M. Grace Gordon
YOU?
Author Swipe
View article: Determining gene specificity from multivariate single-cell RNA sequencing data
Determining gene specificity from multivariate single-cell RNA sequencing data Open
An important application of single-cell genomics experiments is to identify genes specific to biological categories or experimental conditions. Although numerous approaches have been proposed to identify such genes, we consider an axiomati…
View article: Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia
Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia Open
View article: Decoding sequence determinants of gene expression in diverse cellular and disease states
Decoding sequence determinants of gene expression in diverse cellular and disease states Open
Sequence-to-function models that predict gene expression from genomic DNA sequence have proven valuable for many biological tasks, including understanding cis-regulatory syntax and interpreting non-coding genetic variants. However, current…
View article: Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19
Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19 Open
Dexamethasone is the standard of care for critically ill patients with COVID-19, but the mechanisms by which it decreases mortality and its immunological effects in this setting are not understood. Here we perform bulk and single-cell RNA …
View article: Genetic variants associated with cell-type-specific intra-individual gene expression variability reveal new mechanisms of genome regulation
Genetic variants associated with cell-type-specific intra-individual gene expression variability reveal new mechanisms of genome regulation Open
Gene expression levels can vary substantially across cells, even in a seemingly homogeneous cell population. Identifying the relationships between genetic variation and gene expression is critical for understanding the mechanisms of genome…
View article: SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models
SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models Open
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-spe…
View article: Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models
Uncovering context-specific genetic-regulation of gene expression from single-cell RNA-sequencing using latent-factor models Open
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsupervised discovery of context-spe…
View article: Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure
Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure Open
The host’s gene expression and gene regulatory response to pathogen exposure can be influenced by a combination of the host’s genetic background, the type of and exposure time to pathogens. Here we provide a detailed dissection of this usi…
View article: Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus
Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus Open
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (1…
View article: Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals
Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals Open
Summary Tissue- and organism-level biological processes often involve coordinated action of multiple distinct cell types. Current computational methods for the analysis of single-cell RNA-sequencing (scRNA-seq) data, however, are not desig…
View article: FastGxC: Fast and Powerful Context-Specific eQTL Mapping in Bulk and Single-Cell Data
FastGxC: Fast and Powerful Context-Specific eQTL Mapping in Bulk and Single-Cell Data Open
Context-specific eQTLs mediate genetic risk for complex diseases. However, limitations in current methods for identifying these eQTLs have hindered their comprehensive characterization and downstream interpretation of disease-associated va…
View article: Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements
Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements Open
View article: Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding
Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding Open
Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing prote…
View article: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements
lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements Open
View article: Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding
Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding Open
Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, in part due to the challenge of probing protein stru…
View article: Healthy Control Recruitment and Enrollment v4
Healthy Control Recruitment and Enrollment v4 Open
The Immune Cell Census aims to collect expression data from 1000 blood samples collected from healthy individuals. This protocol outlines our inclusion/exclusion criteria and enrollment process.
View article: Participant Recruitment and Enrollment v1
Participant Recruitment and Enrollment v1 Open
The Immune Cell Census aims to collect expression data from 1000 blood samples collected from healthy individuals. This protocol outlines our inclusion/exclusion criteria and enrollment process.
View article: A suite of automated sequence analyses reduces the number of candidate deleterious variants and reveals a difference between probands and unaffected siblings
A suite of automated sequence analyses reduces the number of candidate deleterious variants and reveals a difference between probands and unaffected siblings Open
View article: Genetic determinants of co-accessible chromatin regions in activated T cells across humans
Genetic determinants of co-accessible chromatin regions in activated T cells across humans Open
View article: Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in Drosophila
Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in Drosophila Open