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Dimensionality reduction for visualizing single-cell data using UMAP
TLDR
Comparing the performance of UMAP with five other tools, it is found that UMAP provides the fastest run times, highest reproducibility and the most meaningful organization of cell clusters. Expand
TCR–peptide–MHC interactions in situ show accelerated kinetics and increased affinity
TLDR
It is shown that synaptic TCR–pMHC binding dynamics differ significantly from TCR’s binding in solution, and TCR affinity for pMHC was significantly elevated as the result of a large (about 100-fold) increase in the association rate, a likely consequence of complementary molecular orientation and clustering. Expand
Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species
TLDR
A universal toolbox for the automated identification of DCs through unsupervised analysis of conventional flow cytometry and mass cytometry data obtained from multiple mouse, macaque, and human tissues is provided and validated. Expand
Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates
TLDR
It is shown that human lung and colorectal cancer CD8+ TILs can not only be specific for tumour antigens, but also recognize a wide range of epitopes unrelated to cancer (such as those from Epstein–Barr virus, human cytomegalovirus or influenza virus). Expand
Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow
TLDR
This work found that transcriptional signatures of the cDC1 and cDC2 lineages became evident at the single-cell level from the CDP stage, and identified Siglec-H and Ly6C as lineage markers that distinguished pre-DC subpopulations committed to the c DC1 lineage (SigleC-H−Ly6C− pre- DCs) or c DC2 lineage (CDC2 lineage). Expand
Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline
TLDR
Cytofkit, a new Bioconductor package, which integrates both state-of-the-art bioinformatics methods and in-house novel algorithms to offer a comprehensive toolset for mass cytometry data analysis, is presented. Expand
Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1β Complex Reveal Specific Protein-Protein and Protein-Ca2+ Interactions
TLDR
Structural-based mutations of neuroligin-1 at the interface disrupt binding to neurexin- 1 beta, but not the folding of neurodegeneration, and the validity of the binding interface of the neuroligIn-1/neurex in-1 beta complex is confirmed. Expand
Mapping the human DC lineage through the integration of high-dimensional techniques
TLDR
Two unbiased high-dimensional technologies are employed to characterize the human DC lineage from bone marrow to blood and provide new markers that can be used to identify unambiguously pre-DC from pDC, including CD33, CX3CR1, CD2, CD5, and CD327. Expand
High-dimensional analysis of the murine myeloid cell system
TLDR
A 38-antibody panel for mass cytometry was developed and used dimensionality reduction with machine learning–aided cluster analysis to build a composite of murine (mouse) myeloid cells in the steady state across lymphoid and nonlymphoid tissues, and variations in the monocyte and innate lymphoid cell compartment that were unexpected were identified. Expand
Parallel T-cell cloning and deep sequencing of human MAIT cells reveal stable oligoclonal TCRβ repertoire.
TLDR
Human MAIT cells are remarkably oligoclonal in both the blood and liver, display high inter-individual homology and exhibit a restricted length CDR3β domain of the TCRVβ chain, thus suggesting important protective and immunoregulatory functions of these lymphocytes. Expand
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