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Ben Adler

@benadler.bsky.social
1.9K followers 795 following 105 posts

Postdoc @ Doudna Lab - UC-Berkeley | Bacteriophage engineering | CRISPR | Biotechnology | Microbiology | All Combinations Thereof | He/him. Opinions my own.

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Reposted by Ben Adler
PLOS Biology @plosbiology.org · 16/09/2026
#Phages can evade #bacterial #immunity by disrupting #antiviral signals like cA3, triggering the Panoptes defense systems. @mfwhite2.bsky.social &co show that Type II Panoptes detects cA3 loss and activates a CARF-TM effector to disrupt membranes & stop infection @plosbiology.org 🧪 buff.ly/1ixwg9v
Left: Organisation and mechanism of the Panoptes System. In type I Panoptes systems, mCpol is constitutively active, generating signalling molecules that inactivate the cognate effector, 2TMβ. When an infecting phage expresses a sponge protein, the cyclic oligonucleotide pool is depleted. The Panoptes effector oligomerises, leading to membrane disruption and growth arrest or cell death. Right: CARF-TM model structure and cA3 binding. Alphafold3 model of CARF-TM in complex with cA3, including POPG molecules to simulate the membrane bilayer. The position mutated to generate the truncated CARF protein is shown by black arrows.
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Jase Gehring @skyjase.bsky.social · 13/08/2026
most modern human projects do not have simple bottlenecks. simple bottlenecks are simple to solve, so our systems knock those out and scale up until they face complex, multi-dimensional or self-contradictory bottlenecks (e.g. speed vs safety).
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Siân Owen @sianowen.bsky.social · 06/08/2026
Some good new to share: my lab was recently awarded an NIH R35/MIRA award to continue our work on conjugative plasmids and plasmid-dependent phages! 🥳 🫶NIH🫶 www.wadsworth.org/news/nih-gra...
wadsworth.org
NIH grant awarded to Wadsworth Center scientist to advance research on antimicrobial resistance | New York State Department of Health, Wadsworth Center
Dr. Siân Owen, a Principal Investigator and Research Scientist at the Wadsworth Center, has been awarded a highly competitive five-year, $1.97 million Maximizing Investigators' Research Award (MIRA) f...
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Teresa O'Meara @teresaomeara.bsky.social · 29/07/2026
Bacteriology-Focused Assistant Professor Position in Microbiology and Immunology at the University of Michigan Application deadline: August 15, 2026 Come be my colleague!
Bacteriology-Focused Assistant Professor Position in Microbiology and Immunology at the University of Michigan

Application deadline: August 15, 2026

Applicants are requested to send
1) A cover letter (up to 1 page)
2) A CV
3) A description of research interests and goals (up to 2 pages)
4) A description of teaching experience and philosophy (up to 1 page)
5) Contact information including email to solicit 3 letters of recommendation.
Application materials should be combined into one PDF and addressed to the department chair, Dr. Bethany Moore, and sent via email to Sheryl Smith - sherylhs@umich.edu
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15
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Aude Bernheim @audeber.bsky.social · 21/07/2026
Out @cp-cellhostmicrobe.bsky.social, natural products meet bacterial immunity! We used genomics to identify lanthivirins: a family of >2,000 lanthipeptide BGCs that protect Actinobacteria against phages. Led by @hshomar.bsky.social & @mariegllm.bsky.social www.sciencedirect.com/science/arti...
sciencedirect.com
A family of lanthipeptides with anti-phage function
Bacteria produce natural products to adapt to their environments, with phage interactions as major ecological and evolutionary drivers. While some nat…
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Jase Gehring @skyjase.bsky.social · 03/07/2026
A major pillar of the system is paying its skilled employees below-market “subsistence stipends” and sharing their work for free. private industry knows it’s the biggest beneficiary. It doesn’t want the music to stop
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Jason Rasgon @vectorgen.bsky.social · 03/07/2026
The NIH is an ENORMOUS bargain for the American people. Do folk think that private industry will do the background slog work for drug discovery for 250K direct costs?
