Raymond H. Y. Louie
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View article: Expanded CD16+CD56+Granzyme B+ NK like CD8+ T cells an off target effect of bruton’s tyrosine kinase inhibitors in Waldenström macroglobulinemia
Expanded CD16+CD56+Granzyme B+ NK like CD8+ T cells an off target effect of bruton’s tyrosine kinase inhibitors in Waldenström macroglobulinemia Open
View article: Human axillary lymph node T follicular helper (Tfh) and Precursor‐Tfh cells exhibit functional flexibility following seasonal influenza vaccination
Human axillary lymph node T follicular helper (Tfh) and Precursor‐Tfh cells exhibit functional flexibility following seasonal influenza vaccination Open
Objectives CD4 + T cells partitioned into different cell lineages based on transcription factor, cytokine and chemokine expression have defined functions that work cooperatively to ensure optimum operation of the immune system. This study …
View article: Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease
Expanded T cell clones with lymphoma driver somatic mutations in refractory celiac disease Open
Intestinal inflammation continues in a subset of celiac disease (CD) patients despite a gluten-free diet. Here, by applying multiomic single cell analysis to duodenal biopsies, we find low-grade malignancies with lymphoma driver mutations …
View article: CAR+ and CAR- T cells share a differentiation trajectory into an NK-like subset after CD19 CAR-T cell infusion in patients with B cell malignancies
CAR+ and CAR- T cells share a differentiation trajectory into an NK-like subset after CD19 CAR-T cell infusion in patients with B cell malignancies Open
Supplementary Code and Data for Manuscript submitted to Nature Communications. Abstract: Chimeric antigen receptor (CAR) T cell therapy is effective in treating B-cell malignancies, but factors influencing the persistence of functional CAR…
View article: CAR+ and CAR− T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies
CAR+ and CAR− T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies Open
View article: Chimeric Antigen Receptor T Cell Therapy Targeting Epithelial Cell Adhesion Molecule in Gastric Cancer: Mechanisms of Tumor Resistance
Chimeric Antigen Receptor T Cell Therapy Targeting Epithelial Cell Adhesion Molecule in Gastric Cancer: Mechanisms of Tumor Resistance Open
Epithelial cell adhesion molecule (EpCAM) is a tumor-associated antigen that is frequently overexpressed in various carcinomas. We have developed chimeric antigen receptor (CAR) T cells specifically targeting EpCAM for the treatment of gas…
View article: Multi-omic profiling in coeliac disease reveals somatic driver mutations in rogue T cell clones
Multi-omic profiling in coeliac disease reveals somatic driver mutations in rogue T cell clones Open
It has long been proposed that the pathogenesis of human autoimmune diseases may share common origins with lymphoid cancer. However, a major hurdle in understanding the immune pathogenesis of autoimmune diseases is distinguishing self-reac…
View article: CAR+ and CAR− T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion
CAR+ and CAR− T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion Open
Chimeric antigen receptor (CAR) T cells have demonstrable efficacy in treating B-cell malignancies. Factors such as product composition, lymphodepletion and immune reconstitution are known to influence CAR+ T cell survival and persistence,…
View article: P569: Identification of a novel, deep-intronic alteration in KDM6A: How a multi-omics approach ended a 10+ year diagnostic odyssey*
P569: Identification of a novel, deep-intronic alteration in KDM6A: How a multi-omics approach ended a 10+ year diagnostic odyssey* Open
View article: P657: NSD2 duplication results in distinct phenotype and DNA methylation signature
P657: NSD2 duplication results in distinct phenotype and DNA methylation signature Open
View article: P582: Exon-level copy number variations identified by whole genome sequencing in previously undiagnosed patients with rare hereditary diseases
P582: Exon-level copy number variations identified by whole genome sequencing in previously undiagnosed patients with rare hereditary diseases Open
View article: Identification of human progenitors of exhausted CD8+ T cells associated with elevated IFN-γ response in early phase of viral infection
Identification of human progenitors of exhausted CD8+ T cells associated with elevated IFN-γ response in early phase of viral infection Open
T cell exhaustion is a hallmark of hepatitis C virus (HCV) infection and limits protective immunity in chronic viral infections and cancer. Limited knowledge exists of the initial viral and immune dynamics that characterise exhaustion in h…
View article: High activation levels maintained in receptor‐binding domain–specific memory B cells in people with severe coronavirus disease 2019
High activation levels maintained in receptor‐binding domain–specific memory B cells in people with severe coronavirus disease 2019 Open
The long‐term health consequences of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection are still being understood. The molecular and phenotypic properties of SARS‐CoV‐2 antigen–specific T cells suggest a dysfunctional …
View article: Inferring Epistasis from Genetic Time-series Data
Inferring Epistasis from Genetic Time-series Data Open
Epistasis refers to fitness or functional effects of mutations that depend on the sequence background in which these mutations arise. Epistasis is prevalent in nature, including populations of viruses, bacteria, and cancers, and can contri…
View article: CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion
CAR+ and CAR- T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion Open
