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,
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,
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,
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,
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,
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
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
Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia
  • Barrett et al.,
  • Journal of Allergy and Clinical Immunology,
  • 2019
Biology
Genomics
Immunology
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
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
  • Menon et al.,
  • Nature Communications,
  • 2019
Biology
Cell Atlas
Genomics
Immunology
Medicine
Brittany Goods
Alex K. Shalek
Induction of metabolic quiescence defines the transitional to follicular B cell switch
  • Farmer et al.,
  • Science Signaling,
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
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
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
Dynamic regulatory network controlling TH17 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
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