Join the Start-Up Summer School 2026 by the Centre for Synthetic Biology at Technische Universität Darmstadt and Futury! 🚀🧪 📅 Date: September 7–10, 2026 📍 Location: Darmstadt and Frankfurt 📝 Application: lnkd.in/efkkh5qq ⏰ Deadline: August 21, 2026
Jan Mathony
@jmathony.bsky.social
Scientist with a passion for Synbio | Protein engineering | Optogenetics | ML www.niopeklab.de/mathony-lab/
New preprint! We used protein domain insertion to tighten the editing window of the TadA8e adenine base editor. Bulky domain insertions concentrated editing around position A5, maintained robust on-target activity, and reduced Cas-independent off-target editing. 🧬 doi.org/10.64898/202...
Domain Insertion Improves the Precision of a CRISPR Adenine Base Editor
Adenine base editors (ABEs) enable efficient A:T to G:C conversion, but their broad activity windows frequently cause unintended bystander edits. We hypothesized that insertion of a bulky, inert prote...
biorxiv.org
Very nice news & views about our recent study on thermogenetic protein regulation! www.nature.com/articles/s41...
A familiar newcomer to the thermogenetic toolset - Nature Chemical Biology
Temperature-sensitive proteins promise precise, remote and penetrant control of cells, but few such proteins are currently available. A study finds that certain existing protein switches can moonlight...
nature.com
Check out Nick's thread on his phage-assisted evolution paper that has just been published in @natcomms.nature.com: www.nature.com/articles/s41... Many congrats to Nick and all co-authors.
Phage-assisted evolution of allosteric protein switches - Nature Communications
Allostery enables proteins to respond to signals but remains difficult to engineer. Here, Southern et al. developed a phage-assisted evolution framework for allosteric protein switches yielding high-p...
nature.com
Nicholas Southern@neuroscinikolai.bsky.social · 4mo ago1/28 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🧵
Thermogenetics: How Proteins Are Controllable by Heat – Modular design strategy makes it possible to precisely control cellular functions through minimal temperature changes www.uni-heidelberg.de/en/newsroom/...
Are you interested in working with a fresh team on cutting edge protein design? We're hiring a Technical Assistant for our protein design team at DKFZ Heidelberg: jobs.dkfz.de/en/jobs/1683... Please share!
Technical Assistant
jobs.dkfz.de
🎉🎉 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.
Modular engineering of thermoresponsive allosteric proteins - Nature Chemical Biology
Thermogenetics enables spatiotemporal control of protein activity using temperature. Now, engineering of a compact, insertable thermoresponsive protein module diversifies the classes of proteins amena...
nature.com
Jan Mathony@jmathony.bsky.social · last yr.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...
Check out the open positions in the new Mari Sepp lab. She is a great scientist and mentor!
Mari Sepp@marisepp.bsky.social · 6mo agoI've started my own lab 🎉 PhD/postdoc positions available - reach out if curious about cerebellum evo-devo and autism spectrum disorders. We’re based at Uni Tartu, Institute of Genomics (home to Estonian Biobank), and funded by @simonsfoundation.org @embo.org, and the Estonian Research Council.
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
With this, the last bit of my PhD at @embl.org is finally out! We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models. Paper: nature.com/articles/s42256-… Code: github.com/mjendrusch/salad Data: zenodo.org/records/14711580 1/🧵
EMBL@embl.org · 11mo ago‘Salad’ – a new AI model from EMBL scientists – offers major improvements in synthetic protein design. Salad is significantly faster than comparable methods, and designing proteins that don't exist in nature can have applications in many scientific fields. www.nature.com/articles/s42...
Work by @bene837.bsky.social @jmathony.bsky.social @dominikniopek.bsky.social @uniheidelberg.bsky.social
Nature Methods@natmethods.nature.com · last yr.ProDomino is a machine learning-based method that predicts domain insertion sites and helps guide the engineering of functional multi-domain proteins. www.nature.com/articles/s41...
Publication alert: Our paper on domain insertion predictions in proteins is now out in @natmethods.nature.com in its final form: rdcu.be/ey7w3 Also check out the nice perspective by @noahholzleitner.bsky.social and @grunewald.bsky.social : www.nature.com/articles/s41...
Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites
Nature Methods - ProDomino is a machine leaning-based method, trained on a semisynthetic domain insertion dataset, to guide the engineering of protein domain recombination.
rdcu.be
I'm very excited to finally share the main work of my PhD! We explored the evolutionary dynamics of gene regulation and expression during gonad development in primates. We cover among others: X chromosome dynamics (incl. in a developing XXY testis), gene regulatory networks and cell type evolution.
Kaessmann Lab@kaessmannlab.bsky.social · last yr.We are delighted to share our new preprint “The evolution of gene regulatory programs controlling gonadal development in primates” www.biorxiv.org/content/10.1...
We are delighted to share our new preprint “The evolution of gene regulatory programs controlling gonadal development in primates” www.biorxiv.org/content/10.1...
