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
Reposted by Jonathan Jacobs
First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics
Complete Diploid Genome of the Type Strain Yarrowia lipolytica YB-423 (ATCC 18942™)
Abstract. Here, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a co
academic.oup.com
January 27, 2026 at 5:22 PM
First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics
First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics
Complete Diploid Genome of the Type Strain Yarrowia lipolytica YB-423 (ATCC 18942™)
Abstract. Here, we present the first complete, fully phased diploid genome of type strain Yarrowia lipolytica YB-423 (=ATCC 18942™), constructed using a co
academic.oup.com
January 27, 2026 at 5:22 PM
First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics
Reposted by Jonathan Jacobs
“I just checked—it turns out that Art. II, Sec. 1 of the Constitution of the United States does *not* say ‘The executive Power shall be vested in a bunch of sociopaths who think they can do whatever the f*ck they want and make sh*t up as they go along.’” — George Conway
January 26, 2026 at 12:37 PM
“I just checked—it turns out that Art. II, Sec. 1 of the Constitution of the United States does *not* say ‘The executive Power shall be vested in a bunch of sociopaths who think they can do whatever the f*ck they want and make sh*t up as they go along.’” — George Conway
Wondering how this count of retrotransposons in Yarrowia lipolytica compare to other yeasts... bc it seems really high and may explain why this species has such incredible genomic plasticity at the structural level.
(for context - this is from our recent publication on type-strain in JIMB)
(for context - this is from our recent publication on type-strain in JIMB)
January 20, 2026 at 7:30 PM
Wondering how this count of retrotransposons in Yarrowia lipolytica compare to other yeasts... bc it seems really high and may explain why this species has such incredible genomic plasticity at the structural level.
(for context - this is from our recent publication on type-strain in JIMB)
(for context - this is from our recent publication on type-strain in JIMB)
It's a beautiful thing when this happens...
January 16, 2026 at 2:06 PM
It's a beautiful thing when this happens...
Also realizing that biologists, engineers, data scientists often use the same words differently.
Standards fail when semantic alignment fails.
Also see my post on providence vs provenance — this actually happened today. 🤦🏻♂️
Standards fail when semantic alignment fails.
Also see my post on providence vs provenance — this actually happened today. 🤦🏻♂️
Some takeaways from today’s meeting: 1/n
Engineers: “Why do we need so many replicates?”
Biologists: “Why are you iterating without statistical confidence?”
Engineers: “Why do we need so many replicates?”
Biologists: “Why are you iterating without statistical confidence?”
January 9, 2026 at 6:46 PM
Also realizing that biologists, engineers, data scientists often use the same words differently.
Standards fail when semantic alignment fails.
Also see my post on providence vs provenance — this actually happened today. 🤦🏻♂️
Standards fail when semantic alignment fails.
Also see my post on providence vs provenance — this actually happened today. 🤦🏻♂️
Some takeaways from today’s meeting: 1/n
Engineers: “Why do we need so many replicates?”
Biologists: “Why are you iterating without statistical confidence?”
Engineers: “Why do we need so many replicates?”
Biologists: “Why are you iterating without statistical confidence?”
January 9, 2026 at 6:15 PM
Some takeaways from today’s meeting: 1/n
Engineers: “Why do we need so many replicates?”
Biologists: “Why are you iterating without statistical confidence?”
Engineers: “Why do we need so many replicates?”
Biologists: “Why are you iterating without statistical confidence?”
Looking forward to participating in today’s session at the MidAtlantic Synthetic Biology Symposium on digital biology & data standards in synthetic biology.
Lots of work to do in this space - and very happy NIST is organized a session on this topic.
#synbio
Lots of work to do in this space - and very happy NIST is organized a session on this topic.
#synbio
January 9, 2026 at 5:16 PM
Looking forward to participating in today’s session at the MidAtlantic Synthetic Biology Symposium on digital biology & data standards in synthetic biology.
Lots of work to do in this space - and very happy NIST is organized a session on this topic.
#synbio
Lots of work to do in this space - and very happy NIST is organized a session on this topic.
#synbio
Attending MidAtlantic Synthetic Biology Symposium - happy to see @genegirl007.bsky.social presenting on her work at GATech! “Harnessing synthetic biology for next-generation therapeutics” #synbio #stemcells
January 8, 2026 at 8:58 PM
Attending MidAtlantic Synthetic Biology Symposium - happy to see @genegirl007.bsky.social presenting on her work at GATech! “Harnessing synthetic biology for next-generation therapeutics” #synbio #stemcells
Ok so the salary ranges for bioinformaticians at AI/ML companies (Anthropocene, OpenAI etc) - is ABSOLUTELY INSANE.
$250k - $450k+ salary plus equity… no PhD and only a few years experience required . Whut???
$250k - $450k+ salary plus equity… no PhD and only a few years experience required . Whut???
a man with curly hair and glasses is making a funny face and saying `` wait ... what ? ''
ALT: a man with curly hair and glasses is making a funny face and saying `` wait ... what ? ''
media.tenor.com
January 8, 2026 at 3:49 AM
Ok so the salary ranges for bioinformaticians at AI/ML companies (Anthropocene, OpenAI etc) - is ABSOLUTELY INSANE.
$250k - $450k+ salary plus equity… no PhD and only a few years experience required . Whut???
$250k - $450k+ salary plus equity… no PhD and only a few years experience required . Whut???
Reposted by Jonathan Jacobs
🧪🖥️ This was funny AF so I feel compelled to share it. 🧵
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
January 7, 2026 at 3:03 AM
🧪🖥️ This was funny AF so I feel compelled to share it. 🧵
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
🧪🖥️ This was funny AF so I feel compelled to share it. 🧵
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
January 7, 2026 at 3:03 AM
🧪🖥️ This was funny AF so I feel compelled to share it. 🧵
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
So … if you ever are confused or read / hear / think someone else is confused about
Providence vs. Provenance
Please share this thread. 👇
#AIxBio #Bioinformatics
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