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Tominaga K. (tomiken) @pacyc184.bsky.social · 18/06/2026
YprA-family helicases provide the missing link between diverse prokaryotic immune systems: Cell Host & Microbe www.cell.com/cell-host-microbe/full…
cell.com
YprA-family helicases provide the missing link between diverse prokaryotic immune systems
YprA-family helicases represent a key hub in the prokaryotic defense network. Through phylogenetic analysis of YprA, Bell and colleagues identify a distinct class of defense systems, called ARMADA. ARMADA protects bacteria against diverse phages, synergizing with another defense system, Druantia III. ARMADA, Druantia III, and Zorya II co-occur in phage-like elements.
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Jase Gehring @skyjase.bsky.social · 15/06/2026
i've built laboratories. i've built deep learning models. i've been evangelizing Big Data in Bio my whole career. give me money and i'll do it a lot more
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Jessica Sacher @jessicasacher.bsky.social · 05/06/2026
NIAID (@niaidnews.bsky.social) has awarded $6M to launch a coordinated US phage therapy research network — 3 new centers! Excited our Stanford Center for Phage Pharmaceuticals (@stanfordmedicine.bsky.social) is one, & to work w/ @gladstoneinst.bsky.social & @pghphageprogram.bsky.social! 🧵 1/
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Rafael Pinilla-Redondo (Rafa) @rafomics.bsky.social · 02/06/2026
Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold!
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Ben Adler @benadler.bsky.social · 28/05/2026
This is so cool -- multifunctional-ization of biofilm eDNA with a single protein! Two ideas for anyone interested below:
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Susie Grigson @susiegriggo.bsky.social · 26/05/2026
New preprint! 🚨 Phage proteins don't act alone. Phages rely on homooligomerisation to assemble identical protein subunits into functional forms. But figuring out those exact configurations experimentally is tough. Learn about our approach in our new preprint! 👇 (1/n) www.biorxiv.org/content/10.6...
biorxiv.org
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Di Jiang @dijiang319.bsky.social · 21/05/2026
Ancient wars between microbes gave us key immune defenses | @science.org | AAAS www.science.org/content/arti... #microsky #virosky #immunosky
science.org
Ancient wars between microbes gave us key immune defenses
A better understanding of battles between bacteria and viruses could inspire new medicines
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Ákos T Kovács @evolvedbiofilm.bsky.social · 20/05/2026
Chemical inactivation of a bacterial immune system de-domesticates a temperate phage and promotes its spread bioRxiv from Joseph Gerdt at Indiana University with @annadragos.bsky.social www.biorxiv.org/content/10.6... #PhageSky
biorxiv.org
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Vivek Mutalik @vivekmutalik.bsky.social · 20/05/2026
🎊 New Preprint from phagefoundry.org ! Super excited to share our latest work on generating systematic phage-MDR P. aeruginosa interaction dataset & use of ML to predict phage susceptibility & phage cocktails from target genome sequences alone, w validations www.biorxiv.org/cgi/content/...
Systematic lytic host range characterization of 99 multidrug resistant Pseudomonas aeruginosa strains against 95 diverse double strand DNA phages, and AI/ML workflow to predict phage susceptibility and cocktail formulation based on genomic sequence alone.
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Zach LaTurner @micronaut.bsky.social · 15/05/2026
The paper on my Ph.D. work is fully online! We used a ribozyme that barcodes 16S rRNA to track the transduction range of phage P1 in a synthetic community and real wastewater communities, while diving deeper into the unique range conferred by P1s two tail fibers. www.nature.com/articles/s41...
nature.com
Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding - Nature Communications
Bacteriophages are the most abundant life form on earth and can be applied to eliminate or engineer bacteria. Here, authors demonstrate RNA barcoding as a high throughput tool to measure bacteriophage...
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Ben Adler @benadler.bsky.social · 12/05/2026
Let's get ready to tumble!
