Jeff E. Mold
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View article: Longitudinal human CD8+ T-cell fate following yellow fever vaccination 3548
Longitudinal human CD8+ T-cell fate following yellow fever vaccination 3548 Open
Description CD8+ T-cells are critical effectors in the immune response against viral infections and cancers. A long-standing question within T-cell immunology concerns the mechanisms that govern which cells give rise to long lived memory C…
View article: Multi-cellular phenotypic dynamics during the progression of breast tumors
Multi-cellular phenotypic dynamics during the progression of breast tumors Open
Summary In cancer, improving diagnostics and therapeutic interventions can benefit from understanding the cellular and phenotypic heterogeneity of the tumor microenvironment (TME). In recent years, the TME has been profiled at an unprecede…
View article: Cell lineage inference from mitochondrial mutations
Cell lineage inference from mitochondrial mutations Open
Tissues and organs develop from single founder cells, which give rise to distinct cell lineages that contribute to regeneration and maintenance of homeostasis in the adult. Tracing the genealogical relationships between individual cells an…
View article: Distinct Tissue‐Dependent Composition and Gene Expression of Human Fetal Innate Lymphoid Cells
Distinct Tissue‐Dependent Composition and Gene Expression of Human Fetal Innate Lymphoid Cells Open
The human fetal immune system starts to develop in the first trimester and likely plays a crucial role in fetal development and maternal‐fetal tolerance. Innate lymphoid cells (ILCs) are the earliest lymphoid cells to arise in the human fe…
View article: CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics
CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics Open
Motivation Copy number variations (CNVs) are common genetic alterations in tumour cells. The delineation of CNVs holds promise for enhancing our comprehension of cancer progression. Moreover, accurate inference of CNVs from single-cell seq…
View article: Distinct tissue-dependent composition and gene expression of human fetal innate lymphoid cells
Distinct tissue-dependent composition and gene expression of human fetal innate lymphoid cells Open
The human fetal immune system starts to develop in the first trimester and likely plays a crucial role in fetal development and maternal-fetal tolerance. Innate lymphoid cells (ILCs) are the earliest lymphoid cells to arise in the human fe…
View article: Clonally heritable gene expression imparts a layer of diversity within cell types
Clonally heritable gene expression imparts a layer of diversity within cell types Open
Cell types can be classified according to shared patterns of transcription. Non-genetic variability among individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. Using high-cove…
View article: Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics
Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics Open
The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method …
View article: Intestinal damage is required for the pro-inflammatory differentiation of commensal CBir1-specific T cells
Intestinal damage is required for the pro-inflammatory differentiation of commensal CBir1-specific T cells Open
Commensal-specific clusters of differentiation (CD)4+ T cells are expanded in patients with inflammatory bowel disease (IBD) compared to healthy individuals. How and where commensal-specific CD4+ T cells get activated is yet to be fully un…
View article: Long-read whole-genome analysis of human single cells
Long-read whole-genome analysis of human single cells Open
Long-read sequencing has dramatically increased our understanding of human genome variation. Here, we demonstrate that long-read technology can give new insights into the genomic architecture of individual cells. Clonally expanded CD8+ T-c…
View article: Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue
Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue Open
The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed Spatial Transcriptomics of VDJ sequences (Spatial VDJ), which maps immunoglobulin and TR antigen rec…
View article: Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue.
Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue. Open
This dataset contains a single zipped folder containing: data scripts needed to reproduce the manuscript entitled "Spatial transcriptomics of T and B cell receptors uncovers lymphocyte clonal dynamics in human tissue", deposited on bioRxiv…
View article: Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics.
Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics. Open
This dataset contains a single zipped folder containing: data scripts needed to reproduce the manuscript entitled "Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics". Each folder is organized by tissue t…
View article: Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics.
Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics. Open
This dataset contains a single zipped folder containing: data scripts needed to reproduce the manuscript entitled "Spatial transcriptomics of B and T cell receptors uncovers lymphocyte clonal dynamics". Each folder is organized by tissue t…
View article: Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues
Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues Open
Spatial and genomic heterogeneity of tumors is the key for cancer progression, treatment, and survival. However, a technology for direct mapping the clones in the tumor tissue based on point mutations is lacking. Here, we propose Tumorosco…
View article: Prostate cancer disease recurrence after radical prostatectomy is associated with <scp>HLA</scp> type and local cytomegalovirus immunity
Prostate cancer disease recurrence after radical prostatectomy is associated with <span>HLA</span> type and local cytomegalovirus immunity Open
Prostate cancer is a heterogeneous disease with a need for new prognostic biomarkers. Human leukocyte antigen (HLA) genes are highly polymorphic genes central to antigen presentation to T‐cells. Two alleles, HLA‐A*02:01 and HLA‐A*24:02, ha…
View article: Clonally heritable gene expression imparts a layer of diversity within cell types
Clonally heritable gene expression imparts a layer of diversity within cell types Open
Cell types can be classified based on shared patterns of transcription. Variability in gene expression between individual cells of the same type has been ascribed to stochastic transcriptional bursting and transient cell states. We asked w…
View article: A biliary immune landscape map of primary sclerosing cholangitis reveals a dominant network of neutrophils and tissue-resident T cells
A biliary immune landscape map of primary sclerosing cholangitis reveals a dominant network of neutrophils and tissue-resident T cells Open
Bile ducts from patients with PSC are enriched in neutrophils and biliary-resident CD8 + T cells and differ in composition from liver tissue.
View article: Long-read whole genome analysis of human single cells
Long-read whole genome analysis of human single cells Open
With long-read sequencing, we have entered an era where individual genomes are routinely assembled to near completion and where complex genetic variation can efficiently be resolved. Here, we demonstrate that long reads can be applied to s…
View article: Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood
Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood Open
Significance Respiratory diseases are leading causes of death worldwide. However, the local immune cell composition in the human lung and individual outliers within the population still remain largely undescribed. We here identify adaptive…
View article: PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data
PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data Open
We propose PhylEx: a clonal-tree reconstruction method that integrates bulk genomics and single-cell transcriptomics data. In addition to the clonal-tree, PhylEx also assigns single-cells to clones, which effectively produce clonal express…
View article: Activation of a neural stem cell transcriptional program in parenchymal astrocytes
Activation of a neural stem cell transcriptional program in parenchymal astrocytes Open
Adult neural stem cells, located in discrete brain regions, generate new neurons throughout life. These stem cells are specialized astrocytes, but astrocytes in other brain regions do not generate neurons under physiological conditions. Af…
View article: Author response: Activation of a neural stem cell transcriptional program in parenchymal astrocytes
Author response: Activation of a neural stem cell transcriptional program in parenchymal astrocytes Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Adult neural stem cells, loca…
View article: Activation of a neural stem cell transcriptional program in parenchymal astrocytes
Activation of a neural stem cell transcriptional program in parenchymal astrocytes Open
Neural stem cells, located in discrete niches in the adult brain, generate new neurons throughout life. These stem cells are specialized astrocytes, but astrocytes in other brain regions do not generate neurons under physiological conditio…