Ben Adler
@benadler.bsky.social
Postdoc @ Doudna Lab - UC-Berkeley | Bacteriophage engineering | CRISPR | Biotechnology | Microbiology | All Combinations Thereof | He/him. Opinions my own.
Reposted by Ben Adler
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
doi.org
November 7, 2025 at 4:36 PM
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Reposted by Ben Adler
Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇
November 6, 2025 at 10:39 AM
Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇
tinyurl.com/ch3damp
We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity
Revealed by the amazing Ilya Osterman. See his thread below👇
Reposted by Ben Adler
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted by Ben Adler
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology
An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.
www.nature.com
November 6, 2025 at 1:49 PM
After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...
Reposted by Ben Adler
"We need more institutional experiments for science" makes sense to me @seemaychou.bsky.social. We might not like some of 'em and some'll fail, but given academic science often looks like a feudal system needing an industrial revolution trying things can't hurt.. seemay.substack.com/p/big-experi...
Big experiments are only big if they can fail
Some reflections on Arena Bioworks' unexpected wind down as a fellow institutional experimentalist
seemay.substack.com
November 6, 2025 at 7:08 PM
"We need more institutional experiments for science" makes sense to me @seemaychou.bsky.social. We might not like some of 'em and some'll fail, but given academic science often looks like a feudal system needing an industrial revolution trying things can't hurt.. seemay.substack.com/p/big-experi...
Reposted by Ben Adler
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Ben Adler
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
Wilkinson Lab
We discover and study reverse transcriptases
wilkinsonlab.bio
October 31, 2025 at 7:00 PM
The Wilkinson Lab is open for science! @mskcancercenter.bsky.social
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
🧬We'll be finding funky new RNA biology, mainly by looking at reverse transcriptases (i.e. the Best Enzymes In The World)🧬
annnd: I'm hiring - come join! Especially postdocs and PhD students - please get in touch (NYC is great)
Reposted by Ben Adler
From @plos.org #Computational #Biology | Ten rules for a structural bioinformatic analysis | i like Recommendation #10: Visualize everything! | #Bioinformatics #Education #Recommendations #NotSimpleRules 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Ten rules for a structural bioinformatic analysis
Author summary Here, we provide a roadmap for users to leverage the Protein Data Bank’s vast collection of protein structural models into reliable and valuable insights. It lays out 10 clear rules tha...
journals.plos.org
November 1, 2025 at 12:44 PM
From @plos.org #Computational #Biology | Ten rules for a structural bioinformatic analysis | i like Recommendation #10: Visualize everything! | #Bioinformatics #Education #Recommendations #NotSimpleRules 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
⬇️
journals.plos.org/ploscompbiol...
⬇️
journals.plos.org/ploscompbiol...
Reposted by Ben Adler
The Python Software Foundation won a $1.5m grant from the US government National Science Foundation.
Turned it down because required to affirm that we "will not... operate any programs that advance or promote DEI"
simonwillison.net/2025/Oct/27/...
Turned it down because required to affirm that we "will not... operate any programs that advance or promote DEI"
simonwillison.net/2025/Oct/27/...
The PSF has withdrawn a $1.5 million proposal to US government grant program
The Python Software Foundation was recently "recommended for funding" (NSF terminology) for a $1.5m grant from the US government National Science Foundation to help improve the security of the Python ...
simonwillison.net
October 29, 2025 at 7:21 PM
The Python Software Foundation won a $1.5m grant from the US government National Science Foundation.
Turned it down because required to affirm that we "will not... operate any programs that advance or promote DEI"
simonwillison.net/2025/Oct/27/...
Turned it down because required to affirm that we "will not... operate any programs that advance or promote DEI"
simonwillison.net/2025/Oct/27/...
Reposted by Ben Adler
Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology
Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases
Bacteria are frequently attacked by viruses, known as phages, and rely on diverse defence systems like restriction endonucleases and CRISPR-Cas to survive. While phages can evade these defences by cov...
doi.org
October 30, 2025 at 12:16 PM
Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology
Reposted by Ben Adler
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Ben Adler
Excited to share some new work from the lab, led by @shelbyeandersen.bsky.social where we developed a method and computational pipeline to identify antiphage defenses across diverse bacterial phyla.
Serine recombinases are conserved genetic markers of antiphage defense systems https://www.biorxiv.org/content/10.1101/2025.10.07.681051v1
October 20, 2025 at 5:49 PM
Excited to share some new work from the lab, led by @shelbyeandersen.bsky.social where we developed a method and computational pipeline to identify antiphage defenses across diverse bacterial phyla.
Reposted by Ben Adler
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
www.biorxiv.org
October 17, 2025 at 5:22 PM
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from?
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria.
www.biorxiv.org/content/10.1...
Reposted by Ben Adler
US Academia Be Like
October 16, 2025 at 6:38 PM
US Academia Be Like
Reposted by Ben Adler
The latest preprint from the lab is out!
