The Immunological Genome Project: networks of gene expression in immune cells

A gene atlas of the mouse and human protein-encoding transcriptomes

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Regulatory T Cell Lineage Specification by the Forkhead Transcription Factor Foxp3

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The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

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Interferon and Granulopoiesis Signatures in Systemic Lupus Erythematosus Blood

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Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data

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Molecular and functional profiling of memory CD8 T cell differentiation.

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Standardizing global gene expression analysis between laboratories and across platforms

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Micromanagement of the immune system by microRNAs

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Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data

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Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks

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Addendum: Standardizing global gene expression analysis between laboratories and across platforms

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Relationships Among Murine CD11chigh Dendritic Cell Subsets as Revealed by Baseline Gene Expression Patterns

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Genomic approaches to hematologic malignancies

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Construction of an open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells

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Gene expression microarrays: glimpses of the immunological genome

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Rules for Gene Usage Inferred from a Comparison of Large-Scale Gene Expression Profiles of T and B Lymphocyte Development

Hoffmann, R. F. G., Bruno, L., Seidl, T., Rolink, A. G., & Melchers, F. (2003) · The Journal of Immunology · doi:10.4049/jimmunol.170.3.1339 · Cited by 62 · see citing works

The Regulated Expression of a Diverse Set of Genes during Thymocyte Positive Selection In Vivo

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Progression to Islet Destruction in a Cyclophosphamide-Induced Transgenic Model

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Conceptual-level workflow modeling of scientific experiments using NMR as a case study

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The Genopolis Microarray Database

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Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

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NicheNet: Modeling intercellular communication by linking ligands to target genes

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Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation

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Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages

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NK Cells Stimulate Recruitment of cDC1 into the Tumor Microenvironment Promoting Cancer Immune Control

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TREM2 Lipid Sensing Sustains the Microglial Response in an Alzheimer’s Disease Model

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A rapid and robust method for single cell chromatin accessibility profiling

Chen, X., Miragaia, R. J., Natarajan, K. N., & Teichmann, S. A. (2018) · Nature Communications · doi:10.1038/s41467-018-07771-0 · Cited by 1,147 · see citing works

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

Finucane, H. K., Reshef, Y. A., Anttila, V., Slowikowski, K., Gusev, A., Byrnes, A., Gazal, S., Loh, P.-R., Lareau, C., Shoresh, N., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0081-4 · Cited by 1,097 · see citing works

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

Reyfman, P. A., Walter, J. M., Joshi, N., Anekalla, K. R., McQuattie-Pimentel, A. C., Chiu, S., Fernandez, R., Akbarpour, M., Chen, C.-I., Ren, Z., et al. (2019) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201712-2410oc · Cited by 1,203 · see citing works

A Validated Regulatory Network for Th17 Cell Specification

Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C. N., Muratet, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.016 · Cited by 1,160 · see citing works

PPAR-γ is a major driver of the accumulation and phenotype of adipose tissue Treg cells

Cipolletta, D., Feuerer, M., Li, A., Kamei, N., Lee, J., Shoelson, S. E., Benoist, C., & Mathis, D. (2012) · Nature · doi:10.1038/nature11132 · Cited by 1,143 · see citing works

Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1

Wu, C., Yosef, N., Thalhamer, T., Zhu, C., Xiao, S., Kishi, Y., Regev, A., & Kuchroo, V. K. (2013) · Nature · doi:10.1038/nature11984 · Cited by 1,022 · see citing works

Control of amino-acid transport by antigen receptors coordinates the metabolic reprogramming essential for T cell differentiation

Sinclair, L. V., Rolf, J., Emslie, E., Shi, Y.-B., Taylor, P. M., & Cantrell, D. A. (2013) · Nature Immunology · doi:10.1038/ni.2556 · Cited by 930 · see citing works

Fap2 Mediates Fusobacterium nucleatum Colorectal Adenocarcinoma Enrichment by Binding to Tumor-Expressed Gal-GalNAc

Abed, J., Emgård, J. E. M., Zamir, G., Faroja, M., Almogy, G., Grenov, A., Sol, A., Naor, R., Pikarsky, E., Atlan, K. A., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.07.006 · Cited by 888 · see citing works

Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer’s Disease Not Evident in Mouse Models

Friedman, B. A., Srinivasan, K., Ayalon, G., Meilandt, W. J., Lin, H., Huntley, M. A., Cao, Y., Lee, S.-H., Haddick, P. C. G., Ngu, H., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2017.12.066 · Cited by 662 · see citing works

Dynamic regulatory network controlling TH17 cell differentiation

Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., et al. (2013) · Nature · doi:10.1038/nature11981 · Cited by 682 · see citing works

