Biography

Alex K. Shalek is currently the Pfizer-Laubach Career Development Associate Professor at MIT, as well as a Core Member of the Institute for Medical Engineering and Science (IMES), an Associate Professor of Chemistry, and an Extramural Member of The Koch Institute for Integrative Cancer Research.  He is also an Institute Member of the Broad Institute, an Associate Member of the Ragon Institute, an Assistant in Immunology at MGH, and an Instructor in Health Sciences and Technology at HMS.  His research is directed towards the creation and implementation of new approaches to elucidate cellular and molecular features that inform tissue-level function and dysfunction across the spectrum of human health and disease. This encompasses both the development of broadly enabling technologies as well as their application to characterize, model, and rationally control complex multicellular systems. Dr. Shalek received his bachelor’s degree summa cum laude from Columbia University and his Ph.D. from Harvard University in chemical physics under the guidance of Hongkun Park, and performed postdoctoral training under Hongkun Park and Aviv Regev (Broad/MIT).

Publications

Functional compensation precedes recovery of tissue mass following acute liver injury
  • Walesky et al.,
  • Nature Communications,
  • 2020
  • Immunology
  • Biology
  • Genomics
  • Kellie Kolb
  • Ira Fleming
  • Alex K. Shalek
Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells
  • Pae et al.,
  • bioRxiv,
  • Genomics
  • Immunology
  • Biology
  • Sam Allon
  • José Ordovas-Montañes
  • Alex K. Shalek
Inflammasomes within hyperactive murine dendritic cells stimulate long-lived T cell-mediated anti-tumor immunity
  • Zhivaki et al.,
  • Cell Reports,
  • 2020
  • Biology
  • Medicine
  • Immunology
  • Cancer
  • Genomics
  • Benjamin Doran
  • Ira Fleming
  • Alex K. Shalek
Evolution and diversity of immune responses during acute HIV infection
  • Kazer et al.,
  • Immunity,
  • Immunology
  • Biology
  • Infectious Disease
  • Medicine
  • Sam Kazer
  • Alex K. Shalek
Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu
  • Goods et al.,
  • biorXiv,
  • 2020
  • Medicine
  • Genomics
  • Immunology
  • Biology
  • Brittany Goods
  • Riley Drake
  • Ira Fleming
  • Alex K. Shalek
Single-cell analysis of human primary prostate cancer reveals the heterogeneity of tumor-associated epithelial cell states
  • Song et al.,
  • bioRxiv,
  • 2020
  • Biology
  • Cancer
  • Genomics
  • Immunology
  • Marc Wadsworth II
  • Alex K. Shalek
Single-cell profiling of ebola virus disease in vivo reveals viral and host dynamics
  • Kotliar et al.,
  • Cell,
  • Immunology
  • Cell Atlas
  • Infectious Disease
  • Genomics
  • Biology
  • Travis Hughes
  • Marc Wadsworth II
  • Nancy Tran
  • Alex K. Shalek
Single-cell profiling of tuberculosis lung granulomas reveals functional lymphocyte signatures of bacterial control
  • Gideon et al.,
  • bioRxiv,
  • 2020
  • Biology
  • Genomics
  • Infectious Disease
  • Cell Atlas
  • Immunology
  • Travis Hughes
  • Marc Wadsworth II
  • Conner Kummerlowe
  • Sarah Nyquist
  • José Ordovas-Montañes
  • Alex K. Shalek
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
  • Immunology
  • Technology
  • Genomics
  • Chemistry
  • R&D
  • Cell Atlas
  • Travis Hughes
  • Marc Wadsworth II
  • José Ordovas-Montañes
  • Alex K. Shalek
Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets
  • Berger et al.,
  • Nature Communications,
  • 2020
  • Computational Methods
  • Biology
  • 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,
  • Immunology
  • Biology
  • Genomics
  • Infectious Disease
  • Sam Kazer
  • Alex K. Shalek
Transcriptional subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer
  • Raghavan et al.,
  • bioRxiv,
  • 2020
  • Cancer
  • Immunology
  • Genomics
  • Computational Methods
  • Biology
  • Cell Atlas
  • Technology
  • Medicine
  • 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
  • Genomics
  • Immunology
  • Computational Methods
  • 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
  • Genomics
  • Biology
  • 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
  • Immunology
  • Infectious Disease
  • Genomics
