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.

Humanized Caffeine-Inducible Systems for Controlling Cellular Functions https://www.biorxiv.org/content/10.1101/2025.06.13.659463v1

Check out the new pre-print from our lab on phage-assisted evolution of light-switchable, allosteric proteins. Congrats to first author @neuroscinikolai.bsky.social, co-corresponding author @jmathony.bsky.social and everyone from the @niopeklab.bsky.social involved! www.biorxiv.org/content/10.1...

Check out the longer thread on the project below 👇

Excited to share my main PhD work is finally out! 🥳 We built a phage-assisted evolution platform to evolve allosteric protein switches (POGO-PANCE) and introduce cumulative, targeted mutations/Indels (RAMPhaGE)! See how we evolved ultra-strong, light-switchable AraC variants 🌚🌞

More insights into #glycoRNA, this time found within exosomes! www.nature.com/articles/s41...

Die #Exzellenzcluster stehen fest: Heute hat die Exzellenzkommission 70 Projekte zur Förderung ausgewählt. 45 Cluster werden fortgesetzt, 25 neu eingerichtet. Die Förderung beginnt ab 1. Jan. 2026 für 7 Jahre, die Fördersumme beträgt insg. 539 Mio. €/Jahr. Die Liste: www.dfg.de/resource/blo... 1/3

1/10 Today in @science.org in collaboration with the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...

Genomes encode biological complexity, which is determined by combinations of DNA mutations across millions of bases In new work @arcinstitute.org, we report the discovery and engineering of the first programmable DNA recombinases capable of megabase-scale human genome rearrangement

A lipid nanoparticle–delivered base-editing therapy was custom designed for an infant with a ureacycle disorder. The affected infant was treated at approximately 7 and 8 months of age. Read the Brief Report: nej.md/42XF03F #ASGCT2025 #MedSky @asgct.bsky.social

New paper alert! We introduce the modular allosteric thermo-control of protein activity. Employing the AsLOV2 domain and mutants thereof as thermoreceptors, we engineered diverse hybrid proteins, whose activity can be controlled by small temperature changes (37-40/41 °C). doi.org/10.1101/2025...

Modular Engineering of Thermo-Responsive Allosteric Proteins https://www.biorxiv.org/content/10.1101/2025.05.02.651844v1

We have an exciting new PhD opportunity! If you are fsacinated by proteins and their dynamics and want to engineer them to develop new molecular tools: apply now! We are a young and dynamic team combining state-of-the-art laboratory and bioinformatics approaches. Please share.

Many thanks to @jmathony.bsky.social for presenting his intriguing research on allosteric protein switches, and how to design them using ML-based prediction of insertion sites for domains like the photoreceptor LOV2. And thank you to @bocklab.bsky.social for hosting this impromptu seminar at #CeMM!👏

Francis Collins, the NIH Director for 12 years, led the Human Genome Project and other NIH efforts for 32 years, resigned today. Key words from his resignation letter www.nytimes.com/2025/03/01/u...

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!