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Dominik Niopek @dominikniopek.bsky.social · Aug 6

Our work on opto- and chemogenetic control of broad-spectrum anti-CRISPR proteins is now out in Nucleic Acids Research: academic.oup.com/nar/article/...

A versatile anti-CRISPR platform for opto- and chemogenetic control of CRISPR-Cas9 and Cas12 across a wide range of orthologs

Abstract. CRISPR-Cas technologies have revolutionized life sciences by enabling programmable genome editing across diverse organisms. Achieving dynamic and

academic.oup.com

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Dominik Niopek @dominikniopek.bsky.social · Aug 4

Our work on rationally engineering allosteric protein switches is now out in Nature Methods: www.nature.com/articles/s41... Thanks a lot to @grunewald.bsky.social and @noahholzleitner.bsky.social for the comprehensive news and views: 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.

www.nature.com

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Dominik Niopek @dominikniopek.bsky.social · Jun 13

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...

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...

www.biorxiv.org

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Dominik Niopek @dominikniopek.bsky.social · May 5

www.biorxiv.org/content/10.1...

Modular Engineering of Thermo-Responsive Allosteric Proteins

Thermogenetics enables non-invasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membra...

www.biorxiv.org

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Dominik Niopek @dominikniopek.bsky.social · May 5

www.biorxiv.org/content/10.1...

Modular Engineering of Thermo-Responsive Allosteric Proteins

Thermogenetics enables non-invasive spatiotemporal control over protein activity in living cells and tissues, yet its applications have largely been restricted to transcriptional regulation and membra...

www.biorxiv.org

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Reposted by Dominik Niopek

Jan Mathony @jmathony.bsky.social · May 3

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 Dominik Niopek

Jan Mathony @jmathony.bsky.social · Apr 1

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 Dominik Niopek

CeMM @cemm.oeaw.ac.at · Apr 22

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!👏

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Reposted by Dominik Niopek

jared toettcher @toettch.bsky.social · Apr 21

I'd like to share a little bit of happy lab news in these chaotic times: a new preprint, driven by the brilliant Qinhao Cao!
www.biorxiv.org/content/10.1...
We address a big challenge in synbio: If you give me a protein "X", how can I give you a version of X whose activity is controlled by a kinase?

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Dominik Niopek @dominikniopek.bsky.social · Feb 1

I really enjoyed it. That was a fantastic meeting. See you soon in HD @hellmichgroup.bsky.social

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Reposted by Dominik Niopek

Eric Topol @erictopol.bsky.social · Jan 24

"Humanity's Last Exam" (formerly "Humanity's Last Stand")
Front page NYT today, by @kevinroose.com
Gift link www.nytimes.com/2025/01/23/t...

A Test So Hard No AI System Can Pass It — Yet (Gift Article)

The creators of a new test called “Humanity’s Last Exam” argue we may soon lose the ability to create tests hard enough for A.I. models.

www.nytimes.com

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Dominik Niopek @dominikniopek.bsky.social · Jan 24

Great to see that thermogenetics starts to take off. Very exciting future ahead for the field, indeed. Congrats @bugajlab.bsky.social for laying important groundwork for others to build on.

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Reposted by Dominik Niopek

Rita Strack @ritastrack.bsky.social · Jan 23

Every once in a while we publish a paper that moves a whole field forward. I think that's the case for this one from the Bugaj lab, where they describe proteins for THERMOGENETIC control of cellular behavior. www.nature.com/articles/s41...

A temperature-inducible protein module for control of mammalian cell fate - Nature Methods

The Melt (Membrane localization using temperature) protein translocates to the plasma membrane upon temperature shift. Melt variants with a range of switching temperatures enable straightforward therm...

www.nature.com

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Reposted by Dominik Niopek

Arne Schneuing @rne.bsky.social · Jan 15

Our paper on computational design of chemically induced protein interactions is out in @natureportfolio.bsky.social. Big thanks to all co-authors, especially Anthony Marchand, Stephen Buckley and Bruno Correia!

t.co/vtYlhi8aQm

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Reposted by Dominik Niopek

Kerstin Göpfrich @kgoepfrich.bsky.social · Dec 17

We have an open professorship in #synbio / biological engineering in Heidelberg! jobs.zeit.de/jobs/full-pr... Check it out!

Full Professorship (W3) in Molecular Biology (f/m/d) with a Focus on Biological Engineering - Universität Heidelberg

Universität Heidelberg bietet Stelle als Full Professorship (W3) in Molecular Biology (f/m/d) with a Focus on Biological Engineering in Heidelberg - jetzt bewerben!

jobs.zeit.de

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Reposted by Dominik Niopek

Noelia Ferruz @noeliaferruz.bsky.social · Dec 18

Protein language models excel at generating functional yet remarkably diverse artificial sequences.

They however fail to naturally sample rare datapoints, like very high activities.

In our new preprint, we show that RL can solve this without the need for additional data:

arxiv.org/abs/2412.12979

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Reposted by Dominik Niopek

Niopek Lab @niopeklab.bsky.social · Dec 16

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

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Reposted by Dominik Niopek

Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · Dec 9

We trained a model to co-generate protein sequence and structure by working in the ESMFold latent space, which encodes both. PLAID only requires sequences for training but generates all-atom structures!

Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!

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Reposted by Dominik Niopek

Julian Grünewald @grunewald.bsky.social · Nov 26

Very excited about the first preprint from our lab at TUM! This is a fun gene & cell therapy collaboration led by
@schmidts.bsky.social's lab. We use generative #AI
to design new #CARTcell therapies. Check out Andrea's thread & thanks to the whole team! www.biorxiv.org/content/10.1...

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Dominik Niopek @dominikniopek.bsky.social · Dec 5

Congratulations to first author @bene837.bsky.social, co-senior author @jmathony.bsky.social and all co-authors for making this exciting project happen! Comments are highly appreciated

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Dominik Niopek @dominikniopek.bsky.social · Dec 5

Niopek Lab @niopeklab.bsky.social · Dec 5

We 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...

Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites

Domain insertion engineering is a powerful approach to juxtapose otherwise separate biological functions, resulting in proteins with new-to-nature activities. A prominent example are switchable protei...

www.biorxiv.org

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Reposted by Dominik Niopek

Niopek Lab @niopeklab.bsky.social · Nov 26

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...

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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...

www.biorxiv.org

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Reposted by Dominik Niopek

Niopek Lab @niopeklab.bsky.social · Nov 26

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/...

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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

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