Here we used structural clustering and immunoprecipitations to uncover some networks in our knowledge of giant virons proteomes. An interesting story by Hela Safi and @ambsch.bsky.social.
www.biorxiv.org/content/10.1...
Here we used structural clustering and immunoprecipitations to uncover some networks in our knowledge of giant virons proteomes. An interesting story by Hela Safi and @ambsch.bsky.social.
www.biorxiv.org/content/10.1...
Elucidating the interaction network of one of the largest icosahedral capsids in the virosphere
Giant viruses challenge traditional boundaries of virology with their large particle sizes, complex genomes, and unique replication strategies. Yet, despite its 750 nm diameter and incorporation of do...
www.biorxiv.org
October 15, 2025 at 5:19 AM
The latest preprint from the lab is out!
Here we used structural clustering and immunoprecipitations to uncover some networks in our knowledge of giant virons proteomes. An interesting story by Hela Safi and @ambsch.bsky.social.
www.biorxiv.org/content/10.1...
Here we used structural clustering and immunoprecipitations to uncover some networks in our knowledge of giant virons proteomes. An interesting story by Hela Safi and @ambsch.bsky.social.
www.biorxiv.org/content/10.1...
Reposted by Ben Adler
Panoptes guards the CBASS pathway (bacterial cGAS-STING). One facet of this work that I find particularly exciting is the genetic linkage between Panoptes and CBASS, which significantly co-occur in bacterial genomes. What other phage defense systems may be genetically (and functionally) linked?
October 8, 2025 at 11:14 AM
Panoptes guards the CBASS pathway (bacterial cGAS-STING). One facet of this work that I find particularly exciting is the genetic linkage between Panoptes and CBASS, which significantly co-occur in bacterial genomes. What other phage defense systems may be genetically (and functionally) linked?
Reposted by Ben Adler
Our work on the Panoptes antiphage system is published! Here we find that Panoptes "watches" the cytosol for phage immune evasion proteins–captured in this illustration by Clair Huffine of Insight Illustrations. A beautiful example of the effector triggered immunity paradigm.
October 8, 2025 at 11:14 AM
Our work on the Panoptes antiphage system is published! Here we find that Panoptes "watches" the cytosol for phage immune evasion proteins–captured in this illustration by Clair Huffine of Insight Illustrations. A beautiful example of the effector triggered immunity paradigm.
Reposted by Ben Adler
Check out the complementary story from @doudna-lab.bsky.social led by @erinedoherty.bsky.social and @benadler.bsky.social Their work on OptE oligomerization is particularly crucial to completing our understanding of Panoptes. www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 8, 2025 at 11:14 AM
Check out the complementary story from @doudna-lab.bsky.social led by @erinedoherty.bsky.social and @benadler.bsky.social Their work on OptE oligomerization is particularly crucial to completing our understanding of Panoptes. www.nature.com/articles/s41...
This is how the Craspedochiton zefranki do.
I'm excited to report that a species has been named after my son Ze Frank, "in recognition of his outstanding contributions to science communication, which have inspired curiosity, wonder, and deeper public engagement with the natural world"
October 7, 2025 at 8:24 PM
This is how the Craspedochiton zefranki do.
Reposted by Ben Adler
New preprint!
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages
Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...
www.biorxiv.org
October 6, 2025 at 6:27 AM
New preprint!
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠
Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!
An epic effort by Rosanna Wright
www.biorxiv.org/content/10.1...
Reposted by Ben Adler
Job alert ‼️ UChicago Micro is hiring! Open to tenured/tenure track faculty at all levels in any area of microbiology. Come join our amazing and growing department. apply.interfolio.com/174404
October 4, 2025 at 6:44 PM
Job alert ‼️ UChicago Micro is hiring! Open to tenured/tenure track faculty at all levels in any area of microbiology. Come join our amazing and growing department. apply.interfolio.com/174404
Reposted by Ben Adler
The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...
Technician III - Department of Microbiology
Position Summary This position will be in the lab of Dr. Joseph E. Peters in the Department of Microbiology. Research in the Peters’ lab broadly involves deciphering mechanisms in genome stability and...
cornell.wd1.myworkdayjobs.com
October 3, 2025 at 1:01 PM
The Peters lab is looking for a new team member! The role transposons play in evolution, basic mechanisms regulating transposition, and applying transposons as tools for genome modification with a special focus on guide RNA-directed transposition. cornell.wd1.myworkdayjobs.com/CornellCaree...
Reposted by Ben Adler
A little late to the Panoptes party, but I’m delighted to share that our paper is published! 👁️ www.nature.com/articles/s41...
The Panoptes system uses decoy cyclic nucleotides to defend against phage - Nature
The Panoptes antiphage system defends bacteria by detecting phage-encoded counter-defences that sequester cyclic nucleotide signals, triggering membrane disruption and highlighting a broader strategy of sensing immune evasion through second-messenger surveillance.
www.nature.com
October 3, 2025 at 4:11 PM
A little late to the Panoptes party, but I’m delighted to share that our paper is published! 👁️ www.nature.com/articles/s41...