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Article
Open AccessA community challenge to predict clinical outcomes after immune checkpoint blockade in non-small cell lung cancer
Predictive biomarkers of immune checkpoint inhibitor (ICI) efficacy are currently lacking for non-small cell lung cancer (NSCLC). Here, we describe the results from the Anti–PD-1 Response Prediction DREAM Chal...
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Article
Open AccessHigh-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE
Recent studies have emphasized the importance of single-cell spatial biology, yet available assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here we introduce CytoSPACE,...
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Article
Open AccessMetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment
Recent advances in single-cell RNA sequencing have shown heterogeneous cell types and gene expression states in the non-cancerous cells in tumors. The integration of multiple scRNA-seq datasets across tumors c...
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Article
Open AccessClonal tracing reveals diverse patterns of response to immune checkpoint blockade
Immune checkpoint blockade (ICB) therapy has improved patient survival in a variety of cancers, but only a minority of cancer patients respond. Multiple studies have sought to identify general biomarkers of IC...
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Article
ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells
Programmed DNA recombination in mammalian cells occurs predominantly in a directional manner. While random DNA breaks are typically repaired both by deletion and by inversion at approximately equal proportions...
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Article
Open AccessLarge-scale public data reuse to model immunotherapy response and resistance
Despite growing numbers of immune checkpoint blockade (ICB) trials with available omics data, it remains challenging to evaluate the robustness of ICB response and immune evasion mechanisms comprehensively. To...
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Article
Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute
Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR–Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate...
