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
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Riley Drake
Vincent Miao
Alex K. Shalek
Pro-inflammatory feedback loops define immune responses to pathogenic lentivirus infection
  • Wilk et al.,
  • bioRxiv,
  • 2023
Genomics
Immunology
Infectious Disease
Sam Kazer
Ira Fleming
Vincent Miao
Jennyfer Galvez-Reyes
Alex K. Shalek
Compressed phenotypic screens for complex multicellular models and high-content assays
  • Mead et al.,
  • bioRxiv,
  • 2023
Biology
Cancer
Chemistry
Computational Methods
Genomics
R&D
Statistics
Technology
Ben Mead
Conner Kummerlowe
Ivy Liu
Walaa Kattan
Thomas Nok Hin Cheng
Peter Winter
Alex K. Shalek
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
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
R&D
Technology
Alex Genshaft
Mike Vilme
Riley Drake
Ira Fleming
Nancy Tran
Constantine Tzouanas
Jasmin Joseph-Chazan
Alex K. Shalek
Cellular and transcriptional diversity over the course of human lactation
  • Nyquist et al.,
  • bioRxiv,
  • 2021
Biology
Cell Atlas
Genomics
Immunology
Vincent Miao
Patricia Gao
Riley Drake
Kellie Kolb
Ben Mead
Alex K. Shalek
Brittany Goods
A Treatment-Naive Cellular Atlas of Pediatric Crohn’s Disease Predicts Disease Severity and Therapeutic Response
  • Zheng et al.,
  • bioRxiv,
  • 2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Medicine
Benjamin Doran
Kyle Kimler
Alex K. Shalek
José Ordovas-Montañes
Single-cell profiling of environmental enteropathy reveals signatures of epithelial remodeling and immune activation in severe disease
  • Kummerlowe et al.,
  • bioRxiv,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Conner Kummerlowe
Travis Hughes
Nolawit Mulugeta
Ira Fleming
Marko Vukovic
Benjamin Doran
José Ordovas-Montañes
Alex K. Shalek
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
  • Delorey et al.,
  • bioRxiv,
  • 2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Carly Ziegler
Alex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
  • Ziegler et al.,
  • bioRxiv,
  • 2021
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Carly Ziegler
Vincent Miao
Andrew Navia
Josh Bromley
Micayla George
Riley Drake
Alex K. Shalek
José Ordovas-Montañes
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
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Carly Ziegler
Vincent Miao
Andrew Navia
Josh Bromley
José Ordovas-Montañes
Alex K. Shalek
Single cell and spatial transcriptomics defines the cellular architecture of the antimicrobial response network in human leprosy granulomas
  • Ma et al.,
  • bioRxiv,
  • 2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Travis Hughes
Marc Wadsworth II
Alex K. Shalek
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
  • Pae et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Sam Allon
José Ordovas-Montañes
Alex K. Shalek
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
  • Goods et al.,
  • biorXiv,
  • 2020
Biology
Genomics
Immunology
Medicine
Brittany Goods
Riley Drake
Ira Fleming
Alex K. Shalek
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
  • Song et al.,
  • bioRxiv,
  • 2020
Biology
Cancer
Genomics
Immunology
Marc Wadsworth II
Alex K. Shalek
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
  • Gideon et al.,
  • bioRxiv,
  • 2020
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Travis Hughes
Marc Wadsworth II
Conner Kummerlowe
Sarah Nyquist
José Ordovas-Montañes
Alex K. Shalek
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
  • Raghavan et al.,
  • bioRxiv,
  • 2020
Biology
Cancer
Cell Atlas
Computational Methods
Genomics
Immunology
Medicine
Technology
Peter Winter
Andrew Navia
Jennyfer Galvez-Reyes
Nolawit Mulugeta
Alex K. Shalek
Single-cell profiling of Ebola virus infection ​in vivo​ reveals viral and host transcriptional dynamics
  • Kotliar et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Travis Hughes
Marc Wadsworth II
Nancy Tran
Alex K. Shalek
Alterations of multiple alveolar macrophage states in chronic obstructive pulmonary disease
  • Bassler et al.,
  • bioRxiv,
  • 2020
Computational Methods
Genomics
Immunology
Medicine
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
High-throughput organoid screening enables engineering of intestinal epithelial composition
  • Mead et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Medicine
R&D
Technology
Ben Mead
Marko Vukovic
José Ordovas-Montañes
Alex K. Shalek
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
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Sam Allon
Sarah Nyquist
José Ordovas-Montañes
Marc Wadsworth II
Carly Ziegler
Alex K. Shalek
Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults
  • Cao et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Microbiology
José Ordovas-Montañes
Alex K. Shalek
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
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Medicine
Carly Ziegler
Sam Allon
Sarah Nyquist
Vincent Miao
Marc Wadsworth II
Sam Kazer
Travis Hughes
Benjamin Doran
James Gatter
Marko Vukovic
Constantine Tzouanas
Shaina Carroll
Alex K. Shalek
José Ordovas-Montañes
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
  • Genshaft et al.,
  • bioRxiv,
  • 2020
Biology
Cancer
Chemistry
Genomics
R&D
Technology
Alex Genshaft
Carly Ziegler
Constantine Tzouanas
Ben Mead
Andrew Navia
Alex K. Shalek
Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
  • Huang et al.,
  • bioRxiv,
  • 2019
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Carly Ziegler
Marko Vukovic
José Ordovas-Montañes
Alex K. Shalek
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
Biology
Genomics
Immunology
R&D
Technology
Travis Hughes
Marc Wadsworth II
José Ordovas-Montañes
Alex K. Shalek
Identification of a Master Regulator of Differentiation in Toxoplasma
  • Waldman B.S. et al.,
  • bioRxiv,
  • 2019
Biology
Infectious Disease
Microbiology
Marc Wadsworth II
Alex K. Shalek
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
  • Kazer S.W. et al.,
  • bioRxiv,
  • 2019
Biology
Genomics
Immunology
Infectious Disease
Sam Kazer
Toby Aicher
Shaina Carroll
José Ordovas-Montañes
Carly Ziegler
Sarah Nyquist
Alex K. Shalek
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
  • Smillie et al.,
  • BioRxiv,
  • 2018
Biology
Cell Atlas
Computational Methods
Immunology
Medicine
José Ordovas-Montañes
Alex K. Shalek
Linking single-cell measurements of mass, growth rate, and gene expression
  • Kimmerling et al.,
  • BioRxiv,
  • 2018
Chemistry
Genomics
Technology
Jay Prakadan
Alejandro Gupta
Riley Drake
Alex K. Shalek
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
Cell Atlas
Immunology
Medicine
José Ordovas-Montañes
Sarah Nyquist
Marc Wadsworth II
Travis Hughes
Sam Kazer
Alex K. Shalek