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Jonathan Jacobs

@bioinformer.bsky.social

2.8K followers 1.1K following 580 posts

UofArizona #Aggie > UofMaryland PhD > NIH/NCI PostDoc > Biodefense, Pathogen #Genomics, #Bioinformatics, Data Authenticity, #BioSecurity. ++PC gaming, DnD, EDM, punk, goth, backcountry backpacking, porsche 🎲♟️👾🎮 🎸 🧪 🧬 🖥 🦠🚀🏎️ he/him. On Steam: @bioinformer

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Jonathan Jacobs @bioinformer.bsky.social · 5d

Our Q3 2025 Data Release! 500 new microbial genomes, incl. 474 bacteria, 17 viruses, 9 fungi. 429 unique species, 26 "unclassified" species, and 24 new type-strains.

We now have 6,250 authenticated reference genomes on the AGP. Come by and check it out! more coming! #genomics genomes.atcc.org

Home | ATCC Genome Portal

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

genomes.atcc.org

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Jonathan Jacobs @bioinformer.bsky.social · 3h

Things editors read when reviewing the comments of reviewers for a microbial forensics paper...

"to account for potential batch effects, please include acquisition date, transport conditions, storage conditions and duration for all cadavers included in the study"

👀

Reposted by Jonathan Jacobs

Melanie D’Arrigo @darrigomelanie.bsky.social · 16h

I feel like this photo of masked, armed men pepper spraying a pastor protecting his community is going to be a defining picture of this moment in America for a long, long time.

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Jonathan Jacobs @bioinformer.bsky.social · 5d

We also added genomes for 2 new intracellular microbes (Chlamydia pecorum and C. psychrophilum), 16 new extremophiles, 2 strains of Cedecea davisae, and 5 new ESKAPE pathogen genomes

have fun!

Jonathan Jacobs @bioinformer.bsky.social · 5d

Additional highlights of our latest data release has hybrid genome assemblies (ONT+ILMN) for many novel strains including
10 new Mycobacterium
10 new Nocardia
9 new Bordetella
7 new Streptococcus
8 new Acinetobacter
8 new Ensifer
7 new Pseudomonas
6 new Corynebacterium

Jonathan Jacobs @bioinformer.bsky.social · 5d

Home | ATCC Genome Portal

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

genomes.atcc.org

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Jonathan Jacobs @bioinformer.bsky.social · 5d

"... the American Type Culture Collection (ATCC) Genome Portal (genomes.atcc.org) which is the only authenticated reference genome database for ATCC microbes, the largest general culture collection in the world..." 🎯

www.cell.com/iscience/ful...

😊 cc: @officialatcc.bsky.social

Impact of mycotoxins and glyphosate residue on the gut microbiome and resistome of European fallow deer

Environmental science; Microbiology; Microbiome; Wildlife microbiology; Wildlife toxicology

www.cell.com

Jonathan Jacobs @bioinformer.bsky.social · 14d

“It’s can only good happen.”

LMAO

Jonathan Jacobs @bioinformer.bsky.social · 14d

Agree that with scDNA sequencing you don’t really need biological reps for most experiments.

Jonathan Jacobs @bioinformer.bsky.social · 14d

Latest paper from my group explores the differential response of five model cell lines used in leukemia research to to EF24, a synthetic cucurmin analog.

journals.plos.org/plosone/arti...

#genomics #RNAseq #biopharma #EF24 #naturalproducts #leukemia

Genomic discovery of EF-24 targets unveils antitumorigenic mechanisms in leukemia cells

Curcumin, a polyphenolic compound derived from the plant Curcuma longa L., has demonstrated a wide range of therapeutic properties, including potential anticancer effects. However, its clinical effica...

journals.plos.org

Jonathan Jacobs @bioinformer.bsky.social · 14d

AHAHAHHAHHHAHAHA!!!!

a man with a mustache is smiling and looking up at the sky .

ALT: a man with a mustache is smiling and looking up at the sky .

media.tenor.com

Jonathan Jacobs @bioinformer.bsky.social · 14d

For DNA sequencing - yes agreed. We use the same approach for our whole exome sequencing, but sometimes do technical replicates of the gDNA preps (because WES is generally not great).

but for RNAseq - we do 5x biological reps of each cell line (independent cultures, in parallel).

Jonathan Jacobs @bioinformer.bsky.social · 15d

Hey scRNAseq people… what’s this about not needing to do biological replicates? What now?

I’m sorry - yes it’s expensive to do. Complain to 10X Genomics - not the RA Fisher and his legacy. 🙃

RA Fisher, Jacques Monod, Francois Jacob, and Barbara McClintock are watching. 🤣

Image of RA Fisher, Jacques Monod, Francois Jacob, Barbara McClintock scowling and disappointed with the viewer. Created with ChatGPT5.

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Jonathan Jacobs @bioinformer.bsky.social · 18d

Apparently… this worked. LMAO

Jonathan Jacobs @bioinformer.bsky.social · 18d

Like… what the S F…

“Sorry, I can’t create an image of a rat in this context. Would you like me to adjust the mascot to be a different kind of anthropomorphic animal—like a bear, dog, or fox in a business suit?”

Jonathan Jacobs @bioinformer.bsky.social · 18d

What the F is this…

I can’t create “a mouse in a business suit” who is accepting $10 from a protestor who is also holding a sign that says “Free Speech”

The F’ing irony of this has me fuming…

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Jonathan Jacobs @bioinformer.bsky.social · 22d

This is epic! @officialatcc.bsky.social announced the winners of the 2025 Photo contest! They look amazing! Check the Alt text and follow the link for tons more. www.atcc.org/about-us/upc...

