The latest work from the lab now out in @cp-molcell.bsky.social! New mechanistic insights into TnpB DNA unwinding and hypercompact plant genome editors🌱 Congratulations to leads @zehanzhou.bsky.social, Iren Saffarian, @honglue.bsky.social, Trevor Weiss & team, and Jacobsen, Savage and Bryant labs

Zehan Zhou@zehanzhou.bsky.social · 5h ago

We are PUBLISHED!!! Our mechanistic work on how CRISPR-Cas ancestors unwind DNA and how this can be used to engineer hypercompact plant editors can now be found on Mol Cell- if you are interested in what defines a good genome editor, this read is for you 😎 🔗 www.sciencedirect.com/science/arti...

Super cool symposium in Berkeley!!

Simon Roux@simrouxvirus.bsky.social · 2mo ago

🚨 Registration for VEGA26 is 👏 officially open 👏 🚨 The 5th edition of our Viral EcoGenomics and Applications symposium will be held November 18-19, 2026, on the UC Berkeley campus 🧬 🦠 🔬 🧫 Event website ➡️ jgi.doe.gov/work-with-us... Registration link ➡️ cvent.me/e0RnA0

We are PUBLISHED!!! Our mechanistic work on how CRISPR-Cas ancestors unwind DNA and how this can be used to engineer hypercompact plant editors can now be found on Mol Cell- if you are interested in what defines a good genome editor, this read is for you 😎 🔗 www.sciencedirect.com/science/arti...

Cool preprint. Rather than engineering TdT around reversible terminators, they use the natural sugar specificity of an RNA polymerase to achieve terminator-free, template-free single-nucleotide addition. www.researchsquare.com/article/rs-9...

Repurposing the TIGR-Tas system for programmable transcription activation https://www.biorxiv.org/content/10.64898/2026.07.30.739400v1

Published today in @natchembio.nature.com @natureportfolio.nature.com: a framework for the de novo design of antimicrobial α-helical peptides that assemble into transmembrane barrel-stave nanopores.

Out now! In collaboration with Hiroshi Nishimasu's lab, we uncover how a dual reverse transcriptase immune system builds double-stranded DNA from both RNA and protein templates. www.cell.com/cell/abstrac... Previous thread for the preprint: bsky.app/profile/ster...

Coordinated RNA- and protein-templated synthesis of double-stranded DNA by a dual reverse transcriptase immune system

Bacterial reverse transcriptases defend against viruses, yet how their DNA products stop infection remains unknown. Bacteriophage inhibition of a host recombination enzyme activates the DRT3 defense s...

cell.com

🔬 Microbiology | Tenure-Track Faculty Positions @ Yale University A role focused on the molecular mechanisms of how pathogens invade host cells. https://jobrxiv.org/job/yale-university-27778-tenure-track-faculty-positions-dept-of-microbial-pathogenesis/ #Immunology #ImmunologyJobs

Phage terminase recognition by the bacterial immune sensors Avs2 and Upx | Nature Communications

🚀 Thrilled to share our first metaSPLiT preprint from @annabiosys.bsky.social's lab in collaboration with @gibbological.bsky.social! Explore hidden bacterial phenotypic heterogeneity in the human gut microbiome and discover the concept of "physiological guilds": www.biorxiv.org/content/10.6...

Phenotypic heterogeneity in the human gut microbiome revealed by subspecies-resolution single-cell transcriptomics

Most of our knowledge about bacterial functional roles in microbiomes comes from bulk measurements. Yet microbial communities are complex ecosystems in which functionally distinct bacterial subpopulat...

biorxiv.org

Preprint: biorxiv.org/content/10.6... This is the product of many years of effort, and particularly amazing summer teamwork by Qi Yu, Haedong Kim, @seidels.bsky.social @cxqiu.bsky.social and many others from Shendure Lab & SeaHub (a @alleninstitute.org @biohub.org @uwmedicine.bsky.social colab) 2/n

In vivo reconstruction of the cell lineage history of a developing mouse with DNA Typewriter, from zygote to late organogenesis

The complete cell lineage of C. elegans, mapped over four decades ago, was tractable because the animal is small, transparent, and lineage invariant. Most animals are none of these, having orders of m...

biorxiv.org

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek

We’re so excited to share our new paper, where we tackle the wealth of structural and functional diversity of anti-phage sensors across bacteria (1/6)

Nature@nature.com · last wk.

Nature research paper: Diverse bacterial pattern recognition receptors sense the core phage proteome go.nature.com/45fpXCZ

The manuscript introducing ArchaeaHQ is still under review😴 As science can't wait... I'm making available a version of the dashboard we use. vee-lab.eu/archaeahq Here the user can have quick access to the information in the database, and select specific genomes of interest. Enjoy 🎉

Pedro Leão@pedroleao.bsky.social · 2mo ago

I'm happy to share the first pre-print of out Lab! 🎉 Introducing ArchaeaHQ www.biorxiv.org/content/10.6... We curated 21,644 genomes across all 4 archaeal kingdoms to bridge the gap in public datasets for computational biology What is inside ArchaeaHQ... (1/2)

New Preprint 🥳 Here we wondered how phages that have been extensively studied in laboratory E. coli strains actually behave when they encounter a real pathogen such as O157:H7 strain...one with a far more complex cell surface & one of the most consequential foodborne pathogens in the United States.

