Pre-Prints Archives - Shalek Lab

Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment

Yeo et al.,
bioRxiv,
2024

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

Zhu et al.,
bioRxiv,
2024

Glycan-costumed virus-like particles promote type 1 anti-tumor immunity

Lensch et al.,
biorxiv,
2024

Chronic metabolic stress drives developmental programs and loss of tissue functions in non-transformed liver that mirror tumor states and stratify survival

Tzouanas et al.,
bioRxiv,
2023

scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with clinical malaria

Morang’a et al.,
medRxiv,
2023

Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection

Wilk et al.,
bioRxiv,
2023

Compressed phenotypic screens for complex multicellular models and high-content assays

Mead et al.,
bioRxiv,
2023

Clinical implementation of single-cell RNA sequencing using liver fine needle aspirate tissue sampling and centralized processing captures compartment specific immuno-diversity

Genshaft et al.,
bioRxiv,
2021

A Treatment-Naive Cellular Atlas of Pediatric Crohn's Disease Predicts Disease Severity and Therapeutic Response

Zheng et al.,
bioRxiv,
2021

Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease

Kummerlowe et al.,
bioRxiv,
2021

A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

Delorey et al.,
bioRxiv,
2021

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19

Ziegler et al.,
bioRxiv,
2021

Single cell profiling of COVID-19 patients: an international data resource from multiple tissues

Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia et al.,
medRxiv,
2020

Single cell and spatial transcriptomics defines the cellular architecture of the antimicrobial response network in human leprosy granulomas

Ma et al.,
bioRxiv,
2020

Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells

Pae et al.,
bioRxiv,
2020

Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control

Gideon et al.,
bioRxiv,
2020

The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer

Raghavan et al.,
bioRxiv,
2020

Single-cell profiling of Ebola virus infection in vivo reveals viral and host transcriptional dynamics

Kotliar et al.,
bioRxiv,
2020

Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease

Bassler et al.,
bioRxiv,
2020

High-throughput organoid screening enables engineering of intestinal epithelial composition

Mead et al.,
bioRxiv,
2020

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Muus et al.,
bioRxiv,
2020

Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

Cao et al.,
bioRxiv,
2020

SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues

Ziegler et al.,
SSRN,
2020

Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes

Genshaft et al.,
bioRxiv,
2020

Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes

Huang et al.,
bioRxiv,
2019

Highly efficient, massively-parallel single-cell RNA-Seq reveals cellular states and molecular features of human skin pathology

Hughes T.K. et al.,
bioRxiv,
2019

Identification of a Master Regulator of Differentiation in Toxoplasma

Waldman B.S. et al.,
bioRxiv,
2019

Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection

Kazer S.W. et al.,
bioRxiv,
2019

Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis

Smillie et al.,
BioRxiv,
2018

Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity

Jose Ordovas-Montanes et al.,
bioRxiv,
2017

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