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
wow... crawling motility in Asgard #archaea!! www.biorxiv.org/content/10.1...
look at these crazy moves!! Let's face it, what these cells want for Christmas is #cilia... the best type of motility appendage...
look at these crazy moves!! Let's face it, what these cells want for Christmas is #cilia... the best type of motility appendage...
December 2, 2025 at 10:30 PM
wow... crawling motility in Asgard #archaea!! www.biorxiv.org/content/10.1...
look at these crazy moves!! Let's face it, what these cells want for Christmas is #cilia... the best type of motility appendage...
look at these crazy moves!! Let's face it, what these cells want for Christmas is #cilia... the best type of motility appendage...
Reposted by Alex Crits-Christoph
CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!
Nanoscale imaging of native symbiotic animal tissue using amultimodal large volume imaging pipeline for cryo-electrontomography https://www.biorxiv.org/content/10.1101/2025.11.30.691379v1
December 1, 2025 at 4:35 AM
CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!
Reposted by Alex Crits-Christoph
The grievance blog masquerading as a "journal" founded by Trump HHS appointees (The "Journal" of the "Academy" of Public Health) is now publishing lengthy screeds about how HHS secretary RFK Jr is being treated unfairly by the BMJ and calling it a literature synthesis...
December 2, 2025 at 4:21 PM
The grievance blog masquerading as a "journal" founded by Trump HHS appointees (The "Journal" of the "Academy" of Public Health) is now publishing lengthy screeds about how HHS secretary RFK Jr is being treated unfairly by the BMJ and calling it a literature synthesis...
"There were car gods there: a powerful, serious-faced contingent, with blood on their black gloves and on their chrome teeth: recipients of human sacrifice on a scale undreamed-of since the Aztecs."
Ending road deaths will be one of the greatest public health wins.
www.nytimes.com/2025/12/02/o...
Ending road deaths will be one of the greatest public health wins.
www.nytimes.com/2025/12/02/o...
Opinion | The Data on Self-Driving Cars Is Clear. We Have to Change Course.
www.nytimes.com
December 2, 2025 at 5:05 PM
"There were car gods there: a powerful, serious-faced contingent, with blood on their black gloves and on their chrome teeth: recipients of human sacrifice on a scale undreamed-of since the Aztecs."
Ending road deaths will be one of the greatest public health wins.
www.nytimes.com/2025/12/02/o...
Ending road deaths will be one of the greatest public health wins.
www.nytimes.com/2025/12/02/o...
Reposted by Alex Crits-Christoph
While the administration has said it is cutting “woke programs” that “poison the minds of Americans", it actually funded fewer grants in every area of science and medicine.
“They brought everything to a stop,” said Sarah Kobrin, a branch chief at the N.I.H.’s National Cancer Institute
“They brought everything to a stop,” said Sarah Kobrin, a branch chief at the N.I.H.’s National Cancer Institute
The U.S. Is Funding Fewer Grants in Every Area of Science and Medicine (Gift Article)
A quiet policy change means the government is making fewer bets on long-term science.
www.nytimes.com
December 2, 2025 at 2:31 PM
While the administration has said it is cutting “woke programs” that “poison the minds of Americans", it actually funded fewer grants in every area of science and medicine.
“They brought everything to a stop,” said Sarah Kobrin, a branch chief at the N.I.H.’s National Cancer Institute
“They brought everything to a stop,” said Sarah Kobrin, a branch chief at the N.I.H.’s National Cancer Institute
Reposted by Alex Crits-Christoph
Thanks nature news for featuring our recent preprint on 𝘐𝘯𝘤𝘦𝘯𝘥𝘪𝘢𝘮𝘰𝘦𝘣𝘢 led by @hbrappap.bsky.social
(check out preprint here: doi.org/10.1101/2025...) #protistsonsky
(check out preprint here: doi.org/10.1101/2025...) #protistsonsky
This single-celled amoeba can thrive at temperatures that kill all other known eukaryotic life
go.nature.com/4452LXP
go.nature.com/4452LXP
‘Fire amoeba’ survives in hotter conditions than any other complex cell
The single-celled organism can grow at 63 °C, a record for eukaryotic life.
go.nature.com
December 2, 2025 at 3:15 PM
Thanks nature news for featuring our recent preprint on 𝘐𝘯𝘤𝘦𝘯𝘥𝘪𝘢𝘮𝘰𝘦𝘣𝘢 led by @hbrappap.bsky.social
(check out preprint here: doi.org/10.1101/2025...) #protistsonsky
(check out preprint here: doi.org/10.1101/2025...) #protistsonsky
Reposted by Alex Crits-Christoph
How does a caterpillar completely dissolve inside its chrysalis, before reconstructing itself in the shape of a butterfly?
