Bridge recombinase enables versatile rewriting of bacterial genomes https://www.biorxiv.org/content/10.64898/2026.04.29.721476v1

Excited to share that our AzoTag paper is now out in @natchem.nature.com! 🥳 We demonstrate de novo chemo-optogenetics through the rational design of photoresponsive small molecules and selection of their artificial protein binding pairs. www.nature.com/articles/s41...

Out now in Nature Biotechnology! Alejandro González-Delgado and a fantastic team of collaborators worked across nine labs to get retron recombineering up-and-running in fifteen bacterial species. Molecular parts on addgene: www.addgene.org/browse/artic... Happy editing!

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

GROQ-seq Datasets Across Transcription Factors (LacI, RamR, VanR), T7 RNA Polymerase and TEV Protease https://www.biorxiv.org/content/10.64898/2026.04.15.718744v1

I am so excited to share our new findings with you! We provide the structural evidence for a direct protein-to-DNA information pathway, showing how a bacterial enzyme 'reads' its own structure to 'write' DNA. www.science.org/doi/10.1126/...

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

New paper from the lab on phage-assisted evolution of allosteric light-switches now out in Nature Comms. Congratulations to Nick and all co-authors! www.nature.com/articles/s41...

1/28 How do you optimize a dynamic protein property that emerges from multiple states? Our finally published paper in @NatureComms takes on one of the hardest problems in protein engineering with phage assisted evolution: evolving allosteric switches🧵

Check out this incredible new method for the directed evolution of protein ON/OFF switches!!! www.cell.com/cell/fulltex...

Fantastic opportunity!

Wow congrats to the authors this is truly impressive

Vorholt Lab re-created endosymbiosis in the lab: injected bacteria into a fungus and evolved a heritable partnership. Evolution, fast-forwarded. doi.org/10.1038/s415...

🎉🎉 Our paper on temperature-dependent protein control using AsLOV2 variants is now published at @natchembio.nature.com: www.nature.com/articles/s41... including some new insights from extend variant characterizations.

Our research on magneto-sensitive fluorescent proteins and some of their applications has now been published! Huge thank you to the many many people involved in making this happen. 🧪 www.nature.com/articles/s41...

Nature has a trick to evolve multimeric proteins via gene duplication. 🧬One copy compensates, the other explores.🧬 Although this has only been a theory so far. Until now: Directed evolution of multimeric proteins by dual-compensatory gene duplication. www.biorxiv.org/content/10.6...

With the state of biomedical science in the U.S. becoming increasingly uncertain, definitely consider these options if you’re a student. I’ve had a great experience doing my PhD in Germany—strong research, supportive environment, and a reasonable cost of living. Happy to share advice if interested!

Join us for a 📢 #CIBSS / SFB 1381 Joint Seminar 🗓 13 Jan 2026 | 12:00–13:00 👉 @jmathony.bsky.social (#uniheidelberg) 🎙 Engineering stimulus-controlled proteins through modular domain recombination 📍 Lecture Hall, Institute of Biology I, Hauptstr. 1 🔗 kurzlinks.de/4mlv #SynBio #ProteinEngineering

1/ Check out our newest paper where we ask: How fast can we experimentally discover binders from scratch? And we mean scratch: a blinded study. TLDR: 26 days. And the binders work…and led to new cancer biology. We’re coming for you AI…. chemrxiv.org/engage/chemr...

Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...

We are hiring a lab manager, for our research group, the Synthetic Neurobiology group (aka Boyden Lab) at MIT/HHMI (on the MIT campus, Cambridge, MA)! Please apply if you're qualified and interested, and spread the word! hhmi.wd1.myworkdayjobs.com/External/job...

Anti-CRISPR-mediated continuous directed evolution of CRISPR-Cas9 in human cells https://www.biorxiv.org/content/10.64898/2025.12.11.693673v1

An ultra-low background far-red light-responsive optogenetic tool based on an engineered biliverdin-binding domain https://www.biorxiv.org/content/10.1101/2025.11.29.691301v1

Especially today, as the administration sidelines evidence-based policy decisions and pressures scientific institutions, this bears repeating: A strong, well-funded, and politically independent scientific ecosystem is vital to innovation, national security, and public health. The stakes are clear.