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/🧵
Inspired by how nature evolves trigger responsiveness through alternating pressures, we are excited to present POGO-PANCE and RAMPhaGE: Phage-assisted evolution platforms for engineering allosteric protein switches under dynamic selection. Preprint: doi.org/10.1101/2025...
Phage-Assisted Evolution of Allosteric Protein Switches
Allostery, the transmission of locally induced conformational changes to distant functional sites, is a key mechanism for protein regulation. Artificial allosteric effectors enable remote manipulation...
doi.org
New Preprint on phage-assisted evolution and retron-mediated mutagenesis for protein optimization. Many congrats to @neuroscinikolai.bsky.social for this heroic effort and all other lab members involved!
Dominik Niopek@dominikniopek.bsky.social · last yr.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...
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...
doi.org
Hey #RNA world, we are excited to share our RNA design engine #pyFuRNAce - an integrated tool for RNA origami experts and novices alike. Kudos to @monari-luca.bsky.social @floppleton.bsky.social et al! Preprint: www.biorxiv.org/content/10.1... Try it out at pyfurnace.de Feedback welcome!
PyFuRNAce: An integrated design engine for RNA origami
To realize the full potential of RNA nanotechnology and RNA origami, user-friendly design tools are needed. Here, we present pyFuRNAce, an open-source, Python-based software package with a graphical u...
biorxiv.org
Thank you to @yaseminsaplakoglu.bsky.social, who wrote a fantastic article for @quantamagazine.bsky.social about our studies on the evolution of the avian pallium. Love it! shorturl.at/vmTLq
Intelligence Evolved at Least Twice in Vertebrate Animals | Quanta Magazine
Complex neural circuits likely arose independently in birds and mammals, suggesting that vertebrates evolved intelligence multiple times.
shorturl.at
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.
What a week! I defended my PhD on Monday, and now my first first-author paper was published in @science.org. shorturl.at/fvIGZ I am so incredibly grateful to everyone who made this possible! Especially @kaessmannlab.bsky.social and the García-Moreno lab 💛
So excited to announce that our study on the development and evolution of pallial cell types and structures in birds, led by @bassi-z.bsky.social, is now out in @science.org! www.science.org/doi/10.1126/...
Developmental origins and evolution of pallial cell types and structures in birds
Innovations in the pallium likely facilitated the evolution of advanced cognitive abilities in birds. We therefore scrutinized its cellular composition and evolution using cell type atlases from chick...
science.org
Excited to announce our optogenetic transcriptional deactivation toolbox is now out in its final form at Nucleic Acids research: academic.oup.com/nar/advance-....
A modular toolbox for the optogenetic deactivation of transcription
Abstract. Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high
academic.oup.com
I am super excited and grateful to be funded by the BW-Stiftung within the Postdoc Elite Program. Looking forward to bringing exciting new research from the drawing board into the lab. Many thanks to all my amazing colleagues for all the continued collaboration and support!
We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders! www.biorxiv.org/content/10.1...
Interested in allosteric protein switches? Check our ProDomino - our new model for the prediction of domain insertion sites. With ProDomino we engineered several potent inducible proteins including Cas9 and Cas12a variants.
Niopek Lab@niopeklab.bsky.social · 2y agoWe are thrilled to share ProDomino a model for the prediction of domain insertion sites in proteins. Our approach enables the simple and rapid engineering of highly potent switchable proteins, as we exemplify by creating novel inducible variants of Cas9 and Cas12a. www.biorxiv.org/content/10.1...
Multi-modal control of gene editing with inducible anti-CRISPR proteins! Congrats to first authors @lucabrenker.bsky.social, Sabine and Felix.
Niopek Lab@niopeklab.bsky.social · 2y agoNew pre-print from our group reporting engineered, broad-spectrum anti-CRISPR proteins based on AcrIIA5, a type II inhibitor, and AcrVA1, a type V inhibitor, for opto- and chemogenetic control of CRISPR-Cas9 and -Cas12a: www.biorxiv.org/content/10.1... (1/3)
Now out in Nucleic Acids Research: A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins: doi.org/10.1093/nar/... (1/4)
A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins
Abstract. Deep mutational scanning is a powerful method for exploring the mutational fitness landscape of proteins. Its adaptation to anti-CRISPR proteins,
doi.org
New pre-print from our group reporting engineered, broad-spectrum anti-CRISPR proteins based on AcrIIA5, a type II inhibitor, and AcrVA1, a type V inhibitor, for opto- and chemogenetic control of CRISPR-Cas9 and -Cas12a: www.biorxiv.org/content/10.1... (1/3)
A Versatile Anti-CRISPR Platform for Opto- and Chemogenetic Control of CRISPR-Cas9 and Cas12 across a Wide Range of Orthologs
CRISPR-Cas technologies have revolutionized life sciences by enabling programmable genome editing across diverse organisms. Achieving dynamic and precise control over CRISPR-Cas activity with exogenou...
biorxiv.org