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Jase Gehring @skyjase.bsky.social · 10/05/2026
asymmetry of information permeates academic science. i'm talking: conferences campus visits grant review peer review the right people can put themselves 6 months ahead of the public record.
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Ben Adler @benadler.bsky.social · 27/04/2026
Saying it because @kenjmloi.bsky.social didn't: This is really close to a RNA system that targets protein sequences because of wobble bases in codons. Truly amazing discovery!!
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Jamie Cate @jhdcate.bsky.social · 27/04/2026
The best thing since *before* sliced bread... VIPRs. www.biorxiv.org/content/10.6... www.biorxiv.org/content/10.6...
biorxiv.org
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Alex Gao @algao.bsky.social · 16/04/2026
Excited to share our new findings in @science.org on how the DRT3 bacterial defense system uses a reverse transcriptase that builds DNA repeats without a nucleic acid template. Microbes never cease to amaze! www.science.org/doi/10.1126/...
science.org
Science | AAAS
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Chase Morgan @phagemorgan.bsky.social · 11/04/2026
Excited to share the last installation of my PhD work. Worked with an all-star team on this one who really made this all come together beautifully. @ranidreamer.bsky.social @amardeeep.bsky.social @benadler.bsky.social and many others. www.cell.com/cell-reports...
cell.com
The phage nucleus synergizes with an anti-defense protein to resist bacterial immunity
Morgan et al. show that a phage-encoded protein functions as an antitoxin to counter DarTG2-mediated phage defense. They further explore the interplay between this anti-defense protein, the phage nucleus replication compartment, which encloses chimallivirus genomes, and the DarTG2 phage defense system.
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Ben Adler @benadler.bsky.social · 04/04/2026
10 years ago @vivekmutalik.bsky.social introduced me to the wild world of phages. Today, @lucasmoriniere.bsky.social presents a truly foundational scale bridging genomes, viruses, editing and function. Truly an amazing scale and vision for the future! Congrats to phage foundry 🌶️🌶️🌶️
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Jason Nomburg @jnoms.bsky.social · 26/03/2026
Come join us at AITHYRA! I highly encourage anyone excited about the interplay between AI and life sciences to apply. It's been an amazing place to start a lab. Feel free to reach out to me if you have any questions about our institute
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Ben Adler @benadler.bsky.social · 25/03/2026
I love this concept -- plasmid to Cryo structure in a day! www.biorxiv.org/content/10.1...
biorxiv.org
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Malcolm White @mfwhite2.bsky.social · 16/03/2026
New preprint: Cyclic tri-adenylate signalling by a Panoptes anti-phage guard system with a CARF-TM effector. Great work led by Sabine Grüschow www.biorxiv.org/content/10.6...
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Kranzusch Lab @kranzuschlab.bsky.social · 06/03/2026
After >10 years of our lab studying bacterial cGAS-like enzymes, @hobbslabutah.bsky.social finally reconstitutes viral sensing in vitro and discovers how these ancient receptors sense phage protease enzymes to detect virion assembly and activate antiviral immunity www.biorxiv.org/content/10.6...
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Ben Adler @benadler.bsky.social · 31/01/2026
Really phenomenal work from the Gerdt lab at Indiana University... I hope this becomes a major boon for phage therapy: "Chemical inhibition of a bacterial immune system" www.cell.com/cell-host-mi...
cell.com
Chemical inhibition of a bacterial immune system
Bacteriophages are promising alternatives to antibiotics for treating bacterial infections. However, bacteria possess immune systems that neutralize bacteriophages. Zang et al. discover small molecule...
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Jase Gehring @skyjase.bsky.social · 21/01/2026
Life science research is plagued with repetitive rote work. This system is designed to support, organize and execute tasks across the research stack. procurement, inventory management, equipment telemetry, safety, and regulatory can be managed with and by the system.
