Dominik Niopek

This paper computationally designs light-responsive proteins that undergo conformational changes upon light activation, enabling precise control of biological functions.

The paper inserts bulky domains into a CRISPR adenine base editor to narrow its editing window and reduce off-target effects.

This paper develops a phage-assisted evolution platform to engineer allosteric protein switches, achieving near-binary optogenetic switches with high dynamic range.

This paper engineers thermo-responsive allosteric proteins using temperature-sensitive domains, enabling precise control of protein activity in both bacterial and mammalian systems.

This paper develops an Fc-SPINK1 fusion protein that reduces pancreatic inflammation in mice by extending its half-life and inhibiting trypsin activity.

This paper introduces ProDomino, a machine learning tool for predicting domain insertion sites in proteins, validated experimentally in E. coli and human cells to create opto- and chemogenetic switches.

The paper introduces LOOMINA, an optogenetic system that deactivates transcriptional activation in response to blue light, offering high adaptability and compatibility with various effector proteins.

This paper develops a versatile platform for optogenetic and chemogenetic control of CRISPR-Cas9 and Cas12 across multiple orthologs using engineered anti-CRISPR proteins.

The paper develops a deep mutational scanning pipeline for anti-CRISPR proteins in E. coli, revealing their mutational tolerance and redundancy, and validates findings in mammalian cells.

This study uses time-resolved RNA sequencing and mathematical modeling to analyze SARS-CoV-2 host cell interactions, revealing transcriptional dynamics and identifying druggable host pathways.

This paper introduces an optogenetic tool to control NmeCas9 activity using a light-switchable anti-CRISPR protein, enabling precise genome editing in mammalian cells.

The paper designs improved anti-CRISPR proteins with enhanced inhibition potency and expanded specificity through structure-based engineering.

This paper develops a cell-specific CRISPR/Cas9 activation system using miRNA-regulated anti-CRISPR proteins, demonstrating targeted gene activation in liver and muscle cells.