Chimeric antigen receptor (CAR) T cells have demonstrable efficacy in treating B-cell malignancies. Factors such as product composition, lymphodepletion and immune reconstitution are known to influence functional persistence of CAR+ T cell…
View article: CAR<sup>+</sup> and CAR<sup>-</sup> T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion
CAR<sup>+</sup> and CAR<sup>-</sup> T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion Open
Chimeric antigen receptor (CAR) T cells have demonstrable efficacy in treating B-cell malignancies. Factors such as product composition, lymphodepletion and immune reconstitution are known to influence functional persistence of CAR + T cel…
View article: Single cell multi-omics reveals early elevated function and multiple fates within human progenitor exhausted CD8<sup>+</sup> T cells
Single cell multi-omics reveals early elevated function and multiple fates within human progenitor exhausted CD8<sup>+</sup> T cells Open
T-cell exhaustion is a hallmark of hepatitis C virus (HCV) infection and limits protective immunity in chronic viral infections and cancer. Limited knowledge exists of the initial viral and immune dynamics that characterise exhaustion in h…
View article: Investigation of product-derived lymphoma following infusion of <i>piggyBac</i>-modified CD19 chimeric antigen receptor T cells
Investigation of product-derived lymphoma following infusion of <i>piggyBac</i>-modified CD19 chimeric antigen receptor T cells Open
We performed a phase 1 clinical trial to evaluate outcomes in patients receiving donor-derived CD19-specific chimeric antigen receptor (CAR) T cells for B-cell malignancy that relapsed or persisted after matched related allogeneic hemopoie…
View article: Recent advances in single‐cell multimodal analysis to study immune cells
Recent advances in single‐cell multimodal analysis to study immune cells Open
Recent advances in single‐cell technologies have enabled the profiling of the genome, epigenome, transcriptome and proteome, along with temporal and spatial information of individual cells. These technologies have provided unique opportuni…
View article: MPL resolves genetic linkage in fitness inference from complex evolutionary histories
MPL resolves genetic linkage in fitness inference from complex evolutionary histories Open
View article: Data accompanying the GitHub repository bartonlab/paper-MPL-inference
Data accompanying the GitHub repository bartonlab/paper-MPL-inference Open
This dataset contains data from simulations and analysis of within-host HIV-1 evolution that accompany the GitHub repository bartonlab/paper-MPL-inference. The GitHub repository contains code and data for reproducing results described in t…
View article: Data accompanying the GitHub repository bartonlab/paper-MPL-inference
Data accompanying the GitHub repository bartonlab/paper-MPL-inference Open
This dataset contains data from simulations and analysis of within-host HIV-1 evolution that accompany the GitHub repository bartonlab/paper-MPL-inference. The GitHub repository contains code and data for reproducing results described in t…
View article: Data accompanying the GitHub repository bartonlab/paper-MPL-inference
Data accompanying the GitHub repository bartonlab/paper-MPL-inference Open
This dataset contains data from simulations and analysis of within-host HIV-1 evolution that accompany the GitHub repository bartonlab/paper-MPL-inference. The GitHub repository contains code and data for reproducing results described in t…
View article: MPF–BML: a standalone GUI-based package for maximum entropy model inference
MPF–BML: a standalone GUI-based package for maximum entropy model inference Open
Summary Learning underlying correlation patterns in data is a central problem across scientific fields. Maximum entropy models present an important class of statistical approaches for addressing this problem. However, accurately and effici…
View article: Resolving genetic linkage reveals patterns of selection in HIV-1 evolution
Resolving genetic linkage reveals patterns of selection in HIV-1 evolution Open
Identifying the genetic drivers of adaptation is a necessary step in understanding the dynamics of rapidly evolving pathogens and cancer. However, signals of selection are obscured by the complex, stochastic nature of evolution. Pervasive …
View article: Data accompanying the GitHub repository bartonlab/paper-MPL-inference
Data accompanying the GitHub repository bartonlab/paper-MPL-inference Open
This dataset contains data from simulations and analysis of within-host HIV-1 evolution that accompany the GitHub repository bartonlab/paper-MPL-inference. The GitHub repository contains code and data for reproducing results described in t…
View article: Identifying immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them
Identifying immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them Open
View article: Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies
Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies Open
Significance An effective vaccine for HIV is still not available, although recent hope has emerged through the discovery of antibodies capable of neutralizing diverse HIV strains. Nonetheless, there exist mutational pathways through which …
View article: Analysis and Design of Multiple-Antenna Cognitive Radios With Multiple Primary User Signals
Analysis and Design of Multiple-Antenna Cognitive Radios With Multiple Primary User Signals Open
We consider multiple-antenna signal detection of primary user transmission\nsignals by a secondary user receiver in cognitive radio networks. The optimal\ndetector is analyzed for the scenario where the number of primary user signals\nis n…