“Metamorphosis is wild,” marvels historian Oren Harman in his beautiful new book, which I reviewed for this week's @nature.com
www.nature.com/articles/d41...
“Metamorphosis is wild,” marvels historian Oren Harman in his beautiful new book, which I reviewed for this week's @nature.com
www.nature.com/articles/d41...
December 2, 2025 at 3:55 PM
How does a caterpillar completely dissolve inside its chrysalis, before reconstructing itself in the shape of a butterfly?
“Metamorphosis is wild,” marvels historian Oren Harman in his beautiful new book, which I reviewed for this week's @nature.com
www.nature.com/articles/d41...
“Metamorphosis is wild,” marvels historian Oren Harman in his beautiful new book, which I reviewed for this week's @nature.com
www.nature.com/articles/d41...
Reposted by Alex Crits-Christoph
pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences https://www.biorxiv.org/content/10.1101/2025.11.27.689987v1
December 1, 2025 at 10:46 PM
pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences https://www.biorxiv.org/content/10.1101/2025.11.27.689987v1
Reposted by Alex Crits-Christoph
The worst nightmare I have is not simply that it happens, but that everyone sees it happen, and the question is not simply whether it is unfair (we all agree), but whether I handled it right: should I have said less? Chosen words more carefully? Been more paranoid about who I was speaking to?
December 1, 2025 at 9:59 PM
The worst nightmare I have is not simply that it happens, but that everyone sees it happen, and the question is not simply whether it is unfair (we all agree), but whether I handled it right: should I have said less? Chosen words more carefully? Been more paranoid about who I was speaking to?
Reposted by Alex Crits-Christoph
Here's the most important piece of data (as far as I am concerned). Comparing Earth Microbiome to the new ones (V4EXT) for major phyla. V4EXT by @ppjevac.bsky.social et al cover more diversity than current gold standard😱 Lot's of work, the entire field will benefit! My lab's gonna try V4EXT soon!
November 29, 2025 at 1:41 AM
Here's the most important piece of data (as far as I am concerned). Comparing Earth Microbiome to the new ones (V4EXT) for major phyla. V4EXT by @ppjevac.bsky.social et al cover more diversity than current gold standard😱 Lot's of work, the entire field will benefit! My lab's gonna try V4EXT soon!
Reposted by Alex Crits-Christoph
And as a blast from that terrible past, the motivations are sadly often backed by interests that reward this behavior with power and money. I still think we have not done enough to train scientists to counter the doubt machine... www.nature.com/articles/d41...
Scientists: don’t feed the doubt machine
From climate to COVID, naivety about how science is hijacked promotes more of the same.
www.nature.com
November 30, 2025 at 5:50 PM
And as a blast from that terrible past, the motivations are sadly often backed by interests that reward this behavior with power and money. I still think we have not done enough to train scientists to counter the doubt machine... www.nature.com/articles/d41...
Reposted by Alex Crits-Christoph
Just pointing out how grim the funding situation is. If an institution fights you have no idea where future grants are coming from. Harvard won in court and is still telling researchers to cut everything 20% because they don’t know what happens next. Somehow everybody has to make it to Jan 2029
Yes I agree with this. The problem for grant-dependent researchers is that even if they win in court to get their illegally withheld funds, they’re sure to be denied any new grants by these corrupted agencies. 2026-2028 will be a killing field as institutions hemorrhage their research apparatus
November 29, 2025 at 1:51 PM
Just pointing out how grim the funding situation is. If an institution fights you have no idea where future grants are coming from. Harvard won in court and is still telling researchers to cut everything 20% because they don’t know what happens next. Somehow everybody has to make it to Jan 2029
Reposted by Alex Crits-Christoph
So apparently the administrators at Northwestern have caved to the extortionist demands of the Feds. Faculty voted 595-4 AGAINST this measure.
November 29, 2025 at 3:30 AM
So apparently the administrators at Northwestern have caved to the extortionist demands of the Feds. Faculty voted 595-4 AGAINST this measure.
Reposted by Alex Crits-Christoph
New preprint: 🚀🧬 Starship in the genome of the lichen fungus Xanthoria. Discovery of giant transposons Starships challenged what we thought we knew about fungal genomes. But what about Starships in #lichen fungi? Let us present Tangerine! 🖥️ 🧪 🦠 🧫 #SymbioSky doi.org/10.1101/2025...
