Genomics Archives - Shalek Lab

CellLENS enables cross-domain information fusion for enhanced cell population delineation in single-cell spatial omics data

Zhu et al.,
Nature Immunology,
2025

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

Congenital T cell activation impairs transitional to follicular B cell maturation in humans

Allard-Chamard et al.,
bioRxiv,
2024

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

Lensch et al.,
biorxiv,
2024

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

Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients

Genshaft et al.,
Hepatology,
2023

Comparative analysis of cell–cell communication at single-cell resolution

Wilk et al.,
Nature Biotechnology,
2023

Engineering kinetics of TLR7/8 agonist release from bottlebrush prodrugs enables tumor-focused immune stimulation

Bhagchandani et al.,
Science Advances,
2023

PI3Kβ controls immune evasion in PTEN-deficient breast tumours

Bergholz et al.,
Nature,
2023

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

Wilk et al.,
bioRxiv,
2023

A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery

Crouchet et al.,
Nature Communications,
2023

Mepolizumab targets multiple immune cells in aspirin-exacerbated respiratory disease

Buchheit et al.,
Journal of Allergy and Clinical Immunology,
2023

An ex vivo ovulation system enables the discovery of novel ovulatory pathways and nonhormonal contraceptive candidates

Zhang et al.,
Biology of Reproduction,
2023

Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system

Wang et al.,
Biology of Reproduction,
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

IL-5Rα marks nasal polyp IgG4- and IgE-expressing cells in aspirin-exacerbated respiratory disease

Buchheit et al.,
Journal of Allergy and Clinical Immunology,
2023

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

Mead et al.,
bioRxiv,
2023

Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity

Williams et al.,
Cancer Research,
2023

NIAID Workshop on T Cell Technologies

Gondré-Lewis et al.,
Nature Immunology,
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 transcriptomics of staged oocytes and somatic cells reveal novel regulators of follicle activation

Chen et al.,
Reproduction,
2023

Hypoxic, glycolytic metabolism is a vulnerability of B-acute lymphoblastic leukemia-initiating cells

Morris et al.,
Cell Reports,
2023

Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm

DePasquale et al.,
Frontiers in Immunology,
2023

Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform

Gerdemann et al.,
Frontiers in Immunology,
2023

PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment

Collins et al.,
Journal for Immunotherapy of Cancer,
2023

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

Kummerlowe et al.,
Science Translational Medicine,
2022

Deciphering the immunopeptidome in vivo reveals new tumour antigens

Jaeger et al.,
Nature,
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

Cellular and transcriptional diversity over the course of human lactation

Nyquist et al.,
PNAS,
2022

Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation

Mead et al.,
Nature Biomedical Engineering,
2022

JAK inhibition in a patient with a STAT1 gain-of-function variant reveals STAT1 dysregulation as a common feature of aplastic anemia

Rosenberg et al.,
Med,
2022

Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states

Song et al.,
Nature Communications,
2022

Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer

Raghavan et al.,
Cell,
2021

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

Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice

Hamza et al.,
Nature Communications,
2021

Single cell biology—a Keystone Symposia report

Cable et al.,
Annals of the New York Academy of Sciences,
2021

Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases

Prakadan et al.,
Nature Communications,
2021

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

Zheng et al.,
bioRxiv,
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

Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

Genshaft et al.,
Nature Communications,
2021

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

Ziegler et al.,
Cell,
2021

Expression of Foxp3 by T follicular helper cells in end-stage germinal centers

Jacobsen et al.,
Science,
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

High-fat diet-activated fatty acid oxidation mediates intestinal stemness and tumorigenicity

Mana et al.,
Cell Reports,
2021

Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas

Amoozgar et al.,
Nature Communications,
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

Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation

Dwyer et al.,
Science Immunology,
2021

Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu

Goods et al.,
JCI Insight,
2021

How are methodological developments enabling insights into cell behavior in cellular communities?

