Roman A. Zubarev

The paper introduces ThermoTargetMiner, a database that identifies protein targets of lung cancer therapeutics using the PISA assay, revealing novel targets for 77% of tested compounds.

HOLSER improves proteome coverage and depth for structural analysis of protein-ligand interactions and conformational changes.

The paper improves target identification in chemical proteomics by using Fisher's method to aggregate peptide-level data instead of protein-level data.

The paper introduces AFDIP, a chemical proteomics method that identifies drug target binding sites with high structural resolution using digestion rate analysis and MD simulations.

This study demonstrates that Fourier Transform Isotopic Ratio Mass Spectrometry can reliably analyze isotope ratios from less than 10 ng of protein, enabling single-cell-scale stable isotope analysis.

The study uses a modified PISA assay to identify TNF as the antigen of infliximab among 8,000 proteins in activated monocytes, demonstrating its utility for antibody-antigen interaction analysis.

The paper shows that stochastic resonance enhances detection of low-level peptide signals in single-cell proteomics using TMT and a carrier proteome.

The paper introduces KISSE, a statistical framework for species identification using bone collagen tandem mass spectrometry data, which provides species identification and probability estimates.

The paper challenges the traditional stable isotope paradigm by showing that the discrimination factor {Delta} varies with diet and changes sign, proposing a new model for isotope assimilation.

This study examines how human ovarian cortical and medullary cells respond to acute X-ray exposure, finding transcriptomic shifts and impaired cell-cell adhesion.

This study develops and characterizes 3D models of human ovarian primary cells using Biosilk scaffolds, showing they maintain key cell types and form a hypoxic core.

This study investigates trypsin cleavage preferences in native proteins using AFDIP, finding lysine cleavage is more abundant and faster than arginine in native conditions.

The paper introduces OPTI-PISA, a method that automates and reduces sample requirements for drug target identification, demonstrating its effectiveness in cell lysates with sub-microgram samples.

The paper introduces GAPPIS, a method to recover molecular weight information from shotgun proteomics, identifying novel caspase 3 substrates in apoptotic cells.

This study shows that ultralight Caenorhabditis elegans, grown on isotopically depleted bacteria, have shorter lifespans despite faster growth and maturation.

This study simulates traumatic brain injury using a dummy head to generate g-force and shockwave, revealing proteome solubility changes and identifying shockwave as the main cause of irreversible cell damage.

The paper investigates the link between isoaspartate (isoAsp) and Alzheimer's disease by analyzing isoAsp levels and related biomarkers in blood samples from AD patients and healthy controls.