Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023‏ - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Decoding the tumor microenvironment with spatial technologies

LA Walsh, DF Quail - Nature immunology, 2023‏ - nature.com
Visualization of the cellular heterogeneity and spatial architecture of the tumor
microenvironment (TME) is becoming increasingly important to understand mechanisms of …

BANKSY unifies cell ty** and tissue domain segmentation for scalable spatial omics data analysis

V Singhal, N Chou, J Lee, Y Yue, J Liu, WK Chock… - Nature …, 2024‏ - nature.com
Spatial omics data are clustered to define both cell types and tissue domains. We present
Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an …

CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data

CZI Cell Science Program, S Abdulla… - Nucleic Acids …, 2025‏ - academic.oup.com
Hundreds of millions of single cells have been analyzed using high-throughput
transcriptomic methods. The cumulative knowledge within these datasets provides an …

An allosteric pan-TEAD inhibitor blocks oncogenic YAP/TAZ signaling and overcomes KRAS G12C inhibitor resistance

TJ Hagenbeek, JR Zbieg, M Hafner, R Mroue… - Nature Cancer, 2023‏ - nature.com
The Hippo pathway is a key growth control pathway that is conserved across species. The
downstream effectors of the Hippo pathway, YAP (Yes-associated protein) and TAZ …

Doublet identification in single-cell sequencing data using scDblFinder

PL Germain, A Lun, CG Meixide, W Macnair… - …, 2022‏ - pmc.ncbi.nlm.nih.gov
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A
number of strategies have therefore been proposed to detect them. Building on the strengths …

Intraventricular B7-H3 CAR T cells for diffuse intrinsic pontine glioma: preliminary first-in-human bioactivity and safety

NA Vitanza, AL Wilson, W Huang, K Seidel… - Cancer …, 2023‏ - aacrjournals.org
Diffuse intrinsic pontine glioma (DIPG) remains a fatal brainstem tumor demanding
innovative therapies. As B7-H3 (CD276) is expressed on central nervous system (CNS) …

[HTML][HTML] Astrocytes and oligodendrocytes undergo subtype-specific transcriptional changes in Alzheimer's disease

JS Sadick, MR O'Dea, P Hasel, T Dykstra, A Faustin… - Neuron, 2022‏ - cell.com
Resolving glial contributions to Alzheimer's disease (AD) is necessary because changes in
neuronal function, such as reduced synaptic density, altered electrophysiological properties …

Spatial transcriptomics at subspot resolution with BayesSpace

E Zhao, MR Stone, X Ren, J Guenthoer… - Nature …, 2021‏ - nature.com
Recent spatial gene expression technologies enable comprehensive measurement of
transcriptomic profiles while retaining spatial context. However, existing analysis methods …

LAG-3 and PD-1 synergize on CD8+ T cells to drive T cell exhaustion and hinder autocrine IFN-γ-dependent anti-tumor immunity

LP Andrews, SC Butler, J Cui, AR Cillo, C Cardello… - Cell, 2024‏ - cell.com
Overcoming immune-mediated resistance to PD-1 blockade remains a major clinical
challenge. Enhanced efficacy has been demonstrated in melanoma patients with combined …