Piddini et al.,
Cell Systems,
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

Longitudinal transcriptomics define the stages of myeloid activation in the living human brain after intracerebral hemorrhage

Askenase et al.,
Science Immunology,
2021

Spatiotemporal single-cell profiling reveals that invasive and tissue-resident memory donor CD8+ T cells drive gastrointestinal acute graft-versus-host disease

Tkachev et al.,
Science Translational Medicine,
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

Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential

Huang et al.,
Cell,
2020

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

Pae et al.,
Journal of Experimental Medicine,
2020

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

Ma et al.,
bioRxiv,
2020

Functional compensation precedes recovery of tissue mass following acute liver injury

Walesky et al.,
Nature Communications,
2020

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

Pae et al.,
bioRxiv,
2020

Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity

Zhivaki et al.,
Cell Reports,
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

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

Hughes et al.,
Immunity,
2020

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

Berger et al.,
Nature Communications,
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

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

Raghavan et al.,
bioRxiv,
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 Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease

Mitsialis et al.,
Gastroenterology,
2020

Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states

Tkachev 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

Computational Methods for Single-Cell RNA Sequencing

Hie et al.,
Annual Reviews,
2020

High-throughput organoid screening enables engineering of intestinal epithelial composition

Mead 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

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Rozenblatt-Rosen et al.,
Cell,
2020

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Ding et al.,
Nature Biotechnology,
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

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

Genshaft et al.,
bioRxiv,
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

TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

Tu et al.,
Nature Immunology,
2019

Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia

Barrett et al.,
Journal of Allergy and Clinical Immunology,
2019

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

Huang et al.,
bioRxiv,
2019

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

Menon et al.,
Nature Communications,
2019

Induction of metabolic quiescence defines the transitional to follicular B cell switch

Farmer et al.,
Science Signaling,
2019

The next quarter century

Ablasser et al.,
Immunity,
2019

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

Sangesland et al.,
Immunity,
2019

Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression

Tsankov et al.,
Development,
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

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

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

Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing

Aicher et al.,
Single-Cell Methods,
2019

Mechanisms of lymphoma clearance induced by high-dose alkylating agents

Lossos et al.,
Cancer Discovery,
2019

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration

Pepe-Mooney et al.,
Cell Stem Cell,
2019

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

van Galen et al.,
Cell,
2019

Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer

Hamza B. et al.,
PNAS,
2019

Linking single-cell measurements of mass, growth rate, and gene expression

Kimmerling R.J. et al.,
Genome Biology,
2018

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

Douam F. et al.,
Nature Communications,
2018

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation

Biton et al.,
Cell,
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

Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells

Ordovas-Montanes et al.,
Nature,
2018

Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

Mead B.E.* et al.,
BMC Biology,
2018

Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells

Gaya M. et al.,
Cell,
2017

Science Forum: The Human Cell Atlas

Regev A. et al.,
eLife,
2017

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

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

Prakadan et al.,
Nature Reviews Genetics,
2017

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

Gierahn et al.,
Nature Methods,
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

Regulation of X-linked gene expression during early mouse development by Rlim

Wang et al.,
eLife,
2016

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Genshaft et al.,
Genome Biology,
2016

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

Tirosh et al.,
Science,
2016

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM

Wong et al.,
PNAS,
2016

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

Kløverpris et al.,
Immunity,
2016

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

Kimmerling et al.,
Nature Communications,
2016

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

Gaublomme et al.,
Cell,
2015

Oct1 and OCA-B are selectively required for CD4 memory T cell function

Shakya et al.,
J. Exp. Med.,
2015

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

Avraham et al.,
Cell,
2015

Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics

Wadsworth II et al.,
Genome Biology,
2015

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Macosko et al.,
Cell,
2015

Deconstructing transcriptional heterogeneity in pluripotent stem cells

Kumar et al.,
Nature,
2014

Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL

Wang et al.,
Blood,
2014

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek et al.,
Nature,
2014

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

Patel et al.,
Science,
2014

Heterogeneity in immune responses: from populations to single cells

Satija et al.,
Trends in Immunology,
2014

Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells

Suvà et al.,
Cell,
2014

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

Lohr et al.,
Nature Biotechnology,
2014

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek et al.,
Nature,
2013

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Gifford et al.,
Cell,
2013

Dynamic regulatory network controlling T_H17 cell differentiation

Yosef et al.,
Nature,
2013

Probing Enzymatic Activity inside Living Cells Using a Nanowire−Cell “Sandwich” Assay

Na et al.,
Nano Letters,
2013

Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia

Shalek et al.,
Nano Letters,
2012

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

Chevrier et al.,
Cell,
2011

Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells

Shalek et al.,
PNAS,
2010

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