2020 - Shalek Lab

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

The Human Cell Atlas and equity: lessons learned

Majumder et al.,
Nature 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

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

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

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