  • 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,
  • Computational Methods
  • Genomics
  • Biology
  • Sarah Nyquist
  • Alex K. Shalek
High-throughput organoid screening enables engineering of intestinal epithelial composition
  • Mead et al.,
  • bioRxiv,
  • 2020
  • Genomics
  • Medicine
  • Technology
  • R&D
  • Biology
  • 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
  • Genomics
  • Immunology
  • Biology
  • 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
  • Immunology
  • Cell Atlas
  • Infectious Disease
  • Genomics
  • Biology
  • 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,
  • Infectious Disease
  • Computational Methods
  • Immunology
  • Cell Atlas
  • Genomics
  • Statistics
  • Biology
  • 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
  • Microbiology
  • Immunology
  • Biology
  • Infectious Disease
  • Genomics
  • 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
  • Computational Methods
  • Biology
  • Genomics
  • Cell Atlas
  • Medicine
  • Cancer
  • Immunology
  • Alex K. Shalek
Systematic comparison of single-cell and single-nucleus RNA-sequencing methods
  • Ding et al.,
  • Nature Biotechnology,
  • 2020
  • Computational Methods
  • Technology
  • Genomics
  • R&D
  • 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
  • Genomics
  • Immunology
  • Infectious Disease
  • Computational Methods
  • Statistics
  • Biology
  • 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,
  • Medicine
  • Cell Atlas
  • Immunology
  • Biology
  • Genomics
  • Computational Methods
  • Infectious Disease
  • 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
  • R&D
  • Chemistry
  • Genomics
  • Technology
  • Biology
  • Cancer
  • 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
  • Infectious Disease
  • Immunology
  • José Ordovas-Montañes
  • Alex K. Shalek
Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies
  • Martin-Gayo et al.,
  • Cell Reports,
  • 2020
  • Medicine
  • Infectious Disease
  • Biology
  • Genomics
  • Immunology
  • Kellie Kolb
  • Alex K. Shalek
Identification of a master regulator of differentiation in toxoplasma
  • Waldman et al.,
  • Cell,
  • 2020
  • Genomics
  • Biology
  • Infectious Disease
  • Microbiology
  • Immunology
  • Marc Wadsworth II
  • Alex K. Shalek
Prevention of tuberculosis in macaques after intravenous BCG immunization
  • Darrah et al.,
  • Nature,
  • 2020
  • Infectious Disease
  • Medicine
  • Biology
  • Genomics
  • Immunology
  • 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
  • Cell Atlas
  • Genomics
  • Immunology
  • R&D
  • Biology
  • 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
  • Immunology
  • Genomics
  • 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
  • Immunology
  • Cell Atlas
  • Genomics
  • Biology
  • Computational Methods
  • 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
  • Medicine
  • Immunology
  • Biology
  • Genomics
  • Cell Atlas
  • Brittany Goods
  • Alex K. Shalek
Induction of metabolic quiescence defines the transitional to follicular B cell switch
  • Farmer et al.,
  • Science Signaling,
  • Genomics
  • Biology
  • Immunology
  • Toby Aicher
  • Alex K. Shalek
The next quarter century
  • Ablasser et al.,
  • Immunity,
  • 2019
  • Immunology
  • Biology
  • Genomics
  • Alex K. Shalek
Voices in methods development
  • Anikeeva et al.,
  • Nature Methods,
  • 2019
  • Technology
  • R&D
  • Computational Methods
  • Genomics
  • 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,
  • Medicine
  • Immunology
  • Genomics
  • Biology
  • Infectious Disease
  • 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
Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells
  • Reitman et al.,
  • Nature Communications,
  • 2019
  • Biology
  • Genomics
  • Medicine
  • Cancer
  • Alex K. Shalek
A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases
  • Gawel et al.,
  • Genome Medicine,
  • 2019
  • Computational Methods
  • Genomics
  • Biology
  • Medicine
  • Immunology
  • Alex K. Shalek
Intra- and inter-cellular rewiring of the human colon during ulcerative colitis
  • Smillie et al.,
  • Cell,
  • Immunology
  • Cell Atlas
  • Biology
  • Genomics
  • José Ordovas-Montañes
