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Jan Mathony

@jmathony.bsky.social
111 followers 121 following 28 posts

Scientist with a passion for Synbio | Protein engineering | Optogenetics | ML www.niopeklab.de/mathony-lab/

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Reposted by Jan Mathony
Centre for Synthetic Biology @TUDarmstadt @synbio.bsky.social · 31/07/2026
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
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Reposted by Jan Mathony
Nicholas Southern @neuroscinikolai.bsky.social · 05/07/2026
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...
biorxiv.org
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...
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Jan Mathony @jmathony.bsky.social · 26/04/2026
Very nice news & views about our recent study on thermogenetic protein regulation! www.nature.com/articles/s41...
nature.com
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...
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Jan Mathony @jmathony.bsky.social · 15/04/2026
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.
nature.com
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...
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Reposted by Jan Mathony
Universität Heidelberg @uniheidelberg.bsky.social · 04/03/2026
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/...
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Reposted by Jan Mathony
Michael Jendrusch @mjendrusch.bsky.social · 02/03/2026
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!
jobs.dkfz.de
Technical Assistant
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Jan Mathony @jmathony.bsky.social · 12/02/2026
🎉🎉 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.
nature.com
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...
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Jan Mathony @jmathony.bsky.social · 05/02/2026
Check out the open positions in the new Mari Sepp lab. She is a great scientist and mentor!
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Reposted by Jan Mathony
CIBSS – Centre for Integrative Biological Signalling Studies @cibss.bsky.social · 09/01/2026
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
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Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025
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/🧵
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Reposted by Jan Mathony
Nature Methods @natmethods.nature.com · 04/08/2025
Work by @bene837.bsky.social @jmathony.bsky.social @dominikniopek.bsky.social @uniheidelberg.bsky.social
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Jan Mathony @jmathony.bsky.social · 04/08/2025
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...
rdcu.be
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.
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Reposted by Jan Mathony
Nils Trost @trostnils.bsky.social · 20/06/2025
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.
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Reposted by Jan Mathony
Kaessmann Lab @kaessmannlab.bsky.social · 20/06/2025
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...
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Reposted by Jan Mathony
Michael Jendrusch @mjendrusch.bsky.social · 19/06/2025
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/🧵
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Reposted by Jan Mathony
Niopek Lab @niopeklab.bsky.social · 13/06/2025
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...
doi.org
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...
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Jan Mathony @jmathony.bsky.social · 13/06/2025
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!
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Jan Mathony @jmathony.bsky.social · 03/05/2025
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
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Reposted by Jan Mathony
Kerstin Göpfrich @kgoepfrich.bsky.social · 20/04/2025
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!
biorxiv.org
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...
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Reposted by Jan Mathony
Bastienne Zaremba @bassi-z.bsky.social · 07/04/2025
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
shorturl.at
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.
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Jan Mathony @jmathony.bsky.social · 01/04/2025
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.
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Reposted by Jan Mathony
Bastienne Zaremba @bassi-z.bsky.social · 14/02/2025
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 💛
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Kaessmann Lab @kaessmannlab.bsky.social · 13/02/2025
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/...
science.org
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...
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Reposted by Jan Mathony
Niopek Lab @niopeklab.bsky.social · 16/12/2024
Excited to announce our optogenetic transcriptional deactivation toolbox is now out in its final form at Nucleic Acids research: academic.oup.com/nar/advance-....
academic.oup.com
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
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Jan Mathony @jmathony.bsky.social · 09/12/2024
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!
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Reposted by Jan Mathony
Martin Pacesa @martinpacesa.bsky.social · 08/12/2024
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...
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Jan Mathony @jmathony.bsky.social · 05/12/2024
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.
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Jan Mathony @jmathony.bsky.social · 26/11/2024
Multi-modal control of gene editing with inducible anti-CRISPR proteins! Congrats to first authors @lucabrenker.bsky.social, Sabine and Felix.
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Reposted by Jan Mathony
Niopek Lab @niopeklab.bsky.social · 26/11/2024
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)
doi.org
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,
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Reposted by Jan Mathony
Niopek Lab @niopeklab.bsky.social · 26/11/2024
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)
biorxiv.org
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...
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Reposted by Jan Mathony
bioRxiv Synthetic Biology @biorxiv-synthbio.bsky.social · 26/11/2024
A Versatile Anti-CRISPR Platform for Opto- and Chemogenetic Control of CRISPR-Cas9 and Cas12 across a Wide Range of Orthologs www.biorxiv.org/content/10.1101/202…
biorxiv.org
A Versatile Anti-CRISPR Platform for Opto- and Chemogenetic Control of CRISPR-Cas9 and Cas12 across a Wide Range of Orthologs https://www.biorxiv.org/content/10.1101/2024.11.25.625186v1
CRISPR-Cas technologies have revolutionized life sciences by enabling programmable genome editing ac
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Jan Mathony @jmathony.bsky.social · 22/11/2024
Our paper on DMS of anti-CRISPR proteins is out in it's final form Nucleic Acids Research! Many congrats to first authors Tobias and Michael! It was lots of fun to see the story develop. academic.oup.com/nar/advance-...
academic.oup.com
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,
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