Sergey Kryazhimskiy
@skryazhi.bsky.social
Work in progress | Evolution | Ecology | Systems Biology | Experiments | Theory | Running a lab @ucsdbiosciences | http://sklab.science | https://thoughtsforbreakfast.wordpress.com/
Reposted by Sergey Kryazhimskiy
My quote of the day
Masha Gessen
Masha Gessen
December 22, 2025 at 11:47 AM
My quote of the day
Masha Gessen
Masha Gessen
Reposted by Sergey Kryazhimskiy
I am very excited to announce that a fully funded PhD position is available in my group.
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
November 27, 2025 at 2:24 PM
I am very excited to announce that a fully funded PhD position is available in my group.
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia
Please RT or forward this information to interested candidates.
Deadline: 11.01.26
More info:
shorturl.at/f1TuF
Reposted by Sergey Kryazhimskiy
This year has been brutal for science, especially early career researchers and those working with communities further marginalized by this administration. Please read the experiences of these scientists.
And when you’re done reading, find a way to fight back.
theconversation.com/this-year-ne...
And when you’re done reading, find a way to fight back.
theconversation.com/this-year-ne...
‘This year nearly broke me as a scientist’ – US researchers reflect on how 2025’s science cuts have changed their lives
US science lost a great deal in 2025, including tens of billions of dollars of federal funding, entire research agencies and programs, and a generation of researchers.
theconversation.com
December 19, 2025 at 12:55 AM
This year has been brutal for science, especially early career researchers and those working with communities further marginalized by this administration. Please read the experiences of these scientists.
And when you’re done reading, find a way to fight back.
theconversation.com/this-year-ne...
And when you’re done reading, find a way to fight back.
theconversation.com/this-year-ne...
Reposted by Sergey Kryazhimskiy
Excited that SpaceBar is now out in Nature Methods!🥳
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
SpaceBar enables single-cell-resolution clone tracing with imaging-based spatial transcriptomics
Nature Methods - SpaceBar is a cellular barcoding strategy for simultaneous analysis of cell clonal and spatial identities.
rdcu.be
December 18, 2025 at 7:55 PM
Excited that SpaceBar is now out in Nature Methods!🥳
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
We combined clone tracing with spatial transcriptomics to untangle what drives gene expression in tumors: a cell's identity or its neighborhood?
Most genes were driven by location, but some showed strong clonal patterns.
rdcu.be/eVhpc
Reposted by Sergey Kryazhimskiy
So, after thinking for a bit on this:
-always (and still) good practice to debrief with PO regardless of panel summary
-less ad hoc reviews means you’re going to (overall) get less specific comments and more sporadic frustrating comments
-funding is a shitshow bc of continuing resolutions
-always (and still) good practice to debrief with PO regardless of panel summary
-less ad hoc reviews means you’re going to (overall) get less specific comments and more sporadic frustrating comments
-funding is a shitshow bc of continuing resolutions
Live thread of the NSF biology virtual office hour:
🧵
🧵
December 18, 2025 at 8:34 PM
So, after thinking for a bit on this:
-always (and still) good practice to debrief with PO regardless of panel summary
-less ad hoc reviews means you’re going to (overall) get less specific comments and more sporadic frustrating comments
-funding is a shitshow bc of continuing resolutions
-always (and still) good practice to debrief with PO regardless of panel summary
-less ad hoc reviews means you’re going to (overall) get less specific comments and more sporadic frustrating comments
-funding is a shitshow bc of continuing resolutions
Very excited about this meeting!
📢 Join us in sunny Lisbon 🇵🇹 2-5 June for the @embo.org workshop ☀️
“The rules of the game: biophysical & molecular principles in cellular evolution”
Apply by March 1st!
Please repost to help spread the word!
meetings.embo.org/event/26-cel...
#EMBORulesOfTheGame @gimmfoundation.bsky.social
“The rules of the game: biophysical & molecular principles in cellular evolution”
Apply by March 1st!
Please repost to help spread the word!
meetings.embo.org/event/26-cel...
