Patrick Pausch

BindCraft2 v1.0.4 has been released: with significantly improved VHH, scFv, ARP, and induced fit targeting. WE also improved speed and code stability. Try your difficult campaigns again. Great work by @erikmaeots.bsky.social , Leonardo Tredese and @liza-ch.bsky.social

How does a single methyl group activate bacterial defence? Our new preprint, led by @pspatharas.bsky.social in collaboration with the group of @matthiaswilmanns.bsky.social, explains how a single DNA methylation event activates large retron assemblies. www.biorxiv.org/content/10.6...

Retron biology keeps surprising us. Type VI does things VERY differently! 🧬 Check the paper to see how it works👇 Fun working with the @seth-shipman.bsky.social lab on this story!

Heads up! The Symposium on the Immune System of Bacteria 2027 is now open for registrations! 20-22nd July 2027, Churchill College, University of Cambridge, UK Places are limited, so register soon. Visit the website to see our fantastic line-up of speakers: sisb2027.info #phage

What does it take for a mycobacteriophage to infect M. smegmatis mc² 155? 🦠🗺️ We mapped it for 70 phages using genome-wide CRISPRi. Our new preprint from the Phage Foundry is out! (phagefoundry.org) 🥳🧵 Read the preprint here: www.biorxiv.org/content/10.6...

A new preprint 🎉 from phagefoundry.org Mycobacteriophages are candidate therapies for drug-resistant mycobacterial infections, but we still don't know how most of them get into their hosts. Our new preprint tackles this challenge 👉🏽 www.biorxiv.org/content/10.6...

Excited to share our work on bacterial immune signaling! Our preprint reveals how RNA-guided Cas13 cleaves host tRNAs to generate small-molecule messengers that activate 2TMβ, linking RNA recognition to membrane damage and phage defense. 1/11

We are looking for a new team member! Interested in structural biology, gene expression and organelles? Then apply now to our open PhD position: umg.recruiting-portal.com/r/z11okjqp6v...

Heads-up! I’ll be starting my research group at MedUni Vienna in January 2027, with postdoc and PhD positions available soon. Looking for people interested in bacteria–phage interactions, bacterial defense systems, and phage anti-defense strategies. Please send your CV: anna.lopatina@univie.ac.at

Attention, phage friends! Our new work on predicting phage-host interactions is out in Nature Microbiology since yesterday! 👉 www.nature.com/articles/s41...

🌙 Bringing Archaea to moon! Our latest study with the Orsi lab shows that M. okinawensis can survive, perform methanogenesis, and grow under simulated Enceladus conditions. Yet another reminder of how astonishingly adaptable Archaea are. www.science.org/doi/10.1126/...

The final version of our manuscript on TnSeq in bacteriophages (“HIDEN-SEQ”) is out today – if you have an interesting phage phenotype and want to know the underlying genetic basis, this one is for you! 1/4

ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...

Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team

Some of the smallest 😎 viruses on Earth are all around us. Three or four genes 😍 each, in nearly every environment. We keep finding thousands by sequencing, yet don't know who they infect, can't easily isolate them, or even how the few we have infect a cell. Our new preprint takes this on 🧵👇

I'm excited to share that my newly funded #ERCStG FRONTERA is recruiting two postdoctoral researchers at @ipbhalle.bsky.social 🌱🔬 If you are passionate about plant immunity, proteolysis, membrane proteins, or proteomics, I'd love to hear from you. 🧵 Please RT/share!

Structural biology of retron-mediated immunity against phage pubmed.ncbi.nlm.nih.gov/42658732/ #cryoEM

Do you need to analyze bacterial microscopy data and are looking for an all-in-one tool for Windows or macOS? Check out BactoMate by Lasse Hallenga and Philipp Popp! I'm happy that we were able to contribute to this great work. www.biorxiv.org/content/10.6...

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

1/4 Every good defence needs a backup! 🛡️⚔ Out now in @natrevmicro.nature.com our Comment on "𝗶𝗺𝗺𝘂𝗻𝗲 𝘀𝗮𝗳𝗲𝗴𝘂𝗮𝗿𝗱𝗶𝗻𝗴"! 🎉 🔗 www.nature.com/articles/s41...

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...

🧬 Thrilled to share our latest @biorxiv-microbiol.bsky.social preprint! Here we find that Retron-IX build crazy supramolecular rings scaffolded by DNA molecules that sense phage infection! www.biorxiv.org/content/10.6... Read more below🧵! (1/X)

Our AI-guided design of RNA-guided nucleases is now out in @science.org 💻🧬 We used structure and evolutionary data to generate minimal, active and divergent gene editors! www.science.org/doi/10.1126/... Congrats to @petrskopintsev.bsky.social @isabelesain.bsky.social @evandeturk.bsky.social & team!

