Infectious Disease Archives - Shalek Lab

A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients

Pita-Juarez et al.,
Genome Biology,
2025

Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity

Peters et al.,
biorxiv,
2024

Intrahepatic plasma cells, but not atypical memoryB cells, associate with clinical phases of chronichepatitis B

Osmani et al.,
European Journal of Immunology,
2024

Tobacco smoke exposure recruits inflammatory airspace monocytes that establish permissive lung niches for Mycobacterium tuberculosis

Corleis et al.,
Science Translational Medicine,
2023

Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses

Normandin et al.,
Cell Genomics,
2023

Identification of drug candidates targeting monocyte reprogramming in people living with HIV

Knoll et al.,
Frontiers in Immunology,
2023

CD8+ lymphocytes are critical for early control of tuberculosis in macaques

Winchell et al.,
Journal of Experimental Medicine,
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

Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity

Bui et al.,
Nature Communications,
2023

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Bernardes et al.,
Immunity,
2023

Myocyte-Specific Upregulation of ACE2 in Cardiovascular Disease: Implications for SARS-CoV-2–Mediated Myocarditis

Tucker et al.,
Circulation,
2023

Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)

Jaiswal et al.,
BMC Genomics,
2023

HIV specific CD8+ TRM-like cells in tonsils express exhaustive signatures in the absence of natural HIV control

Fardoos et al.,
Frontiers in Immunology,
2023

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

Kummerlowe et al.,
Science Translational Medicine,
2022

Multimodal profiling of lung granulomas in macaques reveals cellular correlates of tuberculosis control

Gideon et al.,
Immunity,
2022

A single-cell liver atlas of Plasmodium vivax infection

Mancio-Silva et al.,
Cell Host & Microbe,
2022

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

Aggregated Mycobacterium tuberculosis Enhances the Inflammatory Response

Rodel et al.,
Frontiers in Microbiology,
2021

Allelic variation in class I HLA determines CD8+ T cell repertoire shape and cross-reactive memory responses to SARS-CoV-2

Francis et al.,
Science Immunology,
2021

Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip

Bein et al.,
Frontiers in Pharmacology,
2021

Identification of immune correlates of fatal outcomes in critically ill COVID-19 patients

Youngs et al.,
PLOS Pathogens,
2021

HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells

Fardoos et al.,
JCI Insight,
2021

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

Ziegler et al.,
Cell,
2021

The cellular architecture of the antimicrobial response network in human leprosy granulomas

Ma et al.,
Nature Immunology,
2021

Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells

Jiang et al.,
JCI Insight,
2021

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets

Delorey et al.,
Nature,
2021

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

Kummerlowe et al.,
bioRxiv,
2021

MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection

Khuzwayo et al.,
Frontiers in Immunology,
2021

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Muus et al.,
Nature Medicine,
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

Evolution and diversity of immune responses during acute HIV infection

Kazer et al.,
Immunity,
2020

Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics

Kotliar et al.,
Cell,
2020

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

Gideon et al.,
bioRxiv,
2020

Innate Lymphoid Cell Activation and Sustained Depletion in Blood and Tissue of Children Infected with HIV from Birth Despite Antiretroviral Therapy

Singh et al.,
Cell Reports,
2020

A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood

Sangesland et al.,
Cell Reports,
2020

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

Kotliar et al.,
bioRxiv,
2020

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Sungnak et al.,
Nature Medicine,
2020

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

Ziegler et al.,
Cell,
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

Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection

Kazer et al.,
Nature Medicine,
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

Distribution and storage of inflammatory memory in barrier tissues

Ordovas-Montanes et al.,
Nature Reviews Immunology,
2020

Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies

Martin-Gayo et al.,
Cell Reports,
2020

Identification of a master regulator of differentiation in toxoplasma

Waldman et al.,
Cell,
2020

Prevention of tuberculosis in macaques after intravenous BCG immunization

Darrah et al.,
Nature,
2020

Germline-encoded affinity for cognate antigen enables vaccine amplification of a human broadly neutralizing response against influenza virus

Sangesland et al.,
Immunity,
2019

Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis

Ardain A. et al.,
Nature,
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

Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection

Ndhlovu et al.,
Science Translational Medicine,
2019

Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses

Douam F. et al.,
Nature Communications,
2018

High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults

Roider et al.,
frontiers in Immunology,
2018

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

Martin-Gayo et al.,
Genome Biology,
2018

Single-cell analyses to tailor treatments

Shalek A.K. et al.,
Science Translational Medicine,
2017

Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies

Nandin I.S. et al.,
Journal of Experimental Medicine,
2017

Circulating CXCR5+CXCR3+PD-1lo Tfh-like Cells in HIV-1 Controllers with Neutralizing Antibody Breadth

Martin-Gayo et al.,
JCI Insight,
2017

Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion

Ranasinghe et al.,
Immunity,
2016

Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression

Kløverpris et al.,
Immunity,
2016

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

Avraham et al.,
Cell,
2015

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