I love this! Please reshare! #microscopy #biology #research #science #cellbiology #microbiology #biotech 🧪🧬

2025 Most Popular Image Award for Microbiology
Bouquet of Trebouxia
Photographer - Sandra Story, NUBAD, LLC
Trebouxia (ATCC 30426) is a free-living green alga that often forms a symbiotic relationship with certain fungi. Trebouxia has a complex life cycle showing many cellular forms including motile.

2025 Most Popular Image Award for Cell Biology
Mitosis in Color: A Super-Resolution View
Photographer - Avishkar Sawant, Vanderbilt University
Super-resolution image of a fixed hTERT-RPE1 cell (ATCC CRL-4000) undergoing mitosis, highlighting the intricate organization of cytoskeletal networks. DNA (cyan), vimentin (depth color-coded), microtubules (red), and actin (magenta) were visualized using NSPARC. The image is presented as a maximum intensity projection of NSPARC stacks.

2025 ATCC Excellence Image Award for Microbiology
Microbial Minimalism
Photographer - Mindy Engevik, Medical University of South Carolina
This is an SEM image of Lactobacillus reuteri (ATCC 6475).

2025 ATCC Excellence Image Award for Microbiology
The Butterfly Effect
Photographer - Sandra Story, NUBAD, LLC
Klebsiella pneumoniae (ATCC 13883) and Bacillus subtilis (ATCC 6501). Fluorescence microscopy composite image of a mixture of bacteria that can be representative of a chronic poly-bacterial infection. Large masses of cells are Klebsiella pneumoniae exposed to a high dose of ertapenem causing the cells to elongate 10-50 times their normal size. Long rigid filaments are Bacillus subtilis common in soil, while Klebsiella pneumoniae are part of the normal microbial flora of the human lower digestive tract. Mixed genera of bacteria can coexist as poly-bacterial biofilms which supports exchange of drug resistance determinants via inter-species and inter-genus horizontal gene transfer. The biofilm-mode of growth supports other synergistic interactions that enhance virulence and promote resistance to antimicrobials resulting in difficult to treat chronic infections. Bacteria were cocultured in nutrient broth exposed to penicillin and incubated at 37 degrees Celsius to allow biofilm development. Samples of the biofilm were stained with three fluorescent dyes FM-64 (red, membrane stain), DAPI (blue, nucleic acid stain for both live and dead cells) and SYTOX Green (green, nucleic acid stain for dead cells) and then spotted onto an agarose nutrient pad sandwiched between a microscope slide and coverslip. The sample was viewed using a Leica DMi8 and illuminated using Texas red, DAPI and GFP filter sets. Images were taken with a K5 microscope camera. Scale bar 20 uM, 1000X magnification.

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Jonathan Jacobs @bioinformer.bsky.social · Sep 5

TTW you’re totally vibing to a Hendrix cover band’s long long jam session at a local brewery … and they finally end the jam - you’re the only one who yells out “All right!!!” …

a man in a cowboy hat stands in a crowd of people

ALT: a man in a cowboy hat stands in a crowd of people

media.tenor.com

Jonathan Jacobs @bioinformer.bsky.social · Aug 29

Yes!

dwight schrute from the office is wearing glasses and a suit and tie .

ALT: dwight schrute from the office is wearing glasses and a suit and tie .

media.tenor.com

Jonathan Jacobs @bioinformer.bsky.social · Aug 27

paper submitted. 😀

Jonathan Jacobs @bioinformer.bsky.social · Aug 26

Interesting how we are included… considering we’re not a sequencing company. 🙃

Reposted by Jonathan Jacobs

alexjungle.bsky.social @alexjungle.bsky.social · Aug 24

In Germany, scientists have made a breakthrough in treating Parkinson’s by implanting a chip in the brain that sends precise signals to restore movement. A stunning leap in neuroscience—witness the power of innovation and the beauty of science in action.
Powerfull content

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Reposted by Jonathan Jacobs

Christopher Webb @cwebbonline.com · Aug 25

This hits right on time…

My wife and I had the great privilege of visiting the African-American Museum in DC, and let me just tell you if you have not been…It is a masterpiece—go.

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Reposted by Jonathan Jacobs

Aaron Rupar @atrupar.com · Aug 14

Newsom: "He doesn't play by a different set of rules. He doesn't believe in the rules. As a consequence, we need to disabuse ourselves of the way things have been done. It's not enough to just hold hands, have a candlelight vigil, talk about way the world should be...we have got to meet fire w/fire"

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Jonathan Jacobs @bioinformer.bsky.social · Aug 14

🧪 🧬🖥️

Lots of buzz and hype about this - so I’m curious what you think ::

What do you consider “AI ready” data in the life sciences?

#bioinformatics #genomics #AI #AIready

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Reposted by Jonathan Jacobs

Matthew Palmer @so3brocktree.bsky.social · Aug 13

I've written a primer on CBRN, an oft-misunderstood area of defence and security.

I was a CBRN specialist at one point so have some experience of the topic - far too many hours spent in a respirator and full noddy suit!

Let me know thoughts and feelings below.

GAS GAS GAS!

A primer on Chemical, Biological, Nuclear, and Radiological Warfare

crackingdefence.substack.com

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