Statistical and machine learning methods for spatially resolved transcriptomics data analysis
The recent advancement in spatial transcriptomics technology has enabled multiplexed
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …
Engineering cytokine therapeutics
J Deckers, T Anbergen, AM Hokke, A de Dreu… - Nature Reviews …, 2023 - nature.com
Cytokines have pivotal roles in immunity, making them attractive as therapeutics for a variety
of immune-related disorders. However, the widespread clinical use of cytokines has been …
of immune-related disorders. However, the widespread clinical use of cytokines has been …
High-dimensional single-cell analysis of human natural killer cell heterogeneity
L Rebuffet, JE Melsen, B Escalière… - Nature …, 2024 - nature.com
Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to
microbes and tumors. Historically, their classification hinged on a limited array of surface …
microbes and tumors. Historically, their classification hinged on a limited array of surface …
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data
The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools …
increased interest in the inference of cell-cell communication. Many computational tools …
[HTML][HTML] Non-cell-autonomous cancer progression from chromosomal instability
Chromosomal instability (CIN) is a driver of cancer metastasis,,–, yet the extent to which this
effect depends on the immune system remains unknown. Using ContactTracing—a newly …
effect depends on the immune system remains unknown. Using ContactTracing—a newly …
High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer
Non-small cell lung cancer (NSCLC) is characterized by molecular heterogeneity with
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …
diverse immune cell infiltration patterns, which has been linked to therapy sensitivity and …
Dictionary of immune responses to cytokines at single-cell resolution
Cytokines mediate cell–cell communication in the immune system and represent important
therapeutic targets,–. A myriad of studies have highlighted their central role in immune …
therapeutic targets,–. A myriad of studies have highlighted their central role in immune …
[HTML][HTML] Spatial CRISPR genomics identifies regulators of the tumor microenvironment
While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes,
existing approaches are suboptimal for identifying extracellular gene functions, particularly …
existing approaches are suboptimal for identifying extracellular gene functions, particularly …
[HTML][HTML] Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes
Y Yang, X Chen, J Pan, H Ning, Y Zhang, Y Bo, X Ren… - Cell, 2024 - cell.com
Characterizing the compositional and phenotypic characteristics of tumor-infiltrating B cells
(TIBs) is important for advancing our understanding of their role in cancer development …
(TIBs) is important for advancing our understanding of their role in cancer development …
Supervised discovery of interpretable gene programs from single-cell data
Factor analysis decomposes single-cell gene expression data into a minimal set of gene
programs that correspond to processes executed by cells in a sample. However, matrix …
programs that correspond to processes executed by cells in a sample. However, matrix …