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
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
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. 🤣
Apparently… this worked. LMAO
September 19, 2025 at 5:54 PM
Apparently… this worked. LMAO
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?”
“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?”
September 19, 2025 at 5:50 PM
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?”
“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?”
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 🧪🧬
paper submitted. 😀
August 27, 2025 at 9:03 PM
paper submitted. 😀
Reading up on the (apparently?) new organelle discovered in mammalian cell lines — Hemifusomes. Pretty neat. www.nature.com/articles/s41...
But the top comment on Reddit hits home. 🤣😭
But the top comment on Reddit hits home. 🤣😭
August 2, 2025 at 7:44 PM
Reading up on the (apparently?) new organelle discovered in mammalian cell lines — Hemifusomes. Pretty neat. www.nature.com/articles/s41...
But the top comment on Reddit hits home. 🤣😭
But the top comment on Reddit hits home. 🤣😭
Really good meeting! Glad I made the trip - met tons of new people and learned about quite a few things I didn’t know before! #GSC25 Genomic Standards Consortium, Cambridge UK.
July 31, 2025 at 2:57 PM
Really good meeting! Glad I made the trip - met tons of new people and learned about quite a few things I didn’t know before! #GSC25 Genomic Standards Consortium, Cambridge UK.
Absolutely incredible talk by @laraurban42.bsky.social at #GSC25 on the use of @nanoporetech.com data to estimate the viability of bacteria directly from samples - based on ML modeling of squiggle data directly. 😱 #genomics #bioinformatics
July 31, 2025 at 8:35 AM
Absolutely incredible talk by @laraurban42.bsky.social at #GSC25 on the use of @nanoporetech.com data to estimate the viability of bacteria directly from samples - based on ML modeling of squiggle data directly. 😱 #genomics #bioinformatics
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
Sometimes working on slides for a talk ain’t so bad… especially from a rooftop pub in Cambridge, UK.
So far I love this town.
So far I love this town.
July 30, 2025 at 5:58 PM
Sometimes working on slides for a talk ain’t so bad… especially from a rooftop pub in Cambridge, UK.
So far I love this town.
So far I love this town.
We released another 500 DNA methylation datasets for ATCC Genome Portal reference genomes - bringing us up to 2,000 microbes now with that data and on track to have all 6,000+ microbes in the AGP paired with methylation info. What data? this data. (more details below 👇)
July 11, 2025 at 4:15 PM
We released another 500 DNA methylation datasets for ATCC Genome Portal reference genomes - bringing us up to 2,000 microbes now with that data and on track to have all 6,000+ microbes in the AGP paired with methylation info. What data? this data. (more details below 👇)
And like WT actual F is going on with this GC content (from the same ILMN library with the AAAAA kmers above)
July 1, 2025 at 2:08 PM
And like WT actual F is going on with this GC content (from the same ILMN library with the AAAAA kmers above)
It gets worse... here's a breakdown of enriched 5mers for the ILMN library used for the same assembly.
Really weird that AAAAA but not TTTTT is enriched. #NGS
#strandbias
#ATbias
Really weird that AAAAA but not TTTTT is enriched. #NGS
#strandbias
#ATbias
July 1, 2025 at 2:08 PM
It gets worse... here's a breakdown of enriched 5mers for the ILMN library used for the same assembly.
Really weird that AAAAA but not TTTTT is enriched. #NGS
#strandbias
#ATbias
Really weird that AAAAA but not TTTTT is enriched. #NGS
#strandbias
#ATbias
TTW you were "just curious" and pulled the raw FASTQ data from SRA for a fungal genome assembly in RefSeq and you find the GC content for the PacBio reads looks like this... 🤔😐
A/T much? geez...
running a contamination screen now...
A/T much? geez...
running a contamination screen now...
July 1, 2025 at 2:08 PM
TTW you were "just curious" and pulled the raw FASTQ data from SRA for a fungal genome assembly in RefSeq and you find the GC content for the PacBio reads looks like this... 🤔😐
A/T much? geez...
running a contamination screen now...
A/T much? geez...
running a contamination screen now...
Still… with so many corporate sponsors I feel like they could have had the funding to be better organized, hosted it in a larger space, and I dunno made it feel more like a… Festival? 🫠 … they didn’t even spring for carpeting…
June 24, 2025 at 9:04 PM
Still… with so many corporate sponsors I feel like they could have had the funding to be better organized, hosted it in a larger space, and I dunno made it feel more like a… Festival? 🫠 … they didn’t even spring for carpeting…
The murals are awesome. I wish more cities supported street art.
June 22, 2025 at 9:44 PM
The murals are awesome. I wish more cities supported street art.
So if you’re at #ASMicrobe you may have missed an epic night of Karaoke.
@bielleogy.bsky.social @surtlab.bsky.social @drswlong.bsky.social @mightycrobe.bsky.social
@bielleogy.bsky.social @surtlab.bsky.social @drswlong.bsky.social @mightycrobe.bsky.social
June 22, 2025 at 6:06 PM
So if you’re at #ASMicrobe you may have missed an epic night of Karaoke.
@bielleogy.bsky.social @surtlab.bsky.social @drswlong.bsky.social @mightycrobe.bsky.social
@bielleogy.bsky.social @surtlab.bsky.social @drswlong.bsky.social @mightycrobe.bsky.social
Also - don’t miss the poster from Briana Benton on my team! She’s presenting early results on WGS of a cohort of 100s of MDR strains isolated from clinical sources - and their associated methylation data. If you’re into AMR or microbial epigenetics - stop by her poster to chat. #ASMicrobe
June 22, 2025 at 5:33 PM
Also - don’t miss the poster from Briana Benton on my team! She’s presenting early results on WGS of a cohort of 100s of MDR strains isolated from clinical sources - and their associated methylation data. If you’re into AMR or microbial epigenetics - stop by her poster to chat. #ASMicrobe
Hey 👋 #ASMicrobe! If you’re into microbial genomics - stop by during the poster session and chat with Scott Nguyen from my team from ATCC. He’s been working on a whole range of interesting microbial species 🦠many of them have never been sequenced before by anyone.
Please RePost🙏 🧪 🧬🖥️
Please RePost🙏 🧪 🧬🖥️
June 22, 2025 at 5:23 PM
Hey 👋 #ASMicrobe! If you’re into microbial genomics - stop by during the poster session and chat with Scott Nguyen from my team from ATCC. He’s been working on a whole range of interesting microbial species 🦠many of them have never been sequenced before by anyone.
Please RePost🙏 🧪 🧬🖥️
Please RePost🙏 🧪 🧬🖥️
Hey #ASMicrobe ! Are you a photographer? Well - ATCC’s photo contest is BACK! Drop by booth 1413 to learn more. I love this contest - and so happy it’s back. www.atcc.org/photocontest @officialatcc.bsky.social
June 21, 2025 at 8:39 PM
Hey #ASMicrobe ! Are you a photographer? Well - ATCC’s photo contest is BACK! Drop by booth 1413 to learn more. I love this contest - and so happy it’s back. www.atcc.org/photocontest @officialatcc.bsky.social
#ASMicrobe Gold.
These are all great people.
These are all great people.
June 21, 2025 at 5:12 AM
#ASMicrobe Gold.
These are all great people.
These are all great people.
Great group of nerds hanging out at The Perch. #ASMicrobe
June 21, 2025 at 4:05 AM
Great group of nerds hanging out at The Perch. #ASMicrobe