Functional characterization of the dural sinuses as a neuroimmune interface

Rustenhoven, J., Drieu, A., Mamuladze, T., de Lima, K. A., Dykstra, T., Wall, M., Papadopoulos, Z., Kanamori, M., Salvador, A. F., Baker, W., et al. (2021) · Cell · doi:10.1016/j.cell.2020.12.040 · Cited by 685 · see citing works

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

Angelidis, I., Simon, L. M., Fernandez, I. E., Strunz, M., Mayr, C. H., Greiffo, F. R., Tsitsiridis, G., Ansari, M., Graf, E., Strom, T.-M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08831-9 · Cited by 637 · see citing works

A Neurodegeneration-Specific Gene-Expression Signature of Acutely Isolated Microglia from an Amyotrophic Lateral Sclerosis Mouse Model

Chiu, I. M., Morimoto, E. T. A., Goodarzi, H., Liao, J. T., O’Keeffe, S., Phatnani, H. P., Muratet, M., Carroll, M. C., Levy, S., Tavazoie, S., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.06.018 · Cited by 651 · see citing works

Wishbone identifies bifurcating developmental trajectories from single-cell data

Setty, M., Tadmor, M. D., Reich-Zeliger, S., Angel, O., Salame, T. M., Kathail, P., Choi, K., Bendall, S., Friedman, N., & Pe'er, D. (2016) · Nature Biotechnology · doi:10.1038/nbt.3569 · Cited by 558 · see citing works

Stellate Cells, Hepatocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche

Bonnardel, J., T’Jonck, W., Gaublomme, D., Browaeys, R., Scott, C. L., Martens, L., Vanneste, B., De Prijck, S., Nedospasov, S. A., Kremer, A., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.08.017 · Cited by 631 · see citing works

Stability and function of regulatory T cells is maintained by a neuropilin-1–semaphorin-4a axis

Delgoffe, G. M., Woo, S.-R., Turnis, M. E., Gravano, D. M., Guy, C., Overacre, A. E., Bettini, M. L., Vogel, P., Finkelstein, D., Bonnevier, J., et al. (2013) · Nature · doi:10.1038/nature12428 · Cited by 587 · see citing works

Class IIa HDAC inhibition reduces breast tumours and metastases through anti-tumour macrophages

Guerriero, J. L., Sotayo, A., Ponichtera, H. E., Castrillon, J. A., Pourzia, A. L., Schad, S., Johnson, S. F., Carrasco, R. D., Lazo, S., Bronson, R. T., et al. (2017) · Nature · doi:10.1038/nature21409 · Cited by 558 · see citing works

A combination of ontogeny and CNS environment establishes microglial identity

Bennett, F. C., Bennett, M. L., Yaqoob, F., Mulinyawe, S. B., Grant, G. A., Hayden Gephart, M., Plowey, E. D., & Barres, B. A. (2018) · Neuron · doi:10.1016/j.neuron.2018.05.014 · Cited by 524 · see citing works

Determinants of resident tissue macrophage identity and function

Blériot, C., Chakarov, S., & Ginhoux, F. (2020) · Immunity · doi:10.1016/j.immuni.2020.05.014 · Cited by 507 · see citing works

Nociceptive Sensory Fibers Drive Interleukin-23 Production from CD301b+ Dermal Dendritic Cells and Drive Protective Cutaneous Immunity

Kashem, S. W., Riedl, M. S., Yao, C., Honda, C. N., Vulchanova, L., & Kaplan, D. H. (2015) · Immunity · doi:10.1016/j.immuni.2015.08.016 · Cited by 448 · see citing works

Magnitude of Therapeutic STING Activation Determines CD8+ T Cell-Mediated Anti-tumor Immunity

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Heme-mediated SPI-C induction promotes monocyte differentiation into iron-recycling macrophages

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Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

Marsh, S. E., Walker, A. J., Kamath, T., Dissing-Olesen, L., Hammond, T. R., de Soysa, T. Y., Young, A. M. H., Murphy, S., Abdulraouf, A., Nadaf, N., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01022-8 · Cited by 432 · see citing works

Population snapshots predict early haematopoietic and erythroid hierarchies

Tusi, B. K., Wolock, S. L., Weinreb, C., Hwang, Y., Hidalgo, D., Zilionis, R., Waisman, A., Huh, J. R., Klein, A. M., & Socolovsky, M. (2018) · Nature · doi:10.1038/nature25741 · Cited by 384 · see citing works

Peripherally derived macrophages can engraft the brain independent of irradiation and maintain an identity distinct from microglia

Cronk, J. C., Filiano, A. J., Louveau, A., Marin, I., Marsh, R., Ji, E., Goldman, D. H., Smirnov, I., Geraci, N., Acton, S., et al. (2018) · Journal of Experimental Medicine · doi:10.1084/jem.20180247 · Cited by 412 · see citing works

