Chen Zhou

Profiling proteome-level amino acid substitutions in Alzheimer's disease brain tissue

This study identifies proteome-level amino acid substitutions in Alzheimer's disease using proteomic datasets and a specialized pipeline, revealing novel substitutions not detectable through genomic or transcriptomic methods.

Amino acid substitutomics: profiling amino acid substitutions at proteomic scale unveils biological implication and escape mechanism in cancer

This study introduces a proteomic approach to identify amino acid substitutions in cancer, revealing novel substitutions and their roles in drug resistance and immune escape.

PIPI-C: A combinatorial optimization framework for identifying post-translational modification crosstalks in mass spectrometry data

PIPI-C identifies PTM crosstalks in mass spectrometry data using a combinatorial optimization framework, revealing upregulated PTM patterns in cancer datasets.

Searching Post-translational Modifications in Cross-linking Mass Spectrometry Data

This study introduces SeaPIC, an XL-MS tool for identifying post-translational modifications in protein-protein interactions and structures, successfully detecting previously undiscovered PTMs.

Exhaustive Cross-linking Search with Protein Feedback

This paper introduces ECL-PF, a method for cleavable XL-MS data analysis that improves sensitivity in detecting protein-protein interactions and structures.

Capturing the Hierarchically Assorted Modules of Protein Interaction in the Organized Nucleome

The paper introduces a pipeline called CHAMPION that uses qXL-MS and MONET modulomics to identify nuclear protein interactions and modules, revealing novel interactors and hormone-specific variants.