PhD opening in my lab @jagiellonskiuni.bsky.social: using AI to predict how phage enzymes break down bacterial capsules — joint work with ML group GMUM and Zuzanna Drulis-Kawa's phage lab (Wrocław), spanning genomics, AI & evolution. mostowylab.com/job-phd-ai-d... Deadline: 15 August 2026

A DNA-scaffolded Retron Ring Mediates Antiphage Immunity https://www.biorxiv.org/content/10.64898/2026.07.14.737667v1

Join us at the EMBO Young Scientists’ Forum 2026 in Dubrovnik, 28–30 October. All areas of life sciences are welcome! ⏰ Early-bird registration ends 15 July. #EYSF2026 #LifeSciences

Klebsiella phages often modify the bacterial capsule instead of degrading it, stripping acetyl groups. Nobody's traced how this evolves. I'm hiring a computational postdoc to find out — Kraków, apply by 21 July. mostowylab.com/job-postdoc-...

We often talk about complex protein folds but what does that really mean? Turns out we don't have a good metric for it. So we made a game to make one! Head over to our website to vote on which fold you think is more complex and why! pacesalab.com/foldcomplexi...

Do you need a super active #CRISPR Cas for in vivo editing? I have not one, but two options for you. Activities rival SpyCas9, but they fit into an scAAV. Check out our latest paper, co-led by Fedor Gorbenko and Irene Sala. Just out in Genome Research. link.springer.com/article/10.1...

This year #EYSF2026 is in Dubrovnik, Croatia! 🔗 event.fourwaves.com/eysf/pages ▶️ For early-career life scientists across Europe: interdisciplinary presentations, networking, collaborations, and creative scientific exchange. & we have a special session #ProtistsOnSky

1/4 Excited to share our new preprint on phage genome editing: Targeted DNA nicking enables efficient, single-step and counterselection-free editing of bacteriophage genomes Preprint: lnkd.in/dv4g5kW6

Our lab website is finally online! pacesalab.com You can find information about our research, publications, and on-going developments in the lab.

Und das ganze Auditorium schweigt...wir müssen nochmal über Zivilcourage reden.

Phage receptor-binding proteins are known for their LEGO-like modularity, but we still do not fully understand their evolutionary potential and how it shapes phage host range. Our new preprint examines this systematically in Klebsiella phages. 🔗 www.biorxiv.org/content/10.6... Thread 🧵

Phages invented sgRNAs before humans!! 🧬 Obviously, for mischief… 😈 Loved seeing this story unfold!

Thrilled to share a major milestone from our long-running collaboration with Zuzanna Drulis-Kawa's lab in Wrocław — DepoCatalog, is now out in @natcomms.nature.com: 129 Klebsiella phage depolymerases, 75 capsule types, 5-class structural framework and public database. www.nature.com/articles/s41...

📢 Registration for our International Symposium on “New Concepts in Prokaryotic Virus-Host Interactions” is now open! 🗓️ 5–7 October 2026 📍 Harnack House, Berlin, Germany ➡️ Information and registration: spp2330.de/symposium-20...

Polish phage science meets Polish visual storytelling 🇵🇱🦠 To celebrate our last paper, we collaborated with an artist who previously worked on The Witcher 3 — to create a comic about phages and why understanding them matters in the fight against antibiotic-resistant bacteria. Comic below 👇

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.

Bacteriophages are in a constant arms race with bacteria 🦠 The Phage ORFeome pooled library from the Aaron Whiteley lab contains phage proteins that activate antiphage defense systems — a tool to dissect the mechanisms of bacterial immunity. Aaron Whiteley

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/...

PhD student or postdoc in microbiology? 🔬🦠 We are opening a new round of our career orientation program VAAMentoring – Get matched with an experienced scientist 👨‍🔬👩‍🔬 to help you find your direction🎯 Apply by May 15, 2026 More info🔗 t1p.de/2iamo #microbiology #mentoring #VAAM #PhDlife #Postdoc

PostDoc position available! (links in post below) Feel free to share!

‼️Please share‼️ Nemudryi lab is looking for postdocs to join our team and study: 🦠 Bacterial phage defense mechanisms 🧬 RNA repair & CRISPR-based RNA editing Excited about RNA, host-virus interactions & mechanistic biology? Let's talk! Apply: explore.jobs.ufl.edu/en-us/job/53...

How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

A big advance in the field of bacterial immunity, from the Bernheim and Laub labs