Cancer biomarkers have transformed current practices in the oncology clinic. Continued
discovery and validation are crucial for improving early diagnosis, risk stratification, and …

Abstract The Human Proteome Organization (HUPO) launched the Human Proteome Project
(HPP) in 2010, creating an international framework for global collaboration, data sharing …

To the Editor—Here we introduce Philosopher (https://philosopher. nesvilab. org), a free,
open-source, versatile and robust data analysis toolkit designed to bring easy access to a …

We report a comprehensive proteogenomics analysis, including whole-genome sequencing,
RNA sequencing, and proteomics and phosphoproteomics profiling, of 218 tumors across 7 …

Integrated multi-omics evaluation of 823 tumors from advanced renal cell carcinoma (RCC)
patients identifies molecular subsets associated with differential clinical outcomes to …

Introduction: Cytokines are a diverse group of peptides produced by different cell types
including cancer cells and various subpopulations of immune system cells. They exert their …

Reproducible research is the bedrock of experimental science. To enable the deployment of
large-scale proteomics, we assess the reproducibility of mass spectrometry (MS) over time …

Many gene products exhibit great structural heterogeneity because of an array of
modifications. These modifications are not directly encoded in the genomic template but …

Mass spectrometry (MS)-based quantitative proteomics experiments frequently generate
data with missing values, which may profoundly affect downstream analyses. A wide variety …

Loss of the von Hippel–Lindau (VHL) tumor suppressor is a hallmark feature of renal clear
cell carcinoma. VHL inactivation results in the constitutive activation of the hypoxia-inducible …