Animated E. coli Bacteria Drawing

Alt: Animated E. coli Bacteria Drawing

static.klipy.com

It’s #glycotime for phage infecting pathogenic E. coli strains

Vivek Mutalik@vivekmutalik.bsky.social · 2w ago

New Preprint 🥳 Here we wondered how phages that have been extensively studied in laboratory E. coli strains actually behave when they encounter a real pathogen such as O157:H7 strain...one with a far more complex cell surface & one of the most consequential foodborne pathogens in the United States.

🔥My first (co)first-author paper is out🔥 The surfaces of Gram+ and Gram- bacteria are markedly different from each other. How are phages equipped to breach the Gram+ envelope❓ 💡We report a baseplate structure uniquely adapted to infect Gram+ S. aureus. A 🧵⬇️ 1/8 #phagesky #cryoEM 🧪

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

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2w ago

Conserved folds enable immune antagonism across the tree of life https://www.biorxiv.org/content/10.64898/2026.07.21.739742v1

1/11 New preprint from the Sternberg lab in collaboration with the Fernández lab! We are excited to share our structure-function study of DRT10, a bacterial defense-associated reverse transcriptase that synthesizes long tandem-repeat DNA.🧵 Read the full story here: www.biorxiv.org/content/10.6...

Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptase

Defense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection[1][1],[2][2]. We previously showed that DRT10, a tripartite system comprising an RT, a...

biorxiv.org

New preprint from @courtneyrsantos.bsky.social and @kvnforsberg.bsky.social discovering human ISGs are sufficient to block phage replication in bacteria! Amazing to see such strong phenotypes especially against RNA phages: www.biorxiv.org/content/10.6...

How do human cells defend against viruses? @sgfern.bsky.social discovers that human immune proteins named ISGs target ancient features of replication shared between animal and bacterial viruses – opening analysis of human immunity to the power of bacterial genetics www.biorxiv.org/content/10.6...

Our paper on the YprA family of helicases and their roles in bacterial defence is now out! We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs www.sciencedirect.com/science/arti...

YprA-family helicases provide the missing link between diverse prokaryotic immune systems

Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…

sciencedirect.com

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/

Almost time to kick-off this year's ASM Microbe, including some very cool sessions in the next few days in the AEM meeting ! If you're around and want to chat anything metagenomes, phages, viruses, and all that, let me know !

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

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2mo ago

Phage-encoded single-guide RNAs subvert CRISPR-Cas9 immunity https://www.biorxiv.org/content/10.64898/2026.06.01.729453v1

@romihadary.bsky.social and @soreklab.bsky.social 's discovery that sponge proteins constitute enormous families of viral immune evasion factors is now out in @natmicrobiol.nature.com @reneechang.bsky.social and our lab were happy to help with this story! www.nature.com/articles/s41...

Functional diversity of phage sponge proteins that sequester host immune signals - Nature Microbiology

A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.

nature.com

Kranzusch Lab@kranzuschlab.bsky.social · 12mo ago

Two major breakthroughs for the nucleotide immune signaling field in pre-print by @romihadary.bsky.social @soreklab.bsky.social www.biorxiv.org/content/10.1... (1) Beautiful bioinformatic analyses reveal known viral nucleotide sponges are members of enormous protein families ubiquitous in phages

🛠️💉It's time for engineering contractile injection systems! @chipericson.bsky.social & @davidschaumann.bsky.social introduce programmable CIS - PROCIS, combining tail length control, non-native cargo loading, and cell retargeting all in one system! www.biorxiv.org/content/10.6... 🧵 1/5

If you work with R6K plasmids for transient DNA delivery, our latest SHARK strains might be of use! Work out at ACS Synthetic Biology led by Shivang Joshi and strains plus plasmids for their assembly will be available @addgene.bsky.social very soon! doi.org/10.1021/acss...

📣 We are now accepting applications for the second Plant Synthetic Biology Hackathon! 📣 Check out this unique opportunity to learn the newest tools and approaches in plant engineering! Hosted by Nicola Patron and myself as part of the Plant Cell Atlas RCN, July 12-13, 2026 at MIT.

Plant Cell Atlas@plantcellatlas.bsky.social · 3mo ago

The Application deadline for the SynBio Hackathon has been EXTENDED until June 8, 2026! Apply Now Here: www.plantcellatlas.org/2026-synbio-... *Participants will be reimbursed up to $800 for travel and lodging costs.

1/8 🚨 New preprint from the @sternberglab.bsky.social & @martinjinek.bsky.social labs! CRISPR-associated transposases (CASTs) insert large DNA cargoes at precise genomic locations — no double-strand breaks needed.