's finally out! 🧪🧬🖥️ My 50th paper is about a new bacterial species! 🧫🦠 Everybody, welcome Janthinobacterium aestuarii sp. nov.!!! 👉 doi.org/10.1099/ijse...

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.

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

My new favorite virus species, Kayvirus kay.

🚨 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...

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

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

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.

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'.

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...

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...

microbiologyresearch.org

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… 😆

Cc @scottnguyen.bsky.social

Cameron Thrash@jcamthrash.bsky.social · 2y ago

OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes academic.oup.com/nar/advance-... #jcampubs

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

Home | ATCC Genome Portal

The ATCC Genome Portal is a repository of high-quality, authenticated microbial reference genomes.

buff.ly

@ace-gtdb.bsky.social Any idea how soon this will be back up? Thank you!