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Jase Gehring @skyjase.bsky.social · 21/01/2026
I’ve jumped completely off the deep end and I’m building a stateful agentic environment for computational and experimental life science research. Inspired by some of the systems I’ve seen here, but different. It’s goal oriented and research focused
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Sorek Lab @soreklab.bsky.social · 05/01/2026
NLR-like immunity in bacteria A new study from the Alex Gao lab. The scope of this work is incredible!!! www.biorxiv.org/content/10.6...
biorxiv.org
Diverse bacterial pattern recognition receptors sense the conserved phage proteome
Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...
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Alex Crits-Christoph @acritschristoph.bsky.social · 24/12/2025
All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)
Figure 2. Himar1 transposon variant screen on a cohort of 92 bacterial species.
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Ben Adler @benadler.bsky.social · 16/12/2025
On this episode of the "What's in the vault?!?!" saga...
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Stefaan Verwimp @sverwimp.bsky.social · 24/11/2025
Protein domains have no single definition, so why stick to one segmentation? 🧩 Instead of forcing structures into rigid classifications, we built AFragmenter. It uses AlphaFold PAE networks for a tuneable approach to domain parsing. You control the granularity. 👇 🔗 doi.org/10.1093/bioi...
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Dorentina Humolli @humollidorentina.bsky.social · 20/11/2025
🚀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 (🧵)
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Alexander Harms @aharms485.bsky.social · 20/11/2025
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8
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Avery Noonan @averynoonan.bsky.social · 16/11/2025
We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing. www.biorxiv.org/content/10.1...
biorxiv.org
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Vivek Mutalik @vivekmutalik.bsky.social · 16/11/2025
📣 New preprint from us at phagefoundry.org 📣 A solid machine learning framework & to predict strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Avery Noonan from the Arkin Lab led this massive effort www.biorxiv.org/content/10.1...
phagefoundry.org
Phage Foundry
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Simone Alma Evans @simone-alma.bsky.social · 15/11/2025
I am so excited to share our project with you! We find prokaryotic proteases activate toxic enzymes and pores as a modular strategy in phage defense. We studied four fascinating protease-toxin pairs that are abundant across bacterial genomes: www.biorxiv.org/content/10.1...
biorxiv.org
Proteolytic activation of diverse antiviral defense modules in prokaryotes
Linked protease–effector modules are widespread in prokaryotic antiviral defense, yet the mechanisms of most remain poorly understood. Here we show that four of the most prevalent modules—metallo-β-la...
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Reid Oshiro @rtoshiro.bsky.social · 15/11/2025
I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.
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Owen Tuck @owentuck.bsky.social · 15/11/2025
Beautiful preprint from Simone Evans et al. in Alex Gao's group looking at MBL/nuclease and other cool zymogens (pepco, EACC1) in antiphage defense systems. Great to see this paradigm extended - probably many more proteolytically activated effectors out there... www.biorxiv.org/content/10.1...
biorxiv.org
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Vivek Mutalik @vivekmutalik.bsky.social · 15/11/2025
Amazing piece of work from @rtoshiro.bsky.social & Kim Seed at UC Berkeley. 🙌 Played a tiny role in this work. Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses www.biorxiv.org/content/10.1...
bsky.app
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Harris Wang @harriswang.bsky.social · 13/11/2025
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️ www.science.org/doi/10.1126/...
science.org
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
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Emmanuele Severi @emmseveri.bsky.social · 14/11/2025
#microsky #phagesky #phage defence Thanks, @crypticprophage.bsky.social for pointing it out on “the other side” www.science.org/doi/10.1126/...
science.org
Recurrent acquisition of nuclease-protease pairs in antiviral immunity
Antiviral immune systems diversify by integrating new genes into existing pathways, creating new mechanisms of viral resistance. We identified genes encoding a predicted nuclease paired with a trypsin...
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François Rousset @francoisrousset.bsky.social · 14/11/2025
A mysterious lactamase-nuclease module found in multiple defense systems finally solved ! Congrats @owentuck.bsky.social et al. !
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Osterman Ilya @ostermanilya.bsky.social · 14/11/2025
Fascinating discovery - anti-phage defense protein is a proenzyme that is cleaved by partner protease after phage infection and all three! products of cleavage form active nuclease.
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