#EMBORulesOfTheGame @gimmfoundation.bsky.social
The rules of the game: biophysical & molecular principles in cellular evolution
Cells are the fundamental units of life, shaped by evolution into a remarkable diversity of forms and functions. Much is known about the roles of genes and proteins, the regulation of molecular proce…
meetings.embo.org
December 18, 2025 at 6:16 PM
Very excited about this meeting!
Reposted by Sergey Kryazhimskiy
Working on this paper fundamentally changed how I thought about bacterial evolution, and I couldn't ask for a better to Hannukah present than to see it out, at last!
Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature
Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...
www.nature.com
December 17, 2025 at 6:58 PM
Working on this paper fundamentally changed how I thought about bacterial evolution, and I couldn't ask for a better to Hannukah present than to see it out, at last!
Reposted by Sergey Kryazhimskiy
We gave Jay Bhattacharya an opportunity to clarify his vaccine stance: does he REALLY believe that the vaccine is worse than the disease? Instead, he launched into a defense of MAHA as the future of scientific inquiry, and never really gave us a straight answer...
@repauchincloss.bsky.social
@repauchincloss.bsky.social
December 16, 2025 at 2:55 PM
We gave Jay Bhattacharya an opportunity to clarify his vaccine stance: does he REALLY believe that the vaccine is worse than the disease? Instead, he launched into a defense of MAHA as the future of scientific inquiry, and never really gave us a straight answer...
@repauchincloss.bsky.social
@repauchincloss.bsky.social
Reposted by Sergey Kryazhimskiy
This is a disaster. I would not be where I am today without the constructive (and yes, sometimes frustrating) reviews my NSF proposals received as a young investigator. This feedback didn't come from the POs but rather the peer reviewers and panelists who saw how I was trying to enter the field
NSF now planning to let POs largely decide what gets funded, and to send PIs reviews that are only 3-5 sentences long. They don't have to use outside reviewers (except maybe 1) and don't have to convene panels. (1/5)
NSF pares down grant-review process, reducing influence of outside scientists
Memo cites overburdened staff, but some say move also aims to elevate White House priorities
www.science.org
December 16, 2025 at 2:12 AM
This is a disaster. I would not be where I am today without the constructive (and yes, sometimes frustrating) reviews my NSF proposals received as a young investigator. This feedback didn't come from the POs but rather the peer reviewers and panelists who saw how I was trying to enter the field
This is just bad...
NSF now planning to let POs largely decide what gets funded, and to send PIs reviews that are only 3-5 sentences long. They don't have to use outside reviewers (except maybe 1) and don't have to convene panels. (1/5)
NSF pares down grant-review process, reducing influence of outside scientists
Memo cites overburdened staff, but some say move also aims to elevate White House priorities
www.science.org
December 16, 2025 at 6:04 AM
This is just bad...
Reposted by Sergey Kryazhimskiy
I’m so speechless at this meaningless cruelty and disrespect for the best of our citizens who often had to QUIT TENURED JOBS to serve our country instead. Way to make us great again I guess 🤬
NSF
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
- Forced reorg
- POs down ~ 40% (DRP, most rotators not renewed, retirements)
- Forced move (and we have to pack and clean) to a building with no furniture, little to no conference space for panels, inadequate 🛜, …)
I personally love the boxes they gave us for packing.
“Details matter” 🙃
December 11, 2025 at 3:10 PM
I’m so speechless at this meaningless cruelty and disrespect for the best of our citizens who often had to QUIT TENURED JOBS to serve our country instead. Way to make us great again I guess 🤬
Reposted by Sergey Kryazhimskiy
1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
The fitness costs of reproductive specialization scale inversely with organismal size
The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a populatio...
www.biorxiv.org
December 9, 2025 at 7:44 PM
1/28 New preprint up, which I think is the best theoretical idea I've ever had. We asked a simple question: what are the costs of investment into non-reproductive somatic cells? Turns out these costs decrease with the *logarithm* of organism size!
