John N. Weinstein

The paper benchmarks nDIA and related proteomics methods, showing nDIA with DIA-NN and Tesorai Search provides high coverage and reliable results in proteomic analysis.

CROCHET is a pipeline for automated analysis of single-cell spatialomic data and creation of visual atlases, supporting diverse data modalities and downstream analyses.

The paper identifies ASX-173 as a potent ASNS inhibitor that enhances the anti-cancer effects of L-asparaginase in leukemia and shows its potential across multiple cancer types.

The paper uses multi-omic mass spectrometry to analyze drug toxicity mechanisms in mice, identifying pathways involved in ASNase toxicity and proposing potential mitigation strategies.

This study creates a spatial proteomic atlas of SBA tumor-immune microenvironment, revealing cell interactions and immune checkpoint patterns linked to patient survival and therapy.

The paper introduces UFP-MS, a fast proteomics method, and applies it to study drug effects on mouse tissues, revealing tissue-specific metabolic changes.

PCA-Plus enhances principal component analysis to better detect, visualize, and quantify batch effects and group differences in multi-omic data.

DeMixSC improves deconvolution accuracy by using single-cell RNA-seq and a benchmark dataset to account for technological discrepancies in complex tissue samples.

This study identifies molecular changes in bladder mucosa that initiate cancer, revealing inflammation's role and mutation patterns linked to early carcinogenesis.

OmicPioneer-sc provides an interactive visualization tool for single-cell sequencing data, integrating dimensionality reduction, heat maps, and pathway modules to aid in cell-type annotation and multi-omic analysis.

The paper provides a user guide to five online tools for exploring and visualizing PCAWG data, demonstrating their integration with external resources to enhance cancer genomics research.

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

This study identifies distinct genomic and molecular features of sarcomatoid bladder cancer, linking EMT dysregulation to aggressive behavior and immune infiltration.

SoS Notebook provides a web-based environment for multi-language data analysis, enabling seamless integration of different scripting languages in bioinformatics workflows.