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Genomics
Induction of metabolic quiescence defines the transitional to follicular B cell switch
Farmer et al.,
Science Signaling,
2019
Biology
Genomics
Immunology
Toby Aicher
Alex K. Shalek
The next quarter century
Ablasser et al.,
Immunity,
2019
Biology
Genomics
Immunology
Alex K. Shalek
Germline-encoded affinity for cognate antigen enables vaccine amplification of a human broadly neutralizing response against influenza virus
Sangesland et al.,
Immunity,
2019
Biology
Genomics
Immunology
Infectious Disease
Medicine
Sam Kazer
Alex K. Shalek
Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression
Tsankov et al.,
Development,
2019
Biology
Genomics
Marc Wadsworth II
Sam Allon
Ben Mead
Riley Drake
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
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
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
Toby Aicher
Shaina Carroll
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
Mechanisms of lymphoma clearance induced by high-dose alkylating agents
Lossos et al.,
Cancer Discovery,
2019
Biology
Cancer
Immunology
Kellie Kolb
Jay Prakadan
Alex K. Shalek
Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration
Pepe-Mooney et al.,
Cell Stem Cell,
2019
Biology
Cell Atlas
Medicine
José Ordovas-Montañes
Alex K. Shalek
Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity
van Galen et al.,
Cell,
2019
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
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
Jay Prakadan
Andrew Navia
Peter Winter
Riley Drake
Alejandro Gupta
Alex K. Shalek
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
Jay Prakadan
Alejandro Gupta
Riley Drake
Alex K. Shalek
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
Douam F. et al.,
Nature Communications,
2018
Biology
Genomics
Immunology
Infectious Disease
Alex K. Shalek
Carly Ziegler
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
Biton et al.,
Cell,
2018
Genomics
Immunology
Medicine
José Ordovas-Montañes
Alex K. Shalek
High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults
Roider et al.,
frontiers in Immunology,
2018
Toby Aicher
Sam Kazer
Alex K. Shalek
Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
Ordovas-Montanes et al.,
Nature,
2018
Biology
Cell Atlas
Immunology
Medicine
José Ordovas-Montañes
Sarah Nyquist
Marko Vukovic
Marc Wadsworth II
Travis Hughes
Sam Kazer
Alex K. Shalek
Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types
Mead B.E.* et al.,
BMC Biology,
2018
Ben Mead
José Ordovas-Montañes
Travis Hughes
Marc Wadsworth II
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
Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells
Gaya M. et al.,
Cell,
2017
Genomics
Immunology
Andrew Navia
Alex K. Shalek
Science Forum: The Human Cell Atlas
Regev A. et al.,
eLife,
2017
Biology
Cell Atlas
Computational Methods
Genomics
Immunology
Medicine
Technology
Alex K. Shalek
Single-cell analyses to tailor treatments
Shalek A.K. et al.,
Science Translational Medicine,
2017
Immunology
Infectious Disease
Medicine
Technology
Alex K. Shalek
Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies
Nandin I.S. et al.,
Journal of Experimental Medicine,
2017
Genomics
Immunology
Infectious Disease
Medicine
Microbiology
Sam Kazer
José Ordovas-Montañes
Alex K. Shalek
Scaling by shrinking: empowering single-cell ‘omics’ with microfluidic devices
Prakadan et al.,
Nature Reviews Genetics,
2017
Genomics
Technology
Jay Prakadan
Alex K. Shalek
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
Marc Wadsworth II
Travis Hughes
Alex K. Shalek
Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion
Ranasinghe et al.,
Immunity,
2016
Biology
Immunology
Infectious Disease
Sam Kazer
Alex K. Shalek
Regulation of X-linked gene expression during early mouse development by Rlim
Wang et al.,
eLife,
2016
Biology
Genomics
Alex K. Shalek
Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
Genshaft et al.,
Genome Biology,
Biology
Chemistry
Genomics
R&D
Technology
Alex Genshaft
Jay Prakadan
Carly Ziegler
Alex K. Shalek
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh et al.,
Science,
2016
Biology
Cancer
Genomics
Medicine
Jay Prakadan
Marc Wadsworth II
Alex Genshaft
Travis Hughes
Carly Ziegler
Sam Kazer
Aleth Gaillard
Kellie Kolb
Alex K. Shalek
Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM
Wong et al.,
PNAS,
2016
Chemistry
Genomics
Technology
Sam Kazer
Aleth Gaillard
Alex K. Shalek
Innate Lymphoid Cells Are Depleted Irreversibly during Acute HIV-1 Infection in the Absence of Viral Suppression
Kløverpris et al.,
Immunity,
2016
Biology
Genomics
Immunology
Infectious Disease
Sam Kazer
Alex K. Shalek
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
Sam Kazer
Alex K. Shalek
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity
Gaublomme et al.,
Cell,
2015
Biology
Genomics
Immunology
Alex K. Shalek
Oct1 and OCA-B are selectively required for CD4 memory T cell function
Shakya et al.,
J. Exp. Med.,
2015
Biology
Genomics
Immunology
Alex K. Shalek
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
Avraham et al.,
Cell,
2015
Biology
Genomics
Immunology
Infectious Disease
Microbiology
Technology
Alex K. Shalek
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics
Wadsworth II et al.,
Genome Biology,
2015
Genomics
R&D
Technology
Marc Wadsworth II
Travis Hughes
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
Deconstructing transcriptional heterogeneity in pluripotent stem cells
Kumar et al.,
Nature,
2014
Biology
Genomics
Alex K. Shalek
Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL
Wang et al.,
Blood,
2014
Cancer
Genomics
Alex K. Shalek
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
Shalek et al.,
Nature,
2014
Biology
Genomics
Alex K. Shalek
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
Patel et al.,
Science,
2014
Cancer
Genomics
Alex K. Shalek
Heterogeneity in immune responses: from populations to single cells
Satija et al.,
Trends in Immunology,
2014
Genomics
Immunology
Technology
Alex K. Shalek
Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells
Suvà et al.,
Cell,
2014
Biology
Cancer
Genomics
Alex K. Shalek
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
Lohr et al.,
Nature Biotechnology,
2014
Biology
Cancer
Genomics
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
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
Gifford et al.,
Cell,
2013
Biology
Genomics
Alex K. Shalek
Dynamic regulatory network controlling T
H
17 cell differentiation
Yosef 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
Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits
Chevrier et al.,
Cell,
2011
Genomics
Immunology
Infectious Disease
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
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