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Sergey Kryazhimskiy
"Prebunking works by exposing people to the techniques used to create misleading arguments before they encounter them in the wild."
Finland has emerged as a global leader in countering “fake news”. Here's how they've done it
Teaching when to trust
As fake news accelerates, we need to teach our children how to think critically. Finnish schools are leading the charge
newhumanist.org.uk
December 7, 2025 at 5:56 PM
"Prebunking works by exposing people to the techniques used to create misleading arguments before they encounter them in the wild."
Reposted by Sergey Kryazhimskiy
Excited to co-organize with @weieli.bsky.social a symposium at SMBE 2026 on how synthetic & systems biology can illuminate the molecular mechanisms of evolution. Honored to have @christianlandry.bsky.social as invited speaker! Join us!
SMBE2026 Symposium 6 | Synthetic and systems biology approaches to dissecting the molecular mechanisms of evolution
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
📨 Abstract submission
smbe2026.org/abstracts
📋 Programme details
smbe2026.org/programme
#SMBE2026
December 5, 2025 at 11:16 PM
Excited to co-organize with @weieli.bsky.social a symposium at SMBE 2026 on how synthetic & systems biology can illuminate the molecular mechanisms of evolution. Honored to have @christianlandry.bsky.social as invited speaker! Join us!
Reposted by Sergey Kryazhimskiy
22% fewer NIH grants
December 2, 2025 at 3:28 PM
22% fewer NIH grants
Reposted by Sergey Kryazhimskiy
Even a decade ago I'd have far sooner predicted that the US would succumb to authoritarian rule than that it would become a state where vaccines were unavailable.
But if we don't throw RFK Jr. out on his ass, we're headed there fast.
But if we don't throw RFK Jr. out on his ass, we're headed there fast.
RFK Jr. is overhauling the program that helps preserve Americans' access to vaccines
A Kennedy adviser said he wants to preserve the Vaccine Injury Compensation Program. The health secretary's anti-vaccine allies prefer it collapse.
www.politico.com
November 30, 2025 at 4:04 AM
Even a decade ago I'd have far sooner predicted that the US would succumb to authoritarian rule than that it would become a state where vaccines were unavailable.
But if we don't throw RFK Jr. out on his ass, we're headed there fast.
But if we don't throw RFK Jr. out on his ass, we're headed there fast.
Reposted by Sergey Kryazhimskiy
The newly discovered archaean 𝘚𝘶𝘬𝘶𝘯𝘢𝘢𝘳𝘤𝘩𝘢𝘦𝘶𝘮 𝘮𝘪𝘳𝘢𝘣𝘪𝘭𝘦 has a genome with 238,000 base pairs, far fewer than humans (billions) or 𝘌. 𝘤𝘰𝘭𝘪 (millions). The species was named after Sukuna-biko-na, a Shinto deity known for being tiny.
A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine
The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.
www.quantamagazine.org
November 29, 2025 at 9:04 PM
The newly discovered archaean 𝘚𝘶𝘬𝘶𝘯𝘢𝘢𝘳𝘤𝘩𝘢𝘦𝘶𝘮 𝘮𝘪𝘳𝘢𝘣𝘪𝘭𝘦 has a genome with 238,000 base pairs, far fewer than humans (billions) or 𝘌. 𝘤𝘰𝘭𝘪 (millions). The species was named after Sukuna-biko-na, a Shinto deity known for being tiny.
Reposted by Sergey Kryazhimskiy
Every year #ESEB distinguishes a young evolutionary biologist with the John Maynard Smith Prize! Nominations for the 2026 prize are due by January 15th!
Find out more here: eseb.org/prizes-fundi...
Find out more here: eseb.org/prizes-fundi...
November 11, 2025 at 10:50 AM
Every year #ESEB distinguishes a young evolutionary biologist with the John Maynard Smith Prize! Nominations for the 2026 prize are due by January 15th!
Find out more here: eseb.org/prizes-fundi...
Find out more here: eseb.org/prizes-fundi...