  • 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
  • R&D
  • Technology
  • Genomics
  • Immunology
  • Travis Hughes
  • Marc Wadsworth II
  • José Ordovas-Montañes
  • Alex K. Shalek
Group 3 innate lymphoid cells mediate early protective immunity against tuberculosis
  • Ardain A. et al.,
  • Nature,
  • 2019
  • Immunology
  • Infectious Disease
  • Biology
  • Sam Kazer
  • Alex K. Shalek
Identification of a Master Regulator of Differentiation in Toxoplasma
  • Waldman B.S. et al.,
  • bioRxiv,
  • Biology
  • Infectious Disease
  • Microbiology
  • Marc Wadsworth II
  • Alex K. Shalek
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
  • Kazer S.W. et al.,
  • bioRxiv,
  • 2019
  • Genomics
  • Immunology
  • Infectious Disease
  • Biology
  • 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
  • Technology
  • R&D
  • Toby Aicher
  • Shaina Carroll
  • Marc Wadsworth II
  • Travis Hughes
  • Alex K. Shalek
Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection
  • Ndhlovu et al.,
  • Science Translational Medicine,
  • 2019
  • Medicine
  • Immunology
  • Genomics
  • Sam Kazer
  • Alex K. Shalek
Mechanisms of lymphoma clearance induced by high-dose alkylating agents
  • Lossos et al.,
  • Cancer Discovery,
  • 2019
  • Immunology
  • Cancer
  • Biology
  • 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
  • Cell Atlas
  • Medicine
  • Biology
  • 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
  • Technology
  • Biology
  • Cancer
  • Computational Methods
  • R&D
  • 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
  • Physics
  • R&D
  • Technology
  • Genomics
  • 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
  • Immunology
  • Biology
  • Genomics
  • Infectious Disease
  • Alex K. Shalek
  • Carly Ziegler
T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation
  • Biton et al.,
  • Cell,
  • 2018
  • Immunology
  • Genomics
  • Medicine
  • José Ordovas-Montañes
  • Alex K. Shalek
Rewiring of the cellular and inter-cellular landscape of the human colon during ulcerative colitis
  • Smillie et al.,
  • BioRxiv,
  • 2018
  • Computational Methods
  • Biology
  • Medicine
  • Cell Atlas
  • Immunology
  • José Ordovas-Montañes
  • Alex K. Shalek
The Human Cell Atlas White Paper
  • Regev A. et al.,
  • Arxiv,
  • 2018
  • Alex K. Shalek
Allergic Inflammatory Memory in Human Respiratory Epithelial Progenitor Cells
  • Ordovas-Montanes et al.,
  • Nature,
  • 2018
  • Biology
  • Medicine
  • Immunology
  • Cell Atlas
  • 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
  • Technology
  • Genomics
  • Chemistry
  • Jay Prakadan
  • Alejandro Gupta
  • Riley Drake
  • 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
  • Immunology
  • Infectious Disease
  • Genomics
  • Medicine
  • Computational Methods
  • Kellie Kolb
  • José Ordovas-Montañes
  • Alex K. Shalek
Initiation of Antiviral B Cell Immunity Relies on Innate Signals from Spatially Positioned NKT Cells
  • Gaya M. et al.,
  • Cell,
  • 2017
  • Immunology
  • Genomics
  • Andrew Navia
  • Alex K. Shalek
Science Forum: The Human Cell Atlas
  • Regev A. et al.,
  • eLife,
  • 2017
  • Genomics
  • Immunology
  • Biology
  • Medicine
  • Technology
  • Computational Methods
  • Cell Atlas
  • Alex K. Shalek
Reduced cellular diversity and an altered basal progenitor cell state inform epithelial barrier dysfunction in human type 2 immunity
  • Jose Ordovas-Montanes et al.,
  • BioRxiv,
  • 2017
  • Cell Atlas
  • Immunology
  • Medicine
  • José Ordovas-Montañes
  • Sarah Nyquist
  • Marc Wadsworth II
  • Travis Hughes
  • Sam Kazer
  • Alex K. Shalek
Single-cell analyses to tailor treatments
  • Shalek A.K. et al.,
  • Science Translational Medicine,
  • 2017
  • Immunology
  • Technology
  • Infectious Disease
  • Medicine
  • 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
  • Immunology
  • Microbiology
  • Genomics
  • Infectious Disease
  • Medicine
  • Sam Kazer
  • José Ordovas-Montañes
  • Alex K. Shalek
IFNγ-Dependent Tissue-Immune Homeostasis is Co-opted in the Tumor Microenvironment
  • Nirschl et al.,
  • Cell,
  • 2017
  • Genomics
  • Immunology
  • Cancer
  • Jay Prakadan
  • 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
