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  1. Article ; Online: Baring cellular souls.

    Shalek, Alex K

    Science translational medicine

    2017  Volume 9, Issue 377

    Abstract: Coupling chemical approaches for disrupting DNA-protein complexes in intact nuclei with combinatorial barcoding enables high-throughput single-cell DNA sequencing. ...

    Abstract Coupling chemical approaches for disrupting DNA-protein complexes in intact nuclei with combinatorial barcoding enables high-throughput single-cell DNA sequencing.
    MeSH term(s) Cell Nucleus ; DNA Barcoding, Taxonomic ; High-Throughput Nucleotide Sequencing
    Language English
    Publishing date 2017-02-15
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.aam6064
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A case of mistaken identity.

    Shalek, Alex K

    Science translational medicine

    2017  Volume 9, Issue 371

    Language English
    Publishing date 2017-01-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.aal4988
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Comparative analysis of cell-cell communication at single-cell resolution.

    Wilk, Aaron J / Shalek, Alex K / Holmes, Susan / Blish, Catherine A

    Nature biotechnology

    2023  Volume 42, Issue 3, Page(s) 470–483

    Abstract: Inference of cell-cell communication from single-cell RNA sequencing data is a powerful technique to uncover intercellular communication pathways, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell- ...

    Abstract Inference of cell-cell communication from single-cell RNA sequencing data is a powerful technique to uncover intercellular communication pathways, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell-level information. Here we present Scriabin, a flexible and scalable framework for comparative analysis of cell-cell communication at single-cell resolution that is performed without cell aggregation or downsampling. We use multiple published atlas-scale datasets, genetic perturbation screens and direct experimental validation to show that Scriabin accurately recovers expected cell-cell communication edges and identifies communication networks that can be obscured by agglomerative methods. Additionally, we use spatial transcriptomic data to show that Scriabin can uncover spatial features of interaction from dissociated data alone. Finally, we demonstrate applications to longitudinal datasets to follow communication pathways operating between timepoints. Our approach represents a broadly applicable strategy to reveal the full structure of niche-phenotype relationships in health and disease.
    MeSH term(s) Cell Communication/genetics ; Gene Expression Profiling ; Transcriptome ; Single-Cell Analysis
    Language English
    Publishing date 2023-05-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1311932-1
    ISSN 1546-1696 ; 1087-0156
    ISSN (online) 1546-1696
    ISSN 1087-0156
    DOI 10.1038/s41587-023-01782-z
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  4. Article ; Online: Size no longer matters.

    Shalek, Alex K

    Science translational medicine

    2016  Volume 8, Issue 365, Page(s) 365ec185

    Language English
    Publishing date 2016-11-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.aal0073
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Comparative analysis of cell-cell communication at single-cell resolution.

    Wilk, Aaron J / Shalek, Alex K / Holmes, Susan / Blish, Catherine A

    bioRxiv : the preprint server for biology

    2022  

    Abstract: Inference of cell-cell communication (CCC) from single-cell RNA-sequencing data is a powerful technique to uncover putative axes of multicellular coordination, yet existing methods perform this analysis at the level of the cell type or cluster, ... ...

    Abstract Inference of cell-cell communication (CCC) from single-cell RNA-sequencing data is a powerful technique to uncover putative axes of multicellular coordination, yet existing methods perform this analysis at the level of the cell type or cluster, discarding single-cell level information. Here we present Scriabin â€" a flexible and scalable framework for comparative analysis of CCC at single-cell resolution. We leverage multiple published datasets to show that Scriabin recovers expected CCC edges and use spatial transcriptomic data, genetic perturbation screens, and direct experimental manipulation of receptor-ligand interactions to validate that the recovered edges are biologically meaningful. We then apply Scriabin to uncover co-expressed programs of CCC from atlas-scale datasets, validating known communication pathways required for maintaining the intestinal stem cell niche and revealing species-specific communication pathways. Finally, we utilize single-cell communication networks calculated using Scriabin to follow communication pathways that operate between timepoints in longitudinal datasets, highlighting bystander cells as important initiators of inflammatory reactions in acute SARS-CoV-2 infection. Our approach represents a broadly applicable strategy to leverage single-cell resolution data maximally toward uncovering CCC circuitry and rich niche-phenotype relationships in health and disease.
    Language English
    Publishing date 2022-07-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2022.02.04.479209
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Revisiting airway epithelial remodeling in type 2 immunity: Beyond goblet cell metaplasia.

    Barrett, Nora A / Shalek, Alex K

    The Journal of allergy and clinical immunology

    2019  Volume 144, Issue 5, Page(s) 1158–1160

    MeSH term(s) Airway Remodeling ; Animals ; Asthma/immunology ; Cell Differentiation ; Cytokines/metabolism ; Goblet Cells/pathology ; Goblet Cells/physiology ; Humans ; Inflammation/immunology ; Metaplasia ; Mice ; Nasal Polyps/immunology ; Respiratory Mucosa/pathology ; Respiratory Mucosa/physiology ; Sequence Analysis, RNA ; Single-Cell Analysis ; Th2 Cells/immunology
    Chemical Substances Cytokines
    Language English
    Publishing date 2019-10-07
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 121011-7
    ISSN 1097-6825 ; 1085-8725 ; 0091-6749
    ISSN (online) 1097-6825 ; 1085-8725
    ISSN 0091-6749
    DOI 10.1016/j.jaci.2019.09.017
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  7. Article ; Online: The Human Cell Atlas and equity: lessons learned.

