Alex Crits-Christoph
@acritschristoph.bsky.social
Computational microbiologist
I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy
I like to post about: microbial genomics, microbial ecology, evolution, micro+plant biotechnology, climate, symbiosis, virology, ag, sci publishing and policy
Reposted by Alex Crits-Christoph
Our paper is out! Analysis of 30K+ genomes revealed that CPR bacteria assemble their ribosomes in unconventional ways, and that these assembly processes appear to have co-evolved with ribosome structure. doi.org/10.1093/molb... #Ribosome #Evolution #Patescibacteria #MBE
November 24, 2025 at 1:15 PM
Our paper is out! Analysis of 30K+ genomes revealed that CPR bacteria assemble their ribosomes in unconventional ways, and that these assembly processes appear to have co-evolved with ribosome structure. doi.org/10.1093/molb... #Ribosome #Evolution #Patescibacteria #MBE
Reposted by Alex Crits-Christoph
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking
Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...
journals.plos.org
November 21, 2025 at 7:31 PM
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Reposted by Alex Crits-Christoph
Are influenza B viruses really “human only”? New review synthesises evidence from serology & metagenomics for #IBV / IBV-like viruses in animals and aquatic hosts. One Health gaps remain. With @marioskoutsakos.viralvaxlab.com @duckswabber.bsky.social www.mdpi.com/1999-4915/17...
November 25, 2025 at 4:46 AM
Are influenza B viruses really “human only”? New review synthesises evidence from serology & metagenomics for #IBV / IBV-like viruses in animals and aquatic hosts. One Health gaps remain. With @marioskoutsakos.viralvaxlab.com @duckswabber.bsky.social www.mdpi.com/1999-4915/17...
Reposted by Alex Crits-Christoph
Oh hey congratulations @oliverio.bsky.social @rmshepherd.bsky.social @hbrappap.bsky.social on the awesome thermophilic amoeba story!
A geothermal amoeba sets a new upper temperature limit for eukaryotes https://www.biorxiv.org/content/10.1101/2025.11.24.690213v1
November 25, 2025 at 3:25 AM
Oh hey congratulations @oliverio.bsky.social @rmshepherd.bsky.social @hbrappap.bsky.social on the awesome thermophilic amoeba story!
Reposted by Alex Crits-Christoph
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
press.asimov.com
November 24, 2025 at 5:00 PM
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Reposted by Alex Crits-Christoph
Some fantastic sessions being planned for ASM Microbe 2026, including "Long-term Dynamics of Environmental Microbiomes", and "Eco-evolutionary Dynamics of Phages and Their Roles in Horizontal Gene Transfer". Get your abstract(s) ready, and join us June 4–7, 2026 in D.C. ! asm.org/events/asm-m...
November 24, 2025 at 8:13 PM
Some fantastic sessions being planned for ASM Microbe 2026, including "Long-term Dynamics of Environmental Microbiomes", and "Eco-evolutionary Dynamics of Phages and Their Roles in Horizontal Gene Transfer". Get your abstract(s) ready, and join us June 4–7, 2026 in D.C. ! asm.org/events/asm-m...
Reposted by Alex Crits-Christoph
How did AI-generated videos contribute to false narratives about SNAP recipients during the government shutdown, lending credibility to stereotypes about beneficiaries of government assistance?
This and more in this week’s edition of The Monitor: https://on.kff.org/3LTFUbv
This and more in this week’s edition of The Monitor: https://on.kff.org/3LTFUbv
Health Information and Trust: The Monitor
This volume examines how AI-generated videos contributed to false narratives about SNAP recipients; findings from KFF’s Health Tracking Poll on beliefs about undocumented immigrants’ ACA eligibility; ...
on.kff.org
November 24, 2025 at 9:20 PM
How did AI-generated videos contribute to false narratives about SNAP recipients during the government shutdown, lending credibility to stereotypes about beneficiaries of government assistance?
