Dominik Niopek

Research Intern - Machine Learning for Biology and Healthcare | Microsoft Careers Research Interns put inquiry and theory into practice. Alongside fellow doctoral candidates and some of the world's best researchers, Research Interns learn, collaborate, and network for life. Researc...

You have until Dec 1 to apply to the bioml PhD research internship!

This is where you apply to work with me,
@alexijie.bsky.social @avapamini.bsky.social @lcrawford.bsky.social or Kristen Severson!

(new) link and some instructions below

apply.careers.microsoft.com/careers/job/...

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

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/...

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.

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...

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...

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...

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/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/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...

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!👏

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?

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

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.

"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...

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.

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...

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...

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

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!

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

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

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

Excited to announce our optogenetic transcriptional deactivation toolbox is now out in its final form at Nucleic Acids research: academic.oup.com/nar/advance-....

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!

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...

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

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...

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 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,

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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