Reposted by Sergey Kryazhimskiy
15-year-old bug 😐 in an industry that has the highest profit margins possible pretty much
www.theguardian.com/science/2017...
www.theguardian.com/science/2017...
November 23, 2025 at 3:45 PM
15-year-old bug 😐 in an industry that has the highest profit margins possible pretty much
www.theguardian.com/science/2017...
www.theguardian.com/science/2017...
Reposted by Sergey Kryazhimskiy
Absolutely. Even if he weren't a damaged creep, his approach to scientific evidence is completely disqualifying.
We know the answer; We just don't have the science yet
There is no study that says that it is not true.
Bye, bye Bobby. You've "gone wild" enough. You going to kill lots of people.
We know the answer; We just don't have the science yet
There is no study that says that it is not true.
Bye, bye Bobby. You've "gone wild" enough. You going to kill lots of people.
November 21, 2025 at 3:10 PM
Absolutely. Even if he weren't a damaged creep, his approach to scientific evidence is completely disqualifying.
We know the answer; We just don't have the science yet
There is no study that says that it is not true.
Bye, bye Bobby. You've "gone wild" enough. You going to kill lots of people.
We know the answer; We just don't have the science yet
There is no study that says that it is not true.
Bye, bye Bobby. You've "gone wild" enough. You going to kill lots of people.
Reposted by Sergey Kryazhimskiy
Epic paper!!
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:56 PM
Epic paper!!
Reposted by Sergey Kryazhimskiy
It's been a busy few months for our group so wanted to highlight a few other recent preprints we’ve posted that I haven’t had the chance to share yet... (1/n)
Excited to share some new work led by grad student Sophie Walton (w/ @petrovadmitri.bsky.social). We used in vitro gut communities to study how natural selection acts on strains of the same species as they compete within larger communities. Check out Sophie's thread below for details!
Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 16, 2025 at 3:26 PM
It's been a busy few months for our group so wanted to highlight a few other recent preprints we’ve posted that I haven’t had the chance to share yet... (1/n)
Reposted by Sergey Kryazhimskiy
Trump’s HHS put me on “non-disciplinary” admin leave today. This was retaliation for speaking up. Moves like this are designed to silence us. Let’s not let.
www.tiktok.com/t/ZP8Dteoop/
www.tiktok.com/t/ZP8Dteoop/
I guess I am hitting a nerve, because they just put me on admin leave.
TikTok video by Jenna
www.tiktok.com
November 13, 2025 at 11:18 PM
Trump’s HHS put me on “non-disciplinary” admin leave today. This was retaliation for speaking up. Moves like this are designed to silence us. Let’s not let.
www.tiktok.com/t/ZP8Dteoop/
www.tiktok.com/t/ZP8Dteoop/
Reposted by Sergey Kryazhimskiy
PSA for people with NIH grant periods starting January 1st (including most NIGMS MIRAs): your RPPR is due Saturday, but they haven’t sent out the usual automated reminders, presumably due to the shutdown
November 11, 2025 at 1:20 AM
PSA for people with NIH grant periods starting January 1st (including most NIGMS MIRAs): your RPPR is due Saturday, but they haven’t sent out the usual automated reminders, presumably due to the shutdown
Reposted by Sergey Kryazhimskiy
Up to 323 cancelled CSR study sections. That's more than the 204 sections cancelled earlier this year. Rescheduling is going to be a hot mess with NIH staff reductions and study section members heading into finals and holidays that limit availability. 🧪
Been a rough year for federally funded scientists, and I hate to add another tab to this spreadsheet. So far, the shutdown has resulted in cancellation of 161 CSR study sections. 🧪https://docs.google.com/spreadsheets/d/1lLEx14q7HKrlYahQYJaN6aHKpMqSMJwX4aenyL5g_ZU/edit?usp=sharing
2025 Study section tracking
docs.google.com
November 11, 2025 at 9:44 PM
Up to 323 cancelled CSR study sections. That's more than the 204 sections cancelled earlier this year. Rescheduling is going to be a hot mess with NIH staff reductions and study section members heading into finals and holidays that limit availability. 🧪