Jim Rose
@jrose835.bsky.social
Computational biologist. Bioinformatician, dad, scientist, science-fiction lover.
Working on spatial transcriptomics for RNA delivery
Working on spatial transcriptomics for RNA delivery
Reposted by Jim Rose
@biorxivpreprint.bsky.social B-cell follicles act as a critical microanatomical niche for sustained viral replication, virus-host interaction, and tissue damage during SIV chronic infection
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 21, 2025 at 2:30 AM
@biorxivpreprint.bsky.social B-cell follicles act as a critical microanatomical niche for sustained viral replication, virus-host interaction, and tissue damage during SIV chronic infection
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jim Rose
A new NEJM paper just dropped evaluating a quadrivalent modified mRNA (modRNA) influenza vaccine in a phase 3 trial. This is the largest test yet of whether the mRNA platform that transformed COVID-19 vaccination can improve our fight against flu.
www.nejm.org/doi/full/10....
www.nejm.org/doi/full/10....
Efficacy, Immunogenicity, and Safety of Modified mRNA Influenza Vaccine | NEJM
Influenza remains a major health burden despite the use of licensed vaccines. Nucleoside-modified
messenger RNA (modRNA) influenza vaccines have shown promising immunogenicity against
influenza and...
www.nejm.org
November 20, 2025 at 12:26 PM
A new NEJM paper just dropped evaluating a quadrivalent modified mRNA (modRNA) influenza vaccine in a phase 3 trial. This is the largest test yet of whether the mRNA platform that transformed COVID-19 vaccination can improve our fight against flu.
www.nejm.org/doi/full/10....
www.nejm.org/doi/full/10....
Reposted by Jim Rose
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 )
Who knows what will happen now
Just in case, remember Euruope-PMC
(europepmc.org )
a cartoon of donald trump with the words be prepared above him
ALT: a cartoon of donald trump with the words be prepared above him
media.tenor.com
September 29, 2025 at 1:35 PM
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 )
Who knows what will happen now
Just in case, remember Euruope-PMC
(europepmc.org )
Reposted by Jim Rose
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.
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.
September 17, 2025 at 5:17 PM
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.
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.
Reposted by Jim Rose
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.
September 10, 2025 at 10:07 PM
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.
Reposted by Jim Rose
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
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
August 25, 2025 at 3:24 PM
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
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
Reposted by Jim Rose
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.
August 23, 2025 at 12:26 AM
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.
Reposted by Jim Rose
My wife shared this with me and I’m tellin you… it’s worth the read.
August 13, 2025 at 2:55 PM
My wife shared this with me and I’m tellin you… it’s worth the read.
Reposted by Jim Rose
"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
cc: Sen. Bill Cassidy
August 5, 2025 at 9:34 PM
"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
cc: Sen. Bill Cassidy
Reposted by Jim Rose
July 31, 2025 at 2:59 PM
Reposted by Jim Rose
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...
That's the culture worth exporting.
Not the mythology machine built on others' exhaustion.
www.dataandpolitics.net/the-selectio...
The Selection Effect: Exporting Burnout as Best Practice
The tech industry has a selection problem: extreme work culture gets amplified globally while sustainable practices stay quiet. For those learning about Silicon Valley from a distance, this creates a ...
www.dataandpolitics.net
July 22, 2025 at 5:08 PM
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...
That's the culture worth exporting.
Not the mythology machine built on others' exhaustion.
www.dataandpolitics.net/the-selectio...
Reposted by Jim Rose
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.
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.
Hearing rumors from multiple sources that NIH COO Eric Schnabel was terminated yesterday for allegedly trying to award a large contract to his wife (who sometimes uses her maiden name) for "public outreach" associated with the autism data science initiative.
#EndlessGrift
#EndlessGrift
a woman drinking a cup of tea with the words " i got the tea " below her
ALT: a woman drinking a cup of tea with the words " i got the tea " below her
media.tenor.com
July 15, 2025 at 2:02 PM
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.
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.
…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”
“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”
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...
Which Kind of Science Reform
What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.
elevanth.org
July 9, 2025 at 5:23 PM
…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”
“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”
Reposted by Jim Rose
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
#ShareGoodNewsToo
‘This isn’t a gimmick’: the New Yorkers trying to restore the American chestnut
More than 120 years after billions of the trees were wiped out, blight-proof seeds are being planted
buff.ly
July 2, 2025 at 12:50 PM
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
#ShareGoodNewsToo
Reposted by Jim Rose
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:
On all podcast platforms:
Lenacapavir: The miracle drug that could end AIDS
Hard Drugs · Episode
open.spotify.com
June 14, 2025 at 7:12 AM
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:
On all podcast platforms:
Very nice work!
Proud 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
May 29, 2025 at 1:06 PM
Very nice work!
Reposted by Jim Rose
Proud 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
May 28, 2025 at 3:40 PM
Proud 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
Devastating
Original post: mastodon.social/@jeffjarvis/...
Original post: mastodon.social/@jeffjarvis/...
May 22, 2025 at 12:20 PM
Devastating
Original post: mastodon.social/@jeffjarvis/...
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-...
As a mostly ad-hoc'er, I've got workflow issues
Please, let's celebrate doing things the ugly way. For our peers that do things justly as ugly.
www.counting-stuff.com
May 20, 2025 at 1:15 PM
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-...
Reposted by Jim Rose
I 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...
bsky.app/profile/h2so...
April 18, 2025 at 1:02 PM
I 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...
bsky.app/profile/h2so...
Reposted by Jim Rose
I hope this makes you smile as much as it did for me.
April 12, 2025 at 3:05 AM
I hope this makes you smile as much as it did for me.
Reposted by Jim Rose
Once 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
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
March 4, 2025 at 3:10 PM
Once 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
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
Reposted by Jim Rose
Confused about how SBX @RocheSequencing works? Watch this you tube video . You’re welcome youtu.be/G8ECt04qPos?...
Introducing Roche Sequencing by Expansion (SBX) Technology
YouTube video by Roche
youtu.be
February 22, 2025 at 11:27 AM
Confused about how SBX @RocheSequencing works? Watch this you tube video . You’re welcome youtu.be/G8ECt04qPos?...
Reposted by Jim Rose
Howard University is now a R1 university, the first HBCU with a research one designation. H-U definitely knows!
Howard University Receives “Research One” Carnegie Classification Indicating Highest Level of Research Production
The American Council of Education (ACE) today announced that Howard University has been conferred a Research One (R1) Carnegie Classification, indicating “very high research spending and doctorate pro...
thedig.howard.edu
February 13, 2025 at 4:52 PM
Howard University is now a R1 university, the first HBCU with a research one designation. H-U definitely knows!
Reposted by Jim Rose
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
February 13, 2025 at 12:36 AM
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