Samantha A. O’Connor

Resolving Immune Lineage and Cell-State Heterogeneity in Human PBMCs via Mass Spectrometry-Based Single-Cell Proteomics

The paper develops a pipeline for protein-level cell annotation in human PBMCs using mass spectrometry-based single-cell proteomics and validates it on unsorted samples.

Multi-omics characterization of IDH-mutant astrocytoma-derived cell lines reveals NOTCH-regulated plastic quiescent astrocyte-like state

The paper establishes and characterizes IDH-mutant astrocytoma cell lines, revealing NOTCH-regulated plasticity between astrocyte-like and oligodendrocyte-like states.

Characterization of quiescent subpopulations and proliferative compartments in glioblastoma

This study characterizes quiescent subpopulations and proliferative compartments in glioblastoma, finding that quiescent cells continuously cycle and lack stable dormant states.

Classifying cell cycle states and a quiescent-like G0 state using single-cell transcriptomics

The paper introduces ccAFv2, a high-resolution cell cycle classifier for scRNA-seq data, which outperforms existing methods and classifies six cell cycle states and a quiescent-like G0 state.

Systematic integration of protein affecting mutations, gene fusions, and copy number alterations into a comprehensive somatic mutational profile

OncoMerge integrates protein-affecting mutations, gene fusions, and copy number alterations to create a unified somatic mutation profile, improving downstream cancer analysis.