    Majumder, Partha P / Mhlanga, Musa M / Shalek, Alex K

    Nature medicine

    2020  Volume 26, Issue 10, Page(s) 1509–1511

    MeSH term(s) Atlases as Topic ; Biomedical Research/ethics ; Biomedical Research/organization & administration ; Biomedical Research/trends ; Career Choice ; Career Mobility ; Cell Physiological Phenomena ; Cross-Cultural Comparison ; Female ; Health Equity/organization & administration ; Health Equity/trends ; Humans ; Male ; Patient Advocacy ; Patient Selection/ethics ; Racism/prevention & control ; Racism/trends ; Research Subjects ; Science/ethics ; Science/organization & administration ; Science/trends ; Socioeconomic Factors ; Whites
    Keywords covid19
    Language English
    Publishing date 2020-10-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-020-1100-4
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  8. Article ; Online: Evolution and Diversity of Immune Responses during Acute HIV Infection.

    Kazer, Samuel W / Walker, Bruce D / Shalek, Alex K

    Immunity

    2020  Volume 53, Issue 5, Page(s) 908–924

    Abstract: Understanding the earliest immune responses following HIV infection is critical to inform future vaccines and therapeutics. Here, we review recent prospective human studies in at-risk populations that have provided insight into immune responses during ... ...

    Abstract Understanding the earliest immune responses following HIV infection is critical to inform future vaccines and therapeutics. Here, we review recent prospective human studies in at-risk populations that have provided insight into immune responses during acute infection, including additional relevant data from non-human primate (NHP) studies. We discuss the timing, nature, and function of the diverse immune responses induced, the onset of immune dysfunction, and the effects of early anti-retroviral therapy administration. Treatment at onset of viremia mitigates peripheral T and B cell dysfunction, limits seroconversion, and enhances cellular antiviral immunity despite persistence of infection in lymphoid tissues. We highlight pertinent areas for future investigation, and how application of high-throughput technologies, alongside targeted NHP studies, may elucidate immune response features to target in novel preventions and cures.
    MeSH term(s) Acute Disease ; Adaptive Immunity ; Animals ; Antiretroviral Therapy, Highly Active ; Biological Evolution ; CD4 Lymphocyte Count ; CD4-Positive T-Lymphocytes/immunology ; CD4-Positive T-Lymphocytes/metabolism ; Cytokines/metabolism ; Disease Management ; HIV/immunology ; HIV Infections/immunology ; HIV Infections/therapy ; HIV Infections/virology ; Host-Pathogen Interactions/immunology ; Humans ; Immunity ; Immunity, Innate ; Inflammation Mediators/metabolism ; Lymphoid Tissue/immunology ; Lymphoid Tissue/metabolism ; Simian Acquired Immunodeficiency Syndrome/immunology ; Simian Acquired Immunodeficiency Syndrome/virology ; Simian Immunodeficiency Virus/immunology ; Time-to-Treatment ; Treatment Outcome ; Viral Load
    Chemical Substances Cytokines ; Inflammation Mediators
    Language English
    Publishing date 2020-11-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1217235-2
    ISSN 1097-4180 ; 1074-7613
    ISSN (online) 1097-4180
    ISSN 1074-7613
    DOI 10.1016/j.immuni.2020.10.015
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  9. Article ; Online: Single-cell analyses to tailor treatments.

    Shalek, Alex K / Benson, Mikael

    Science translational medicine

    2017  Volume 9, Issue 408

    Abstract: Single-cell RNA-seq could play a key role in personalized medicine by facilitating characterization of cells, pathways, and genes associated with human diseases such as cancer. ...

    Abstract Single-cell RNA-seq could play a key role in personalized medicine by facilitating characterization of cells, pathways, and genes associated with human diseases such as cancer.
    Language English
    Publishing date 2017-09-20
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.aan4730
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  10. Article ; Online: Vitrification preserves follicular transcriptomic dynamics during ex vivo ovulation†.

    Zhang, Jiyang / Russo, Daniela D / Wang, Yingzheng / Zhang, Qiang / Zelinski, Mary B / Shalek, Alex K / Goods, Brittany A / Xiao, Shuo

    Biology of reproduction

    2023  Volume 109, Issue 3, Page(s) 240–243

    MeSH term(s) Female ; Humans ; Vitrification ; Transcriptome ; Ovulation ; Ovarian Follicle ; Cryopreservation
    Language English
    Publishing date 2023-08-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1118-6
    ISSN 1529-7268 ; 0006-3363
    ISSN (online) 1529-7268
    ISSN 0006-3363
    DOI 10.1093/biolre/ioad083
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