Bernhard Küster

This study investigates the role of PIMREG in DNA damage response in GBM cells, finding that its loss impairs double-strand break signaling and repair.

This study shows brassinosteroids repress plant immunity by inducing DNA methylation and altering splicing of immune receptor genes through bHLH transcription factors.

The paper identifies CEM198 as a TTL binder through chemoproteomics, showing it disrupts microtubule dynamics via dual mechanisms in different cell lines.

The paper generates an organ-resolved phosphoproteome map from FFPE rat tissues, showing it preserves signaling biology and enables kinase activity inference.

TOPAS converts phosphoproteomic data into patient-specific reports for molecular tumor boards, focusing on clinically relevant signaling and therapeutic targets.

This study uses pan-cancer phosphoproteomics to identify therapeutic targets and improve precision oncology by analyzing 1,998 tumor samples and developing new scores for kinase activity and immune response.

This study uses multi-omics approaches to show that barley responds to Fusarium infection by upregulating aromatic amino acid-derived defense compounds.

This study shows that high-speed mass spectrometers reduce performance differences between DDA and DIA proteomics, but current LC-MS methods still lack comprehensive proteome coverage.

GAP-MS improves gene prediction accuracy in plant genomes by integrating mass spectrometry evidence, identifying hundreds of previously unannotated protein-coding loci.

This paper introduces a method using high-intensity longwave UV light to rapidly perform in-cell photo-crosslinking with minimal photodamage, enabling fast analysis of biomolecular interactions.

The paper develops a chemical proteomics workflow to profile protein citrullination dynamics, achieving high sensitivity and throughput in detecting citrullinated peptides across biological systems.

The paper identifies inhibitor-induced kinase destabilization as a common phenomenon and reveals that it occurs through endogenous proteolytic mechanisms rather than classical ubiquitination.

The paper develops a method to identify and validate kinase-substrate relationships using phosphoproteomics data and applies it to estimate kinase activity in cancer biopsies.

This paper introduces Prosit-PTM, a deep learning model for PTM discovery that improves zero-shot prediction using a synthetic dataset and chemically-informed encoding.

The paper introduces pepR-MS and SALT to map protein-RNA interfaces at single-amino acid and nucleotide resolution, identifying over 34,000 crosslinks in breast cancer cells.

The paper uses chemical proteomics to analyze KRAS inhibitor effects on signaling networks in cancer cells, revealing cell-specific responses and phosphorylation changes.

This study identifies RACB interaction partners in barley-Bh pathosystem and shows their roles in disease resistance or susceptibility through lipid interactions.

The paper quantifies proteins directly interacting with DNA in human cells and identifies key transcription factors and DNA damage proteins in response to treatments.

CHIMERYS deconvolves chimeric spectra in proteomic data, enabling unified analysis across DDA, DIA, and PRM experiments by accurately identifying and quantifying multiple peptides per spectrum.

The paper evaluates proteome analysis performance across different chromatographic flow rates and shows that all are suitable for high-quality analysis, with capLC being a robust alternative to nanoLC.

This study identifies KIPK and KIPKL1 as regulators that suppress overbending during hypocotyl gravitropic growth by modulating ARK kinesins and cortical microtubules.

This study identifies ATR inhibitors as synergistic with gemcitabine in killing PDAC cells by blocking the DNA damage response pathway.

PTMNavigator visualizes differentially regulated PTMs in cellular pathways using phosphoproteomics data to enhance pathway enrichment analysis and drug response visualization.

This study shows that spermidine supplementation improves depression symptoms by enhancing autophagy and correcting polyamine imbalances in both humans and mice.

The paper profiles proteomes from 1,220 FFPE tumors across six cancers, identifies a new normalization method, and reports a comprehensive pan-cancer proteome resource.

The paper uses proteomics to identify secreted markers linked to drug-induced liver injury and adverse drug reactions by analyzing the secretome of hepatocytes exposed to various drugs.

This study quantifies the transport properties of canonical PIN-FORMED proteins and shows the loop domain's role in auxin transport beyond activation.

This study identifies HMGA2 as a master regulator of mutant RAS-driven gene expression by analyzing time-resolved transcriptome and proteome changes in epithelial cells.

The study identifies the role of Clade IB ZmRALF2/3 in regulating cell wall integrity during maize pollen tube growth through interactions with receptor kinases, co-receptors, and cell wall proteins.

CurveCurator assesses and classifies dose-response curve significance using a recalibrated F-statistic and provides p-values and false discovery rates for improved analysis.