This and more in this week’s edition of The Monitor: https://on.kff.org/3LTFUbv
This and more in this week’s edition of The Monitor: https://on.kff.org/3LTFUbv
"These may feel like grim times. Perhaps you feel powerless, even paralyzed. But we’re not at all helpless. Each of us has almost miraculous powers to save or transform lives"
These are the nonprofits in my holiday giving guide this year, sharing a $1.15m prize:
@MutualAidSudan tackles famine in Sudan.
@HelenKellerIntl prevents terrible diseases for 75 cents per child.
@VisionToLearn gets glasses to US kids so they can read.
Join in: www.nytimes.com/2025/11/22/o...
@MutualAidSudan tackles famine in Sudan.
@HelenKellerIntl prevents terrible diseases for 75 cents per child.
@VisionToLearn gets glasses to US kids so they can read.
Join in: www.nytimes.com/2025/11/22/o...
November 24, 2025 at 4:52 AM
"These may feel like grim times. Perhaps you feel powerless, even paralyzed. But we’re not at all helpless. Each of us has almost miraculous powers to save or transform lives"
Reposted by Alex Crits-Christoph
My best Holiday Giving Guide yet, highlighting three superb nonprofits saving and transforming lives abroad and at home. And because of matches from @bloombergdotorg.bsky.social & others, each $1 from you means $4 reaches the nonprofits. Join in! Spread the word. www.nytimes.com/2025/11/22/o...
Opinion | Gifts That Save Lives
www.nytimes.com
November 22, 2025 at 1:25 PM
My best Holiday Giving Guide yet, highlighting three superb nonprofits saving and transforming lives abroad and at home. And because of matches from @bloombergdotorg.bsky.social & others, each $1 from you means $4 reaches the nonprofits. Join in! Spread the word. www.nytimes.com/2025/11/22/o...
Reposted by Alex Crits-Christoph
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 23, 2025 at 7:22 PM
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
Have a look if you are interested in how the team at @cultivarium.bsky.social is finding electroporation protocols for new microbes: both screening lots of conditions on a custom built electroporator concurrently, and cyclical iteration using bayesian optimization
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Active learning guides automated discovery of DNA delivery via electroporation for non-model microbes
Delivery of recombinant DNA is foundational for understanding and engineering a target organism. Electroporation can be applied to any cell type, yet identification of a working protocol for new organ...
www.biorxiv.org
November 22, 2025 at 12:23 AM
Have a look if you are interested in how the team at @cultivarium.bsky.social is finding electroporation protocols for new microbes: both screening lots of conditions on a custom built electroporator concurrently, and cyclical iteration using bayesian optimization
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Crits-Christoph
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 21, 2025 at 10:34 PM
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
Reposted by Alex Crits-Christoph
Reading from AI summaries (via LLMs) rather than doing your own minimal reading impairs learning and produces shallower knowledge.
"...learning from LLM syntheses (vs. web links) can, at times, limit the development of deeper, more original knowledge."
🧪
academic.oup.com/pnasnexus/ar...
"...learning from LLM syntheses (vs. web links) can, at times, limit the development of deeper, more original knowledge."
🧪
academic.oup.com/pnasnexus/ar...
Experimental evidence of the effects of large language models versus web search on depth of learning
Abstract. The effects of using large language models (LLMs) versus traditional web search on depth of learning are explored. A theory is proposed that when
academic.oup.com
November 17, 2025 at 11:55 PM
Reading from AI summaries (via LLMs) rather than doing your own minimal reading impairs learning and produces shallower knowledge.
"...learning from LLM syntheses (vs. web links) can, at times, limit the development of deeper, more original knowledge."
🧪
academic.oup.com/pnasnexus/ar...
"...learning from LLM syntheses (vs. web links) can, at times, limit the development of deeper, more original knowledge."
🧪
academic.oup.com/pnasnexus/ar...
Reposted by Alex Crits-Christoph
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:17 PM
Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!
Reposted by Alex Crits-Christoph
"Climate shock." New study shows that rising property insurance premiums caused by growing weather extremes are cascading into the real estate market. Homes in the ZIP codes most exposed to hurricanes and wildfires would sell for an average of $43,900 less than they would otherwise.
