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Hello World πŸ‘¨πŸΎβ€πŸ”¬πŸ‘©πŸΎβ€πŸ”¬

Our lab employs genomics tools to understand, diagnose and treat pulmonary disease such as asthma, lung cancer and infectious diseases, including the novel coronavirus.

We have developed a number of techniques to study the molecular profiles of circulating and airway immune cells from patients with asthma and other diseases, using fewer cells than previously possible.

We carry a large-scale effort to map epigenomic modifications in more than a dozen different types of human immune cells from normal individuals to understand how epigenetic variations cause susceptibility to disease. For many human diseases, large-scale genomic studies have identified common genetic variants that occur more frequently in people with cardiovascular, autoimmune, inflammatory and infectious diseases, diabetes and asthma than in those without these diseases. However, it has been difficult to pinpoint which genetic changes are truly relevant to disease, or in what specific cell types the genetic variation has the largest effect on one’s health. Mapping the epigenome will enable scientists to zoom in on those genes with the greatest likelihood to contribute to disease, and the cell types in which they act, and therefore will help identify novel therapeutic targets.

⚑ Fun facts:

πŸ“š Highlighted publications:

  • Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants Nature Genetics
  • Imbalance of regulatory and cytotoxic SARS-CoV-2-reactive CD4^[+] T cells in COVID-19 Cell
  • Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma Science Immunology
  • Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer JEM
  • Single-cell eQTL analysis of activated T cell subsets reveals activation and cell type-dependent effects of disease-risk variants Science Immunology
  • Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression Cell

πŸ“« Please feel free to reach us at our GitHub email. Or any of the lab members here. Contributors to this account are:

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Vijay Lab's Projects

asthma_airways_2023 icon asthma_airways_2023

This repository contains the scripts used to analyzed our asthma airways bulk and single-cell data.

covid19_2020 icon covid19_2020

This repository contains scripts used for the analysis of our data and to generate figures in our work titled "Single-cell transcriptomic analysis of SARS-CoV-2 reactive CD4+ T cells"

covid19_2022b icon covid19_2022b

Final version of the code used to pre-process the raw data and create figures and tables for the first version of the manuscript.

dgea icon dgea

Differential expression analyses infrastructure

handy_functions icon handy_functions

This repository contains the most used functions across projects and tasks in the Vijay Lab

hdm_2019 icon hdm_2019

This repository contains scripts used to generate figures in our work titled "Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma"

migec icon migec

MIGEC pipeline for bulk TCR data preprocessing.

pi3kd_2022 icon pi3kd_2022

This repository contains scripts to perform the data analysis of our PI3Kd paper.

project_guides icon project_guides

We place the steps a project had to follow for reproducibility purposes.

scrublet icon scrublet

Detect doublets in single-cell RNA-seq data

tfr_2021 icon tfr_2021

This repository contains scripts used to analyse and create figures for our TFR paper data

uc_2024 icon uc_2024

Final version of the code used to pre-process the raw data and create figures and tables for the manuscript titled "Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans." by Yingcong Li, et al.

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