November 28, 2025 at 2:20 PM
New preprint: 🚀🧬 Starship in the genome of the lichen fungus Xanthoria. Discovery of giant transposons Starships challenged what we thought we knew about fungal genomes. But what about Starships in #lichen fungi? Let us present Tangerine! 🖥️ 🧪 🦠 🧫 #SymbioSky doi.org/10.1101/2025...
Reposted by Alex Crits-Christoph
Out after peer-review: www.science.org/doi/full/10....
Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead!
We now also account for regression and nested cross-validation, with more extensive benchmarking.
Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead!
We now also account for regression and nested cross-validation, with more extensive benchmarking.
November 28, 2025 at 7:32 PM
Out after peer-review: www.science.org/doi/full/10....
Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead!
We now also account for regression and nested cross-validation, with more extensive benchmarking.
Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead!
We now also account for regression and nested cross-validation, with more extensive benchmarking.
Reposted by Alex Crits-Christoph
Authoritarians typically neither like science nor scientists
We are seeing this everywhere
So, fighting for science is also fighting for democracy
www.thelancet.com/journals/lan...
We are seeing this everywhere
So, fighting for science is also fighting for democracy
www.thelancet.com/journals/lan...
From doing science to saving science
Science and scientists are under assault. From denial of vaccines to climate change,
political leaders are increasingly sacrificing democracy as well as science on the
altar of populism and authoritar...
www.thelancet.com
November 28, 2025 at 7:23 PM
Authoritarians typically neither like science nor scientists
We are seeing this everywhere
So, fighting for science is also fighting for democracy
www.thelancet.com/journals/lan...
We are seeing this everywhere
So, fighting for science is also fighting for democracy
www.thelancet.com/journals/lan...
Reposted by Alex Crits-Christoph
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology
Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.
www.nature.com
November 28, 2025 at 4:43 PM
Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...
Reposted by Alex Crits-Christoph
Hard choices for preprint servers.
bioRxiv has always declined reviews/hypotheses b/c of concern about signal:noise and a wish to avoid subjective judgments. AI slop makes screening certain content similarly challenging so other servers are adopting new restrictions. Two thoughts... 1/3
bioRxiv has always declined reviews/hypotheses b/c of concern about signal:noise and a wish to avoid subjective judgments. AI slop makes screening certain content similarly challenging so other servers are adopting new restrictions. Two thoughts... 1/3
In light of record submission rates and a large volume of AI-generated slop, SocArXiv recently implemented a policy requiring ORCIDs linked in the OSF profile of submitting authors, and narrowing our focus to social science subjects. Today we are taking two more steps:
/1
/1
November 27, 2025 at 5:46 PM
Hard choices for preprint servers.
bioRxiv has always declined reviews/hypotheses b/c of concern about signal:noise and a wish to avoid subjective judgments. AI slop makes screening certain content similarly challenging so other servers are adopting new restrictions. Two thoughts... 1/3
bioRxiv has always declined reviews/hypotheses b/c of concern about signal:noise and a wish to avoid subjective judgments. AI slop makes screening certain content similarly challenging so other servers are adopting new restrictions. Two thoughts... 1/3
Reposted by Alex Crits-Christoph
Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
BarTn7: Optimizing Bacterial Lineage Tracking at Sub-Species Resolution for Population Dynamics in Ecological and Evolutionary Studies
Communities of bacteria undergo population bottlenecks which are crucial to their population, ecological, and evolutionary dynamics. However, conventional amplicon sequencing cannot distinguish such d...
www.biorxiv.org
November 25, 2025 at 10:38 PM
Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Alex Crits-Christoph
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:55 PM
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
This is a pretty useful page en.wikipedia.org/wiki/Wikiped...
Wikipedia:Signs of AI writing - Wikipedia
en.wikipedia.org
November 26, 2025 at 10:13 PM
This is a pretty useful page en.wikipedia.org/wiki/Wikiped...
Reposted by Alex Crits-Christoph
In a pretty stark contrast, @melodyschreiber.com understands the truth: the pundit class helped make the moment, and truly cares for nothing (including public health). The elites are the ones behind the steering wheel. Health workers are picking up the pieces newrepublic.com/article/2035...
Olivia Nuzzi’s Real Victims
More than her fiancé, or fellow female journalists, the public will pay the price for these misdeeds. RFK Jr. will see to that.
newrepublic.com
November 26, 2025 at 3:01 AM
In a pretty stark contrast, @melodyschreiber.com understands the truth: the pundit class helped make the moment, and truly cares for nothing (including public health). The elites are the ones behind the steering wheel. Health workers are picking up the pieces newrepublic.com/article/2035...
Reposted by Alex Crits-Christoph
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
November 25, 2025 at 8:41 PM
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
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: 👇