Joshua Fein
@joshuafein.bsky.social
Pinned
Joshua Fein
@joshuafein.bsky.social
· Dec 13
Impossible Dream
This is "Impossible Dream" by Joshua Fein on Vimeo, the home for high quality videos and the people who love them.
vimeo.com
It’s been 13 years since I started down the road to a medical career and left music behind… but I’m delighted to say that last night I had my got to sing on a stage again for the first time in about a decade! Hoping to make time for voice lessons and occasional performing as an attending
Outstanding articles. I’ve only just begun experimenting with Claude and Gemini CLIs and they’re incredibly powerful. This is extremely valuable best practice advice.
The last five months with Claude Code have completely changed how we work.
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
matsen.group/agentic.html details:
• How agents work (& why it matters)
• Git Flow with agents
• Using agents for science
• The human-agent interface
Questions? What has your experience been?
Agentic Coding For Scientists
A four-part series on using coding agents like Claude Code for scientific programming, covering fundamentals, workflows, best practices, and the human side of AI-assisted development.
matsen.group
November 14, 2025 at 5:01 AM
Outstanding articles. I’ve only just begun experimenting with Claude and Gemini CLIs and they’re incredibly powerful. This is extremely valuable best practice advice.
Reposted by Joshua Fein
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
a cartoon says hey everybody an old man 's talking while bart simpson looks on
ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on
media.tenor.com
November 8, 2025 at 1:58 PM
Bluetorial-Jim Watson
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
I met Jim Watson a few times but did not know him well. However, I was greatly influenced by his book “The Double Helix”. He was a complicated human being with some very, very bad features, but some good contributions.
What follows is my personal perspective.
1/41
My favorite feature of the @developers.google.com Gemini CLI is the snarky comments while it's working on something... especially "Rewriting in Rust for no particular reason."
November 7, 2025 at 10:45 AM
My favorite feature of the @developers.google.com Gemini CLI is the snarky comments while it's working on something... especially "Rewriting in Rust for no particular reason."
Proper way to start the day.
November 7, 2025 at 10:43 AM
Proper way to start the day.
Congrats to the authors on this huge accomplishment. Fascinating and so much to build on here.
Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com/articles/s41...
PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 16, 2025 at 9:51 AM
Congrats to the authors on this huge accomplishment. Fascinating and so much to build on here.
Has anyone had success 3D printing storage boxes for -80s? What fiber have you used? any special settings to reinforce?
I'm thinking of making either custom inserts or entire boxes to better keep track of which sample goes where...
I'm thinking of making either custom inserts or entire boxes to better keep track of which sample goes where...
August 13, 2025 at 1:36 PM
Has anyone had success 3D printing storage boxes for -80s? What fiber have you used? any special settings to reinforce?
I'm thinking of making either custom inserts or entire boxes to better keep track of which sample goes where...
I'm thinking of making either custom inserts or entire boxes to better keep track of which sample goes where...
Reposted by Joshua Fein
Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.
May 29, 2025 at 2:39 PM
Industry friends, now is the time for MUCH more speaking out on behalf of academic colleagues under duress. Here are core open source methods that many of your products doubtlessly depend on either directly or indirectly (see en.wikipedia.org/wiki/HMMER) being abruptly defunded. Make noise.
Reminds me of Oliver Sacks’ musings on seeing azure.
This will surely be commercialised and available as an “experience” (hopefully safely) around the world soon, but absolutely sign me up.
This will surely be commercialised and available as an “experience” (hopefully safely) around the world soon, but absolutely sign me up.
The ‘Profound’ Experience of Seeing a New Color
The ecstasy of “olo”
www.theatlantic.com
April 27, 2025 at 4:21 PM
Reminds me of Oliver Sacks’ musings on seeing azure.
This will surely be commercialised and available as an “experience” (hopefully safely) around the world soon, but absolutely sign me up.
This will surely be commercialised and available as an “experience” (hopefully safely) around the world soon, but absolutely sign me up.
I think the reason I like #systemsimmunology #cshlsysimm is because network diagrams are so pretty.
April 23, 2025 at 1:04 PM
I think the reason I like #systemsimmunology #cshlsysimm is because network diagrams are so pretty.
This is simply insanity.
Federal funding for the Women’s Health Initiative, which as one of the largest research projects in women’s health has shaped treatment of menopause, osteoporosis, and nutrition, will stop in September.
Women’s Health Initiative, known for hormone therapy trials, to lose federal funding
The Women's Health Initiative, the enormous study that shaped treatment of menopause and other conditions, is on the verge of shutting down.
buff.ly
April 23, 2025 at 12:59 AM
This is simply insanity.
This disc is a revelation.
I thought I knew these pieces-the D minor concerto was one of the first pieces I fell in love with as a kid.
Beatrice Rana’s playing is simply enchanting.
I thought I knew these pieces-the D minor concerto was one of the first pieces I fell in love with as a kid.
Beatrice Rana’s playing is simply enchanting.
Bach: Keyboard Concertos, BWV 1052, 1053, 1054 & 1056 by Beatrice Rana - Apple Music Classical
Listen to Bach: Keyboard Concertos, BWV 1052, 1053, 1054 & 1056 by Beatrice Rana. 2025. 12 tracks. 1 hour, 2 minutes.
classical.music.apple.com
April 19, 2025 at 8:27 AM
This disc is a revelation.
