@jrose835.bsky.social
Computational biologist. Bioinformatician, dad, scientist, science-fiction lover. Working on spatial transcriptomics for RNA delivery
When I was at NIH and shutdowns loomed, it was discovered that the administration was planning to shut down PubMed. The head of NCBI called the powers that be and pointed out that this would threaten patient safety
Who knows what will happen now
Just in case, remember Euruope-PMC
(europepmc.org )
This is the most exciting time ever to be working in data, and I'm not talking about AI.
3 years ago, I wrote a database-centric guide in my book for analyzing the full 92 million record 1910 Census.
Now, with #rstats and @duckdb?
Analyze those 92 million rows in seconds.
Was helping a client today with a 500 million row dataset. It took about 42 GB as a CSV & 7 GB as a parquet file. We needed a count of rows per ID. We tried Arrow but gave up after staring at the console for a few minutes. Switched to @duckdb.org & got an answer in less than a second.
10.09.2025 22:07 — 👍 11 🔁 2 💬 1 📌 0
We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
got some drinks and talked some shit tonight with @rohitforatlanta.bsky.social. i simply cannot imagine a better human being to lead ATL’s city council. vote for him if you’re ready for an end to typical atlanta way nonsense. we deserve better, and we’re right on the cusp of real change imho.
23.08.2025 00:26 — 👍 29 🔁 4 💬 1 📌 1
My wife shared this with me and I’m tellin you… it’s worth the read.
13.08.2025 14:55 — 👍 14510 🔁 3534 💬 1593 📌 877
"The U.S. Department of Health and Human Services (HHS) today announced the beginning of a coordinated wind-down of its mRNA vaccine development activities...."
cc: Sen. Bill Cassidy
One by one, he watched them start new lives elsewhere. Many of them went to the U.S. At the time, America was the most compelling destination for scientific talent in the world. It would remain so until earlier this year.
An incredibly depressing sentence.
www.theatlantic.com/science/arch...
The future of tech doesn't hinge on who can suffer the longest. It rests on those who can build wisely, lead humanely, and sustain what they start.
That's the culture worth exporting.
Not the mythology machine built on others' exhaustion.
www.dataandpolitics.net/the-selectio...
Hearing the same: that Schnabel was walked off the NIH campus yesterday. If so, that will be a positive step.
Schnabel seemed to have more power at NIH than Jay Bhattacharya—whose work so far seems to involve (?) making podcasts and appearing on Fox and Bari Weiss to push far-right talking points.
“But the whole scholarly career track still pretends that only the mythical Principle Investigator deserves a permanent job and recognition for their contributions.” 🔥🔥
09.07.2025 17:41 — 👍 0 🔁 0 💬 0 📌 0”I think the biggest thing we could do to improve research is to stop rewarding individuals but instead reward teams. Science is done in teams with division of labor.”🙌🙌
09.07.2025 17:41 — 👍 0 🔁 0 💬 1 📌 0…ahem…single cell psuedotime analysis…cough cough 👀#bioinformatics #scRNAseq 🧬🔬
“It’s one of open science’s failure modes: Sharing illogical methods that produce exciting false results just makes it easier for others to publish false results. It’s the ongoing natural selection of bad science”
New York plants 400 chestnuts in effort to restore near-extinct native tree. Once dominant in eastern forests, the American chestnut was nearly wiped out by blight a century ago. The project marks a shift toward urban ecosystems as active sites of species recovery buff.ly/BrPZeqE
#ShareGoodNewsToo
Why not listen to our "brilliant, majestic and expansive" five-hour long episode — on the whole scientific journey, from the 1980s, of turning HIV/AIDS from a fatal to a manageable condition, and why now's the time to be ambitious in fighting HIV worldwide.
On all podcast platforms:
Very nice work!
29.05.2025 13:06 — 👍 1 🔁 0 💬 0 📌 0Proud to announce our new technique for tracking relative B cell clonality in situ with B Cell Receptor MERFISH (BCR-MERFISH)! Congratulations to Evan Yang and our colleagues in the Carroll laboratory! Check out our bioRxiv: www.biorxiv.org/content/10.1... 1/9
28.05.2025 15:40 — 👍 13 🔁 5 💬 2 📌 1
Devastating
Original post: mastodon.social/@jeffjarvis/...
As a scientist working on a mix of bespoke data analysis and reproducible pipeline creation this article ressonates. Very different skillsets! #bioinformatics #genomics #datasci www.counting-stuff.com/as-a-mostly-...
20.05.2025 13:15 — 👍 4 🔁 0 💬 0 📌 0I made a feed for all things Omics! Have your posts included in it by adding a 🧬plus any additional omics related emoji🧪🧫🔬🖥️💉🦠🥼. Anything Genomics, Epigenomics, Transcriptomics, Proteomics, Metabolomics, or Metagenomics related (or adjacent!) is welcome!
bsky.app/profile/h2so...
The image shows a round, fluffy black cat with large, striking yellow eyes looking up at the camera. The cat is seated on a light-colored tiled floor and against a white wall. The cat’s fur is smooth and glossy, creating a stark contrast with its bright eyes. There are two beige letters, "F" and "D," superimposed on the image. The "F" is placed near the cat's left eye, and the "D" near its right eye.
I hope this makes you smile as much as it did for me.
12.04.2025 03:05 — 👍 11305 🔁 1556 💬 195 📌 75Once upon a time, in the late 1800s, people in Japan got really into breeding mice.
Coloured mice. Patterned mice. Even mice that danced.
They became known as Japanese Fancy Mice, and that caught the attention of researchers in Europe and America, who imported them for study.
2/n
Confused about how SBX @RocheSequencing works? Watch this you tube video . You’re welcome youtu.be/G8ECt04qPos?...
22.02.2025 11:27 — 👍 9 🔁 2 💬 0 📌 0
Howard University is now a R1 university, the first HBCU with a research one designation. H-U definitely knows!
13.02.2025 16:52 — 👍 3393 🔁 560 💬 16 📌 32
It became clear in the discussion that investing energy in more biologically meaningful ways to embed the data (compared to existing approaches) is likely where comp biologists can have a huge impact with these models. 2/n
13.02.2025 00:36 — 👍 12 🔁 4 💬 1 📌 0“They’re turning off the lights on cancer research.” That’s the framing.
08.02.2025 16:38 — 👍 28 🔁 11 💬 3 📌 3ATTENTION
If you are someone who had an F31-Diversity (or similar) application submitted this cycle, please DM me here, contact me on signal (jeremymberg.78), or email me at jeremymberg@gmail.com.
I will keep all information confidential.
2/n
My student's diversity F31 has been pulled from study section even though it's the SAME APPLICATION as regular F31s, normally reviewed together in the same panel. Throwing out all the applications from URMs while the ones from white/privileged students get to be reviewed is blatant discrimination.
07.02.2025 03:31 — 👍 220 🔁 91 💬 8 📌 11The immune system balances barrier defenses and systemic responses to maintain health. Diversity in antigen receptors enables pathogen recognition, but some epitopes are historically excluded due to biased selection. Cytokines polarize responses, influencing cell inclusion and immune status.
04.02.2025 21:12 — 👍 51 🔁 16 💬 2 📌 2
"Becoming a #Scientist: The Graphic Novel" goes through the stories of my amazing lab members. Every one has a unique pathway, overcoming personal challenges. They are an inspirational #team!
www.thegreatbritishbookshop.co.uk/products/bec...
