Jonathan Jacobs
@bioinformer.bsky.social
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
🎲♟️👾🎮 🎸 🧪 🧬 🖥 🦠🚀🏎️
he/him. On Steam: @bioinformer
Pinned
Home | ATCC Genome Portal
The ATCC Genome Portal is a repository of high-quality, authenticated microbial reference genomes.
genomes.atcc.org
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
We now have 6,250 authenticated reference genomes on the AGP. Come by and check it out! more coming! #genomics genomes.atcc.org
Reposted by Jonathan Jacobs
Just a reminder that Large Language Models is just one type of AI. It is not synonymous with AI and indeed the key aspects which make LLMs work - big attention networks, very large embedding spaces - have many applications.
December 5, 2025 at 9:15 AM
Just a reminder that Large Language Models is just one type of AI. It is not synonymous with AI and indeed the key aspects which make LLMs work - big attention networks, very large embedding spaces - have many applications.
Oh hey… what’s all this now?
THATS RIGHT!
The ATCC Genome Portal now has whole exome and RNAseq data for 900+ cell lines and organoids models, with more data coming. Currently >4k datasets : all produced in house by my team under ISO using benchmarked and standardized methods.
genomes.ATCC.org
THATS RIGHT!
The ATCC Genome Portal now has whole exome and RNAseq data for 900+ cell lines and organoids models, with more data coming. Currently >4k datasets : all produced in house by my team under ISO using benchmarked and standardized methods.
genomes.ATCC.org
December 2, 2025 at 11:34 AM
Oh hey… what’s all this now?
THATS RIGHT!
The ATCC Genome Portal now has whole exome and RNAseq data for 900+ cell lines and organoids models, with more data coming. Currently >4k datasets : all produced in house by my team under ISO using benchmarked and standardized methods.
genomes.ATCC.org
THATS RIGHT!
The ATCC Genome Portal now has whole exome and RNAseq data for 900+ cell lines and organoids models, with more data coming. Currently >4k datasets : all produced in house by my team under ISO using benchmarked and standardized methods.
genomes.ATCC.org
Something wicked this way comes... 🧬🧬🧬
(to the ATCC Genome Portal on Monday, Dec 1st...)
(wicked in a good, different, leap forward way... 😄)
(to the ATCC Genome Portal on Monday, Dec 1st...)
(wicked in a good, different, leap forward way... 😄)
November 26, 2025 at 1:52 PM
Something wicked this way comes... 🧬🧬🧬
(to the ATCC Genome Portal on Monday, Dec 1st...)
(wicked in a good, different, leap forward way... 😄)
(to the ATCC Genome Portal on Monday, Dec 1st...)
(wicked in a good, different, leap forward way... 😄)
In 2003, Dr. Nathan Myhrvold pointed out that GenBank was doubling in size every 18 months - much like Moore's Law.
22 years later - that trend is continuing. (www.ncbi.nlm.nih.gov/genbank/stat...)
How much longer is that going to be sustainable?
#bioinformatics #genomics
22 years later - that trend is continuing. (www.ncbi.nlm.nih.gov/genbank/stat...)
How much longer is that going to be sustainable?
#bioinformatics #genomics
GenBank and WGS Statistics
www.ncbi.nlm.nih.gov
November 14, 2025 at 2:21 PM
In 2003, Dr. Nathan Myhrvold pointed out that GenBank was doubling in size every 18 months - much like Moore's Law.
22 years later - that trend is continuing. (www.ncbi.nlm.nih.gov/genbank/stat...)
How much longer is that going to be sustainable?
#bioinformatics #genomics
22 years later - that trend is continuing. (www.ncbi.nlm.nih.gov/genbank/stat...)
How much longer is that going to be sustainable?
#bioinformatics #genomics
🧵 Several months ago I started a Friday afternoon journal club focused on Yarrowia lipolytica, metabolic engineering, and functional genomics.
November 7, 2025 at 5:59 PM
🧵 Several months ago I started a Friday afternoon journal club focused on Yarrowia lipolytica, metabolic engineering, and functional genomics.
Good read about terrible things www.thehastingscenter.org/what-researc...
