Dominik Niopek
@dominikniopek.bsky.social
Science enthusiast. Synbio and Protein Enginnering Researcher. Professor @Heidelberg University. Enjoying drumming, guitar, hiking, biking, reading and, foremost, family & friends. All views are my own
Reposted by Dominik Niopek
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/...
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/...
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...
apply.careers.microsoft.com
November 20, 2025 at 3:30 PM
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/...
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/...
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
August 6, 2025 at 6:20 PM
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/...
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
August 4, 2025 at 11:41 AM
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...
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...
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
June 13, 2025 at 10:13 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Dominik Niopek
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/10.1101/2025...
doi.org
May 3, 2025 at 11:03 AM
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/10.1101/2025...
Reposted by Dominik Niopek
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.
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.
April 1, 2025 at 11:52 AM
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.
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.
Reposted by Dominik Niopek
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!👏
April 22, 2025 at 1:25 PM
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!👏
Reposted by Dominik Niopek
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?
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?
April 21, 2025 at 4:07 PM
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?
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?
Reposted by Dominik Niopek
"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...
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
January 24, 2025 at 6:22 PM
"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...
Front page NYT today, by @kevinroose.com
Gift link www.nytimes.com/2025/01/23/t...
Reposted by Dominik Niopek
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
January 23, 2025 at 6:34 PM
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...
Reposted by Dominik Niopek
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
t.co/vtYlhi8aQm
January 15, 2025 at 4:37 PM
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
t.co/vtYlhi8aQm
Reposted by Dominik Niopek
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
December 17, 2024 at 11:49 AM
We have an open professorship in #synbio / biological engineering in Heidelberg! jobs.zeit.de/jobs/full-pr... Check it out!
Reposted by Dominik Niopek
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
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
December 18, 2024 at 9:06 PM
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
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
Reposted by Dominik Niopek
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
December 16, 2024 at 12:54 PM
Excited to announce our optogenetic transcriptional deactivation toolbox is now out in its final form at Nucleic Acids research: academic.oup.com/nar/advance-....
Reposted by Dominik Niopek
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!
Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!
December 9, 2024 at 2:58 PM
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!
Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!
Reposted by Dominik Niopek
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...
@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...
November 26, 2024 at 2:13 PM
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...
@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...
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...
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
December 5, 2024 at 12:31 PM
Reposted by Dominik Niopek
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)
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...
www.biorxiv.org
November 26, 2024 at 11:34 AM
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)
www.biorxiv.org/content/10.1...
(1/3)
Reposted by Dominik Niopek
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)
(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
November 26, 2024 at 11:30 AM
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)
(1/4)