Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
  • Berger et al.,
  • Nature Communications,
  • 2020
Biology
Computational Methods
Statistics
Sarah Nyquist
Alex K. Shalek
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
Biology
Genomics
Immunology
Infectious Disease
Vincent Miao
Sam Kazer
Alex K. Shalek
Transcriptional subtype-specific microenvironmental crosstalk and tumor cell 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
A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood
  • Sangesland et al.,
  • Cell Reports,
  • 2020
Biology
Computational Methods
Genomics
Immunology
Infectious Disease
Sam Kazer
James Gatter
Alex K. Shalek
Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn’s Disease
  • Mitsialis et al.,
  • Gastroenterology,
  • 2020
Biology
Genomics
Immunology
José Ordovas-Montañes
Marko Vukovic
Alex K. Shalek
Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states
  • Tkachev et al.,
  • bioRxiv,
  • 2020
Biology
Genomics
Immunology
Jim Kaminski
José Ordovas-Montañes
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
Computational Methods for Single-Cell RNA Sequencing
  • Hie et al.,
  • Annual Reviews,
  • 2020
Biology
Computational Methods
Genomics
Sarah Nyquist
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
SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes
  • Sungnak et al.,
  • Nature Medicine,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
José Ordovas-Montañes
Alex K. Shalek
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
Biology
Cell Atlas
Genomics
Immunology
Infectious Disease
Statistics
Carly Ziegler
Sam Allon
Sarah Nyquist
Vincent Miao
Constantine Tzouanas
Marc Wadsworth II
Sam Kazer
Travis Hughes
Benjamin Doran
James Gatter
Marko Vukovic
Ben Mead
Shaina Carroll
Alex K. Shalek
José Ordovas-Montañes
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
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
  • Rozenblatt-Rosen et al.,
  • Cell,
  • 2020
Biology
Cancer
Cell Atlas
Computational Methods
Genomics
Immunology
Medicine
Alex K. Shalek
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
  • Ding et al.,
  • Nature Biotechnology,
  • 2020
Computational Methods
Genomics
R&D
Technology
Travis Hughes
Marc Wadsworth II
Shaina Carroll
Alex K. Shalek
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
  • Kazer et al.,
  • Nature Medicine,
  • 2020
Biology
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Sam Kazer
Toby Aicher
Shaina Carroll
José Ordovas-Montañes
Vincent Miao
Carly Ziegler
Sarah Nyquist
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
Distribution and storage of inflammatory memory in barrier tissues
  • Ordovas-Montanes et al.,
  • Nature Reviews Immunology,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
José Ordovas-Montañes
Alex K. Shalek
Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
  • Martin-Gayo et al.,
  • Cell Reports,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Medicine
Kellie Kolb
Alex K. Shalek
Identification of a master regulator of differentiation in toxoplasma
  • Waldman et al.,
  • Cell,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Marc Wadsworth II
Alex K. Shalek
Prevention of tuberculosis in macaques after intravenous BCG immunization
  • Darrah et al.,
  • Nature,
  • 2020
Biology
Genomics
Immunology
Infectious Disease
Medicine
Marc Wadsworth II
Travis Hughes
Alex K. Shalek