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR

Zemmour, D., Zilionis, R., Kiner, E., Klein, A. M., Mathis, D., & Benoist, C. (2018) · Nature Immunology · doi:10.1038/s41590-018-0051-0 · Cited by 384 · see citing works

Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states

Furman, D., Chang, J., Lartigue, L., Bolen, C. R., Haddad, F., Gaudilliere, B., Ganio, E. A., Fragiadakis, G. K., Spitzer, M. H., Douchet, I., et al. (2017) · Nature Medicine · doi:10.1038/nm.4267 · Cited by 389 · see citing works

Epigenetic regulation of the innate immune response to infection

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Parsing the interferon transcriptional network and its disease associations

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Immune Signaling in Neurodegeneration

Hammond, T. R., Marsh, S. E., & Stevens, B. (2019) · Immunity · doi:10.1016/j.immuni.2019.03.016 · Cited by 336 · see citing works

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

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A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies

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Epigenetic therapy inhibits metastases by disrupting premetastatic niches

Lu, Z., Zou, J., Li, S., Topper, M. J., Tao, Y., Zhang, H., Jiao, X., Xie, W., Kong, X., Vaz, M., et al. (2020) · Nature · doi:10.1038/s41586-020-2054-x · Cited by 330 · see citing works

Mitochondrial fragmentation limits NK cell-based tumor immunosurveillance

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ImmGen report: sexual dimorphism in the immune system transcriptome

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Tet2 restrains inflammatory gene expression in macrophages

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Loss-of-function mutations in the <i>C9ORF72</i> mouse ortholog cause fatal autoimmune disease

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C9orf72 ablation causes immune dysregulation characterized by leukocyte expansion, autoantibody production and glomerulonephropathy in mice

Atanasio, A., Decman, V., White, D., Ramos, M., Ikiz, B., Lee, H.-C., Siao, C.-J., Brydges, S., LaRosa, E., Bai, Y., et al. (2016) · Scientific Reports · doi:10.1038/srep23204 · Cited by 263 · see citing works

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses

Xu, H., Ding, J., Porter, C. B. M., Wallrapp, A., Tabaka, M., Ma, S., Fu, S., Guo, X., Riesenfeld, S. J., Su, C., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.09.004 · Cited by 273 · see citing works

The cytotoxic T cell proteome and its shaping by the kinase mTOR

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The expanding incretin universe: from basic biology to clinical translation

Drucker, D. J., & Holst, J. J. (2023) · Diabetologia · doi:10.1007/s00125-023-05906-7 · Cited by 243 · see citing works

Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and weight regain in mice

Cottam, M. A., Caslin, H. L., Winn, N. C., & Hasty, A. H. (2022) · Nature Communications · doi:10.1038/s41467-022-30646-4 · Cited by 216 · see citing works

Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells

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Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells

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Cxcr4 distinguishes HSC-derived monocytes from microglia and reveals monocyte immune responses to experimental stroke

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CNS fibroblasts form a fibrotic scar in response to immune cell infiltration.

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Microglia and C9orf72 in neuroinflammation and ALS and frontotemporal dementia

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Immunomodulation by anticancer cell cycle inhibitors

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A Transcriptomic Method to Determine Airway Immune Dysfunction in T2-High and T2-Low Asthma

Peters, M. C., Ringel, L., Dyjack, N., Herrin, R., Woodruff, P. G., Rios, C., O’Connor, B., Fahy, J. V., & Seibold, M. A. (2019) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201807-1291oc · Cited by 151 · see citing works

Divergent roles for the gut intraepithelial lymphocyte GLP-1R in control of metabolism, microbiota, and T cell-induced inflammation

Wong, C. K., Yusta, B., Koehler, J. A., Baggio, L. L., McLean, B. A., Matthews, D., Seeley, R. J., & Drucker, D. J. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.08.003 · Cited by 138 · see citing works

clustifyr: an R package for automated single-cell RNA sequencing cluster classification

Fu, R., Gillen, A. E., Sheridan, R. M., Tian, C., Daya, M., Hao, Y., Hesselberth, J. R., & Riemondy, K. A. (2020) · F1000Research · doi:10.12688/f1000research.22969.2 · Cited by 135 · see citing works

Efficient Generation of Transcriptomic Profiles by Random Composite Measurements

Cleary, B., Cong, L., Cheung, A., Lander, E. S., & Regev, A. (2017) · Cell · doi:10.1016/j.cell.2017.10.023 · Cited by 114 · see citing works

Interferon regulatory factor 5 controls necrotic core formation in atherosclerotic lesions by impairing efferocytosis

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