November 20, 2025 at 11:12 PM
"Climate shock." New study shows that rising property insurance premiums caused by growing weather extremes are cascading into the real estate market. Homes in the ZIP codes most exposed to hurricanes and wildfires would sell for an average of $43,900 less than they would otherwise.
Reposted by Alex Crits-Christoph
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
November 20, 2025 at 6:52 PM
🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)
Reposted by Alex Crits-Christoph
Reposted by Alex Crits-Christoph
Is it a flagellate? A tiny ball with tentacles? Contamination in my ciliate culture? NEW SUPERGROUP OF EUKARYOTES? Yes to all 4! Meet Solarion - just out in #Nature doi.org/10.1038/s415... Huge congrats to Marek Valt, Cepicka Lab & the star team! Very happy to be part of this project. #ProtistsOnSky
November 19, 2025 at 9:39 PM
Is it a flagellate? A tiny ball with tentacles? Contamination in my ciliate culture? NEW SUPERGROUP OF EUKARYOTES? Yes to all 4! Meet Solarion - just out in #Nature doi.org/10.1038/s415... Huge congrats to Marek Valt, Cepicka Lab & the star team! Very happy to be part of this project. #ProtistsOnSky
Reposted by Alex Crits-Christoph
JAMA study: NIH grant terminations disrupted 3.5% of active clinical trials, affecting over 74,000 patients and resulting in a $1.81 billion funding loss. More than 115 active cancer trials were disrupted. www.ajmc.com/view/nih-gra...
NIH Grant Terminations Disrupt 1 in 30 Clinical Trials, Impacting Over 74,000 Participants | AJMC
Infectious disease was hit hardest by funding cuts to NIH grant for clinical trials that did not align with the Trump administration's priorities.
www.ajmc.com
November 19, 2025 at 8:31 PM
JAMA study: NIH grant terminations disrupted 3.5% of active clinical trials, affecting over 74,000 patients and resulting in a $1.81 billion funding loss. More than 115 active cancer trials were disrupted. www.ajmc.com/view/nih-gra...
Reposted by Alex Crits-Christoph
Trump Moves to Weaken the Endangered Species Act
Trump Moves to Weaken the Endangered Species Act
Four proposed rules could make it easier to drill for oil or harvest timber in areas where endangered species live.
www.nytimes.com
November 19, 2025 at 9:16 PM
Trump Moves to Weaken the Endangered Species Act
Reposted by Alex Crits-Christoph
What if we could autocomplete DNA based on function?
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
November 19, 2025 at 4:31 PM
What if we could autocomplete DNA based on function?
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
Today in @Nature, we share semantic design—a strategy for function-guided design with genomic language models that leverages genomic context to create de novo genes and systems with desired functions. 🧵
www.nature.com/articles/s41...
This part is actually pretty cool. Prompting the DNA LLM with an adjacent gene.
They next evaluated whether the approach extended to anti-CRISPR systems.
Evo was able to produce novel proteins that inhibited SpCas9 and improved phage survival, demonstrating its ability to propose functional products in systems where sequence-based approaches often fail.
Evo was able to produce novel proteins that inhibited SpCas9 and improved phage survival, demonstrating its ability to propose functional products in systems where sequence-based approaches often fail.
November 19, 2025 at 7:31 PM
This part is actually pretty cool. Prompting the DNA LLM with an adjacent gene.
Reposted by Alex Crits-Christoph
The bigger change is presentation, historically, these emails were visually chaotic: sudden colour changes, ALL CAPS, screenshots pasted at random. Classic signs of disordered thinking. Now they’re neat, structured, and grammatically consistent. The delusion hasn't changed, but the formatting has.
November 19, 2025 at 2:19 PM
The bigger change is presentation, historically, these emails were visually chaotic: sudden colour changes, ALL CAPS, screenshots pasted at random. Classic signs of disordered thinking. Now they’re neat, structured, and grammatically consistent. The delusion hasn't changed, but the formatting has.
Reposted by Alex Crits-Christoph
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
PhyloWeaver – Interactive phylogenetic tree editor
Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.
yawak.jp
November 18, 2025 at 1:59 AM
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.