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Publications
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Computational Methods
Comparative analysis of cell–cell communication at single-cell resolution
Wilk et al.,
Nature Biotechnology,
2023
Computational Methods
Genomics
R&D
Statistics
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
NIAID Workshop on T Cell Technologies
Gondré-Lewis et al.,
Nature Immunology,
2023
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
R&D
Alex K. Shalek
Identification and characterization of the T cell receptor (TCR) repertoire of the cynomolgus macaque (Macaca Fascicularis)
Jaiswal et al.,
BMC Genomics,
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
R&D
Sarah Nyquist
Tasneem Jivanjee
Samira Ibrahim
Josh Bromley
James Gatter
Alex K. Shalek
Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform
Gerdemann et al.,
Frontiers in Immunology,
2023
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
R&D
Technology
Jim Kaminski
Alex K. Shalek
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
Biology
Computational Methods
Genomics
Immunology
Medicine
R&D
Technology
Ben Mead
Marko Vukovic
Conner Kummerlowe
José Ordovas-Montañes
Alex K. Shalek
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
Raghavan et al.,
Cell,
2021
Cancer
Computational Methods
Genomics
Immunology
Medicine
R&D
Technology
Peter Winter
Andrew Navia
Jennyfer Galvez-Reyes
Nolawit Mulugeta
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
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
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Ziegler et al.,
Cell,
2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Carly Ziegler
Vincent Miao
Andrew Navia
Josh Bromley
Micayla George
Riley Drake
Alex K. Shalek
José Ordovas-Montañes
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
Delorey et al.,
Nature,
2021
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Carly Ziegler
Alex K. Shalek
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Muus et al.,
Nature Medicine,
2021
Cell Atlas
Computational Methods
Genomics
Immunology
Infectious Disease
Statistics
Sam Allon
Sarah Nyquist
Marc Wadsworth II
Carly Ziegler
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
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
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
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
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,
Biology
Computational Methods
Genomics
Sarah Nyquist
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
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,
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
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
Voices in methods development
Anikeeva et al.,
Nature Methods,
2019
Computational Methods
Genomics
R&D
Technology
Alex K. Shalek
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
Computational Methods
Genomics
Immunology
Infectious Disease
Medicine
Kellie Kolb
José Ordovas-Montañes
Alex K. Shalek
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
Finak et al.,
Genome Biology,
2015
Computational Methods
Statistics
Alex K. Shalek
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Macosko et al.,
Cell,
2015
Genomics
R&D
Technology
Alex K. Shalek
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