I thought I knew these pieces-the D minor concerto was one of the first pieces I fell in love with as a kid.
Beatrice Rana’s playing is simply enchanting.
I thought I knew these pieces-the D minor concerto was one of the first pieces I fell in love with as a kid.
Beatrice Rana’s playing is simply enchanting.
Does anyone have experience with momelotinib for AGvHD in MF patients?
April 18, 2025 at 3:28 PM
Does anyone have experience with momelotinib for AGvHD in MF patients?
Reposted by Joshua Fein
I’m very specifically looking for a tech with mouse experience for my new lab! Message me or apply through the link if you’re interested!
aprecruit.ucsf.edu/JPF05438
aprecruit.ucsf.edu/JPF05438
Minnie Lab - Junior, Assistant, or Associate Specialist
University of California, San Francisco is hiring. Apply now!
aprecruit.ucsf.edu
April 17, 2025 at 4:15 PM
I’m very specifically looking for a tech with mouse experience for my new lab! Message me or apply through the link if you’re interested!
aprecruit.ucsf.edu/JPF05438
aprecruit.ucsf.edu/JPF05438
Excited to attend #cshlsysimm next week. I am just starting to find my way in this fascinating field and look forward to learning from the extraordinary lineup of speakers! Please reach out if you’ll be there—looking forward to connecting. @cshlnews.bsky.social
April 16, 2025 at 2:14 PM
Excited to attend #cshlsysimm next week. I am just starting to find my way in this fascinating field and look forward to learning from the extraordinary lineup of speakers! Please reach out if you’ll be there—looking forward to connecting. @cshlnews.bsky.social
I remain strongly in favor of fishing expeditions.
April 11, 2025 at 1:32 PM
I remain strongly in favor of fishing expeditions.
In light of recent news regarding funding, I have asked ChatGPT to help figure out how to do ATAC-Seq with only an abacus and stone tools.
April 9, 2025 at 1:53 PM
In light of recent news regarding funding, I have asked ChatGPT to help figure out how to do ATAC-Seq with only an abacus and stone tools.
Reposted by Joshua Fein
1/ Excited to share my first-ever first-author paper out now in Science Immunology! from @knapplab.bsky.social and co-supervised by @miershawig.bsky.social
We show that hematopoietic aging, independent of lung tissue aging, is sufficient to exacerbate fibrosis.
🔗 www.science.org/doi/10.1126/...
We show that hematopoietic aging, independent of lung tissue aging, is sufficient to exacerbate fibrosis.
🔗 www.science.org/doi/10.1126/...
An aging bone marrow exacerbates lung fibrosis by fueling profibrotic macrophage persistence
Hematopoietic aging drives lung fibrosis and profibrotic macrophage influx, stalling their maturation via reduced Treg-derived IL-10.
www.science.org
March 28, 2025 at 7:10 PM
1/ Excited to share my first-ever first-author paper out now in Science Immunology! from @knapplab.bsky.social and co-supervised by @miershawig.bsky.social
We show that hematopoietic aging, independent of lung tissue aging, is sufficient to exacerbate fibrosis.
🔗 www.science.org/doi/10.1126/...
We show that hematopoietic aging, independent of lung tissue aging, is sufficient to exacerbate fibrosis.
🔗 www.science.org/doi/10.1126/...
It dawned on me today that I really should’ve named one of my kids Luke, so that I could legitimately say “Luke, I am your father.”
Oh well.
Oh well.
March 20, 2025 at 10:56 PM
It dawned on me today that I really should’ve named one of my kids Luke, so that I could legitimately say “Luke, I am your father.”
Oh well.
Oh well.
Highly recommended escape from these dark times.
The Road to 1066: Anglo-Saxon Apocalypse (Part 1)
Podcast Episode · The Rest Is History · 03/17/2025 · 55m
podcasts.apple.com
March 17, 2025 at 9:27 AM
Highly recommended escape from these dark times.
Reposted by Joshua Fein
1) I am delighted to share a manuscript long in the making (7 years), elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm www.biorxiv.org/content/10.1...
Transcriptomic plasticity is a hallmark of metastatic pancreatic cancer
Metastasis is the leading cause of cancer deaths; nonetheless, how tumor cells adapt to vastly different organ contexts is largely unknown. To investigate this question, we generated a transcriptomic ...
www.biorxiv.org
March 7, 2025 at 11:26 AM
1) I am delighted to share a manuscript long in the making (7 years), elucidating the forces that shape metastatic adaptation PDAC using scRNA-seq across multiple organs from a rapid autopsy combined with a powerful new clonal phylogeny inference algorithm www.biorxiv.org/content/10.1...
Having determined that the transplant immunology community is shamefully lacking for pompously named journals, I propose the establishment of Acta Transplantiana A (solid organs) and B (haematopoietic tissues).
Paper distribution only, on heavy cream-coloured paper stock. Figures hand-drawn.
Paper distribution only, on heavy cream-coloured paper stock. Figures hand-drawn.
March 6, 2025 at 12:45 PM
Having determined that the transplant immunology community is shamefully lacking for pompously named journals, I propose the establishment of Acta Transplantiana A (solid organs) and B (haematopoietic tissues).
Paper distribution only, on heavy cream-coloured paper stock. Figures hand-drawn.
Paper distribution only, on heavy cream-coloured paper stock. Figures hand-drawn.