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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
Biology
Cell Atlas
Genomics
Immunology
R&D
Technology
Alex Genshaft
Alex K. Shalek
Constantine Tzouanas
Ira Fleming
Jasmin Joseph-Chazan
Mike Vilme
Nancy Tran
Riley Drake
Engineering kinetics of TLR7/8 agonist release from bottlebrush prodrugs enables tumor-focused immune stimulation
Bhagchandani et al.,
Science Advances,
2023
Biology
Cancer
Chemistry
Genomics
Immunology
Medicine
R&D
Technology
Alex K. Shalek
Evelyn Yuzhou Tong
Michelle Ramseier
A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery
Crouchet et al.,
Nature Communications,
2023
Biology
Cancer
Genomics
Immunology
R&D
Technology
Alex K. Shalek
Vitrification preserves murine ovarian follicular cell transcriptome in a 3D encapsulated in vitro follicle growth system
Wang et al.,
Biology of Reproduction,
2023
Biology
Genomics
Immunology
R&D
Technology
Alex K. Shalek
Brittany Goods
Daniela Russo
Riley Drake
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
Alex K. Shalek
Ben Mead
Conner Kummerlowe
Ivy Liu
Peter Winter
Thomas Nok Hin Cheng
Walaa Kattan
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
Alex K. Shalek
Ben Mead
Conner Kummerlowe
José Ordovas-Montañes
Marko Vukovic
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
Alex K. Shalek
Constantine Tzouanas
Ira Fleming
Jasmin Joseph-Chazan
Mike Vilme
Nancy Tran
Riley Drake
Enteric Coronavirus Infection and Treatment Modeled With an Immunocompetent Human Intestine-On-A-Chip
Bein et al.,
Frontiers in Pharmacology,
2021
Biology
Genomics
Immunology
Infectious Disease
Medicine
R&D
Technology
Alex K. Shalek
Andrew Navia
Carly Ziegler
José Ordovas-Montañes
Vincent Miao
Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice
Hamza et al.,
Nature Communications,
2021
Biology
Cancer
Genomics
Immunology
Physics
R&D
Technology
Alex K. Shalek
Nolawit Mulugeta
Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes
Genshaft et al.,
Nature Communications,
2021
Genomics
R&D
Technology
Alex Genshaft
Alex K. Shalek
Andrew Navia
Ben Mead
Carly Ziegler
Constantine Tzouanas
Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies
Hughes et al.,
Immunity,
2020
Biology
Cell Atlas
Chemistry
Genomics
Immunology
R&D
Technology
Alex K. Shalek
José Ordovas-Montañes
Marc Wadsworth II
Travis Hughes
High-throughput organoid screening enables engineering of intestinal epithelial composition
Mead et al.,
bioRxiv,
2020
Biology
Genomics
Medicine
R&D
Technology
Alex K. Shalek
Ben Mead
José Ordovas-Montañes
Marko Vukovic
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
Ding et al.,
Nature Biotechnology,
2020
Computational Methods
Genomics
R&D
Technology
Alex K. Shalek
Marc Wadsworth II
Shaina Carroll
Travis Hughes
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
Alex K. Shalek
Andrew Navia
Ben Mead
Carly Ziegler
Constantine Tzouanas
TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
Tu et al.,
Nature Immunology,
2019
Biology
Cell Atlas
Genomics
Immunology
R&D
Technology
Alex K. Shalek
Voices in methods development
Anikeeva et al.,
Nature Methods,
2019
Computational Methods
Genomics
R&D
Technology
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
Alex K. Shalek
José Ordovas-Montañes
Marc Wadsworth II
Travis Hughes
Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing
Aicher et al.,
Single-Cell Methods,
2019
R&D
Technology
Alex K. Shalek
Marc Wadsworth II
Shaina Carroll
Toby Aicher
Travis Hughes
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
van Galen et al.,
Cell,
2019
Alex K. Shalek
Marc Wadsworth II
Travis Hughes
Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer
Hamza B. et al.,
PNAS,
2019
Biology
Cancer
Computational Methods
R&D
Technology
Alejandro Gupta
Alex K. Shalek
Andrew Navia
Jay Prakadan
Peter Winter
Riley Drake
Linking single-cell measurements of mass, growth rate, and gene expression
Kimmerling R.J. et al.,
Genome Biology,
2018
Biology
Cancer
Genomics
Physics
R&D
Technology
Alejandro Gupta
Alex K. Shalek
Jay Prakadan
Riley Drake
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Mead B.E.* et al.,
BMC Biology,
2018
Alex K. Shalek
Ben Mead
José Ordovas-Montañes
Marc Wadsworth II
Travis Hughes
Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices
Prakadan et al.,
Nature Reviews Genetics,
2017
Genomics
Technology
Alex K. Shalek
Jay Prakadan
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
Gierahn et al.,
Nature Methods,
2017
Chemistry
Genomics
R&D
Technology
Travel
Alex K. Shalek
Marc Wadsworth II
Travis Hughes
Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Genshaft et al.,
Genome Biology,
2016
Biology
Chemistry
Genomics
R&D
Technology
Alex Genshaft
Alex K. Shalek
Carly Ziegler
Jay Prakadan
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM
Wong et al.,
PNAS,
2016
Chemistry
Genomics
Technology
Aleth Gaillard
Alex K. Shalek
Sam Kazer
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
Kimmerling et al.,
Nat. Commun.,
2016
Biology
Genomics
Immunology
R&D
Technology
Alex Genshaft
Alex K. Shalek
Sam Kazer
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics
Wadsworth II et al.,
Genome Biology,
2015
Genomics
R&D
Technology
Alex K. Shalek
Marc Wadsworth II
Travis Hughes
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Macosko et al.,
Cell,
2015
Genomics
R&D
Technology
Alex K. Shalek
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing
Trombetta et al.,
Current Protocols in Molecular Biology,
2014
R&D
Technology
Alex K. Shalek
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Shalek et al.,
Nature,
2013
Biology
Genomics
Immunology
Alex K. Shalek
Probing Enzymatic Activity inside Living Cells Using a Nanowire−Cell “Sandwich” Assay
Na et al.,
Nano Letters,
2013
Biology
Chemistry
Immunology
Technology
Alex K. Shalek
Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia
Shalek et al.,
Nano Letters,
2012
Cancer
Genomics
R&D
Technology
Alex K. Shalek
Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits
Robinson et al.,
Nature Nanotechnology,
2012
Biology
Chemistry
Technology
Alex K. Shalek
Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells
Shalek et al.,
PNAS,
2010
Chemistry
Genomics
Physics
R&D
Technology
Alex K. Shalek
Photoinduced Interfacial Charging and “Explosion” of Monolayer Pentacene Islands
Chen L. et al.,
Nano Lett,
2005
Chemistry
Physics
R&D
Technology
Alex K. Shalek
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