  • Technology
  • Genomics
  • Travel
  • R&D
  • Chemistry
  • Marc Wadsworth II
  • Travis Hughes
  • Alex K. Shalek
Circulating CXCR5+CXCR3+PD-1lo Tfh-like Cells in HIV-1 Controllers with Neutralizing Antibody Breadth
  • Martin-Gayo et al.,
  • JCI Insight,
  • 2017
  • Immunology
  • Infectious Disease
  • Biology
  • Kellie Kolb
  • 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
  • Infectious Disease
  • Immunology
  • 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,
  • R&D
  • Genomics
  • Chemistry
  • Biology
  • 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
  • Cancer
  • Genomics
  • Biology
  • 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
  • Infectious Disease
  • Biology
  • Immunology
  • Genomics
  • Sam Kazer
  • Alex K. Shalek
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
  • Kimmerling et al.,
  • Nat. Commun.,
  • 2016
  • Technology
  • Immunology
  • R&D
  • Genomics
  • Biology
  • Alex Genshaft
  • Sam Kazer
  • Alex K. Shalek
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity
  • Gaublomme et al.,
  • Cell,
  • 2015
  • Genomics
  • Biology
  • Immunology
  • Alex K. Shalek
Oct1 and OCA-B are selectively required for CD4 memory T cell function
  • Shakya et al.,
  • J. Exp. Med.,
  • 2015
  • Genomics
  • Immunology
  • Biology
  • Alex K. Shalek
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
  • Avraham et al.,
  • Cell,
  • 2015
  • Microbiology
  • Infectious Disease
  • Biology
  • Technology
  • Genomics
  • Immunology
  • Alex K. Shalek
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics
  • Wadsworth II et al.,
  • Genome Biology,
  • 2015
  • Genomics
  • Technology
  • R&D
  • 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
  • Technology
  • R&D
  • Genomics
  • 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
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 RNA-seq reveals dynamic paracrine control of cellular variation
  • Shalek et al.,
  • Nature,
  • 2014
  • Genomics
  • Biology
  • Alex K. Shalek
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
  • Patel et al.,
  • Science,
  • 2014
  • Genomics
  • Cancer
  • Alex K. Shalek
Heterogeneity in immune responses: from populations to single cells
  • Satija et al.,
  • Trends in Immunology,
  • 2014
  • Genomics
  • Technology
  • Immunology
  • Alex K. Shalek
Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells
  • Suvà et al.,
  • Cell,
  • 2014
  • Biology
  • Genomics
  • Cancer
  • Alex K. Shalek
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
  • Lohr et al.,
  • Nature Biotechnology,
  • 2014
  • Genomics
  • Cancer
  • Biology
  • Alex K. Shalek
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
  • Shalek et al.,
  • Nature,
  • 2013
  • Genomics
  • Immunology
  • Biology
  • Alex K. Shalek
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
  • Gifford et al.,
  • Cell,
  • 2013
  • Genomics
  • Biology
  • Alex K. Shalek
Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli
  • Gat-Viks et al.,
  • Nature Biotechnology,
  • 2013
  • Biology
  • Immunology
  • Alex K. Shalek
Dynamic regulatory network controlling TH17 cell differentiation
  • Yosef et al.,
  • Nature,
  • 2013
  • Immunology
  • Genomics
  • Biology
  • Alex K. Shalek
Probing Enzymatic Activity inside Living Cells Using a Nanowire−Cell “Sandwich” Assay
  • Na et al.,
  • Nano Letters,
  • 2013
  • Chemistry
  • Immunology
  • Biology
  • Technology
  • Alex K. Shalek
Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits
  • Robinson et al.,
  • Nature Nanotechnology,
  • 2012
  • Technology
  • Biology
  • Chemistry
  • Alex K. Shalek
Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits
  • Chevrier et al.,
  • Cell,
  • 2011
  • Immunology
  • Genomics
  • Infectious Disease
  • Alex K. Shalek
Vertical silicon nanowires as a universal platform for delivering biomolecules into living cells
  • Shalek et al.,
  • PNAS,
  • 2010
  • Physics
  • Technology
  • R&D
  • Genomics
  • Chemistry
  • Alex K. Shalek
Photoinduced Interfacial Charging and “Explosion” of Monolayer Pentacene Islands
  • Chen L. et al.,
  • Nano Lett,
  • 2005
  • R&D
  • Chemistry
  • Technology
  • Physics
  • Alex K. Shalek