Great to see our MOSAIC story about an easy, cloning-free efficient protocol for mutating plasmids using recombineering is out now officially and the cover story of ASC Synthetic Biology pubs.acs.org/toc/asbcd6/1... ! Great shoutout to Marijn van den Brink, Tim Althuis and Christophe Danelon!

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...

Mapping the diverse topologies of protein-protein interaction fitness landscapes https://www.biorxiv.org/content/10.1101/2025.10.14.682342v1

New Hot Topics piece from @rphillips3.bsky.social and Stephanie Page in @npp-journal.bsky.social describing emerging insights on roles of molecularly-defined cell types in the lateral septum, which serves as a hub for coordinating diverse social behaviors. www.nature.com/articles/s41...

In the early years of my PhD I remember being asked if we'd ever treat or cure diseases like HIV or Huntington's. I remember saying maybe, but not knowing if I believed. Seeing research pay off as real impact on human lives is - incredible. www.bbc.com/news/article... www.bbc.com/news/article...

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

Been having a lot of fun lately listening to the Night Science Podcast after stumbling on it from the article series by @itaiyanai.bsky.social and Martin Lercher, definitely recommend it if you have a passing interest in the creative aspects of how the scientific process is conducted 😄

🚀 New publication alert! 🚀 We just published in @natbiotech.nature.com: 👉 Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes doi.org/10.1038/s415...

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

Growth, dissolution and segregation of genetically encoded RNA droplets by ribozyme catalysis https://www.biorxiv.org/content/10.1101/2025.08.29.673008v1

Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators. www.nature.com/articles/s41...

A terrorist targeted federal workers last week. There wasn’t much reporting on it. But I’m not finished thinking about it! 🧵 An anti-vaxxer fired more than 500 gunshots into CDC Atlanta, shattering 150 “blast-proof” windows on 6 buildings. Employees were pinned down in terror.

De novo design of light-regulated dynamic proteins using deep learning https://www.biorxiv.org/content/10.1101/2025.08.12.669910v1

Well, this is a huge Executive Order power grab... www.whitehouse.gov/presidential... 1/3

PANCS-Binders (phage-assisted noncontinuous selection of protein binders) screens multiple high-diversity protein libraries against a panel of dozens of targets for high-throughput binder discovery. @chembiobryan.bsky.social @mstyles-chembiol.bsky.social www.nature.com/articles/s41...

Work by @bene837.bsky.social @jmathony.bsky.social @dominikniopek.bsky.social @uniheidelberg.bsky.social

Pretty sure my grandfather, who was a NASA engineer that worked on Saturn and Apollo missions in Alabama in the 1960s and 1970s, would be alarmed to see what’s happening now. This is faded but here is a technical drawing he produced for fiber optic viewing of the liquid oxygen supply for Saturn V.

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

Engineering site-specific nucleic acid-protein conjugates by utilizing a natural RNAylation reaction https://www.biorxiv.org/content/10.1101/2025.07.11.664405v1

Words cannot describe how excited I am to share the findings from the second half of my postdoc in @aaronwhiteley.bsky.social's lab where we discover that bacteria use functional amyloids to defend themselves from predatory bacteria. rdcu.be/euu5Y. See thread for details on this epic adventure 1/.

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

Let’s we flip this script. “Is academia producing too few jobs?”

We have developed an entirely new mechanism of action for gene knockdown -> trafficking of targeted mRNAs to the lysosomal, using lysosomal trafficking oligonucleotides (LyTONs)! Published in @chemicalscience.rsc.org Led by Disha Kashyap #chemsky 🧪 pubs.rsc.org/en/content/a...

Happy to announce the first paper from my PhD at Korbel group at @embl.org has finally been published: embopress.org/doi/full/10.1038… Collaborating with @typaslab.bsky.social, @hennig-lab.bsky.social and the EMBL PEPCF, we designed de novo inhibitors to a bacterial phage defense system 1/🧵

A synthetic cell phage cycle https://www.biorxiv.org/content/10.1101/2025.06.14.659709v1

I left the US in 2022 to pursue a PhD abroad, partly out of concern for the sustainability of our politics. I’m grateful to live where people reckon with the dangers of unchecked power, and I stand—both as an American and a scientist—with those who defend truth, integrity, and limits on authority.