What Research Scandals? Welcome to the Bioethics Memory Hole : The Hastings Center for Bioethics
It is striking how many notorious cases of abuses of human research subjects go almost entirely unmentioned in the bioethics literature.
www.thehastingscenter.org
November 7, 2025 at 1:05 PM
Good read about terrible things www.thehastingscenter.org/what-researc...
Currently attending the annual Virginia Tech CEZAP Symposium on Emerging Infectious Diseases - and Dr. Vincent Racaniello (host of TWIV / MicrobeTV podcast) is the key note. Really love his career talk - I hope the students and postdoc here take his advice to heart.
October 17, 2025 at 1:11 PM
Currently attending the annual Virginia Tech CEZAP Symposium on Emerging Infectious Diseases - and Dr. Vincent Racaniello (host of TWIV / MicrobeTV podcast) is the key note. Really love his career talk - I hope the students and postdoc here take his advice to heart.
Reposted by Jonathan Jacobs
The 400 richest Americans are now worth a record $6.6 trillion.
The entire bottom 50% of America is worth just $4.2 trillion.
Read that back.
When 400 people control more wealth than half a country’s population, we have a very serious problem.
The entire bottom 50% of America is worth just $4.2 trillion.
Read that back.
When 400 people control more wealth than half a country’s population, we have a very serious problem.
October 12, 2025 at 11:30 PM
The 400 richest Americans are now worth a record $6.6 trillion.
The entire bottom 50% of America is worth just $4.2 trillion.
Read that back.
When 400 people control more wealth than half a country’s population, we have a very serious problem.
The entire bottom 50% of America is worth just $4.2 trillion.
Read that back.
When 400 people control more wealth than half a country’s population, we have a very serious problem.
Reposted by Jonathan Jacobs
The following is REAL footage from Portland, 2025. Viewer discretion is advised.
October 9, 2025 at 8:23 PM
The following is REAL footage from Portland, 2025. Viewer discretion is advised.
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"
👀
"to account for potential batch effects, please include acquisition date, transport conditions, storage conditions and duration for all cadavers included in the study"
👀
October 8, 2025 at 12:51 PM
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"
👀
"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
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.
October 7, 2025 at 11:29 PM
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.
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
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
October 2, 2025 at 4:17 PM
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
We now have 6,250 authenticated reference genomes on the AGP. Come by and check it out! more coming! #genomics genomes.atcc.org
"... 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
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
October 2, 2025 at 4:12 PM
"... 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
www.cell.com/iscience/ful...
😊 cc: @officialatcc.bsky.social
“It’s can only good happen.”
LMAO
LMAO
September 24, 2025 at 4:23 AM
“It’s can only good happen.”
LMAO
LMAO
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
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
September 24, 2025 at 12:33 AM
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
journals.plos.org/plosone/arti...
#genomics #RNAseq #biopharma #EF24 #naturalproducts #leukemia
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. 🤣
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. 🤣
September 23, 2025 at 12:48 PM
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. 🤣
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. 🤣
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…
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…
September 19, 2025 at 5:47 PM
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…
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…
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 🧪🧬
I love this! Please reshare! #microscopy #biology #research #science #cellbiology #microbiology #biotech 🧪🧬
September 15, 2025 at 5:07 PM
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 🧪🧬
I love this! Please reshare! #microscopy #biology #research #science #cellbiology #microbiology #biotech 🧪🧬
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
September 5, 2025 at 11:16 PM
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!!!” …
paper submitted. 😀
August 27, 2025 at 9:03 PM
paper submitted. 😀
Reposted by Jonathan Jacobs
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
Powerfull content
August 24, 2025 at 11:14 PM
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
Powerfull content
Reposted by Jonathan Jacobs
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.
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.
August 25, 2025 at 2:34 AM
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.
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.
Reposted by Jonathan Jacobs
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"
August 14, 2025 at 7:29 PM
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"
🧪 🧬🖥️
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
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
August 14, 2025 at 10:19 PM
🧪 🧬🖥️
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
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
Reposted by Jonathan Jacobs
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.
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
August 13, 2025 at 11:26 AM
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.
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.