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2021
Deciphering the state of immune silence in fatal COVID-19 patients
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NASH limits anti-tumour surveillance in immunotherapy-treated HCC
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Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing
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Meningeal lymphoid structures are activated under acute and chronic spinal cord pathologies
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NF-κB activity during pancreas development regulates adult β-cell mass by modulating neonatal β-cell proliferation and apoptosis
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Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors
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2020
A single cell atlas of the human liver tumor microenvironment
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Elevated Calprotectin and Abnormal Myeloid Cell Subsets Discriminate Severe from Mild COVID-19
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LifeTime and improving European healthcare through cell-based interceptive medicine
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Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer
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Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4(+) and PDPN+ CAFs to clinical outcome
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Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma
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Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19
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The Physiology, Pathology, and Potential Therapeutic Applications of the TREM2 Signaling Pathway
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Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients
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C/EBP beta-Dependent Epigenetic Memory Induces Trained Immunity in Hematopoietic Stem Cells
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Cxcl10(+) monocytes define a pathogenic subset in the central nervous system during autoimmune neuroinflammation
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Maternal Type-I interferon signaling adversely affects the microglia and the behavior of the offspring accompanied by increased sensitivity to stress
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Lgr5+telocytes are a signaling source at the intestinal villus tip
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Dissecting cellular crosstalk by sequencing physically interacting cells
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Bystander IFN-gamma activity promotes widespread and sustained cytokine signaling altering the tumor microenvironment
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Single-cell genomic approaches for developing the next generation of immunotherapies
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Spatiotemporal regulation of type I interferon expression determines the antiviral polarization of CD4(+) T cells
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2019
Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program
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ETS Proteins Bind with Glucocorticoid Receptors: Relevance for Treatment of Ewing Sarcoma
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Plasmacytoid dendritic cells develop from Ly6D(+) lymphoid progenitors distinct from the myeloid lineage
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A niche-dependent myeloid transcriptome signature defines dormant myeloma cells
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Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations
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MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing
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Corticosteroid signaling at the brain-immune interface impedes coping with severe psychological stress
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Cell composition analysis of bulk genomics using single-cell data
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DC Respond to Cognate T Cell Interaction in the Antigen-Challenged Lymph Node
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Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma
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Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules
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Single-Cell Analysis of Diverse Pathogen Responses Defines a Molecular Roadmap for Generating Antigen-Specific Immunity
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PD-1/PD-L1 checkpoint blockade harnesses monocyte-derived macrophages to combat cognitive impairment in a tauopathy mouse model
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2018
Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma
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Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting
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From the Human Cell Atlas to dynamic immune maps in human disease
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Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling
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Differences in Cell Cycle Status Underlie Transcriptional Heterogeneity in the HSC Compartment
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Early metazoan cell type diversity and the evolution of multicellular gene regulation
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Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis
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The bone marrow is patrolled by NK cells that are primed and expand in response to systemic viral activation
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Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells
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Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing
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Trained Memory of Human Uterine NK Cells Enhances Their Function in Subsequent Pregnancies
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Disease-Associated Microglia: A Universal Immune Sensor of Neurodegeneration
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Microglial immune checkpoint mechanisms
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Salient experiences are represented by unique transcriptional signatures in the mouse brain
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Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries
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A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies
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Microbiome Influences Prenatal and Adult Microglia in a Sex-Specific Manner
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2017
Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq
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Science Forum: The Human Cell Atlas
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High-Resolution Dissection of Conducive Reprogramming Trajectory to Ground State Pluripotency
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Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner
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Immunology, one cell at a time
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MicroRNA-142 controls thymocyte proliferation
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A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease
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Dicer Deficiency Differentially Impacts Microglia of the Developing and Adult Brain
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Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses
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Genomic Characterization of Murine Monocytes Reveals C/EBP beta Transcription Factor Dependence of Ly6C(-) Cells
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Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression
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Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation
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Single-cell transcriptome conservation in cryopreserved cells and tissues
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Transcriptional programs that control expression of the autoimmune regulator gene Aire
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CD74 is a novel transcription regulator
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Autonomous TNF is critical for in vivo monocyte survival in steady state and inflammation
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2016
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq
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Extracellular Matrix Proteolysis by MT1-MMP Contributes to InfluenzaInfluenza-Related Tissue Damage and Mortality
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Distinct biological events generated by ECM proteolysis by two homologous collagenases
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Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution.
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M-sec regulates polarized secretion of inflammatory endothelial chemokines and facilitates CCL2-mediated lymphocyte transendothelial migration
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Microglia development follows a stepwise program to regulate brain homeostasis.
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Voices Of Biotech
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Sumoylation coordinates the repression of inflammatory and anti-viral gene-expression programs during innate sensing
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PD-1 immune checkpoint blockade reduces pathology and improves memory in mouse models of Alzheimer's disease
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The role of the local environment and epigenetics in shaping macrophage identity and their effect on tissue homeostasis
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2015
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors
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Making the case for chromatin profiling: a new tool to investigate the immune-regulatory landscape
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From mass cytometry to cancer prognosis
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Distinct Murine Mucosal Langerhans Cell Subsets Develop from Pre-dendritic Cells and Monocytes
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DCs are ready to commit
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Simultaneous measurement of genome-wide transcription elongation speeds and rates of RNA polymerase II transition into active elongation with 4sUDRB-seq
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Derivation of novel human ground state naive pluripotent stem cells (vol 504, pg 282, 2013)
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Deterministic direct reprogramming of somatic cells to pluripotency (vol 502, pg 65, 2013)
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High-Resolution Chromatin Dynamics during a Yeast Stress Response
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Transcription factor binding dynamics during human ES cell differentiation
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m(6)A mRNA methylation facilitates resolution of naive pluripotency toward differentiation
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Each cell counts: Hematopoiesis and immunity research in the era of single cell genomics
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2014
A Negative Feedback Loop of Transcription Factors Specifies Alternative Dendritic Cell Chromatin States
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Chronic exposure to TGF beta 1 regulates myeloid cell inflammatory response in an IRF7-dependent manner
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Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment
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High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies
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Sequential Feedback Induction Stabilizes the Phosphate Starvation Response in Budding Yeast
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Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function
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Aging-induced immunological signature of the brain's choroid plexus negatively regulates neurogenesis and cognitive function
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Aging-induced type I interferon response at the choroid plexus negatively affects brain function
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The central nervous system microenvironment imprints microglial inability to switch from pro- to anti-inflammatory phenotype
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The role of chromatin dynamics in immune cell development
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Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators
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Chromatin state dynamics during blood formation
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Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types
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Digital cell quantification identifies global immune cell dynamics during influenza infection
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4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells
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2013
Derivation of novel human ground state naive pluripotent stem cells
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Semiconductor-based DNA sequencing of histone modification states
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Deterministic direct reprogramming of somatic cells to pluripotency
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Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli
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High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states
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Mononuclear phagocyte miRNome analysis identifies miR-142 as critical regulator of murine dendritic cell homeostasis
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2012
The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming
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Expression Noise and Acetylation Profiles Distinguish HDAC Functions
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M(odu)LLating the Innate Response
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EGR1 and the ERK-ERF axis drive mammary cell migration in response to EGF
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2011
Strategies to discover regulatory circuits of the mammalian immune system
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2010
EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors
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2007
Evolvable signaling networks of receptor tyrosine kinases: relevance of robustness to malignancy and to cancer therapy
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Systems approach to growth factor signaling and to therapeutic intervention
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A reciprocal tensin-3-cten switch mediates EGF-driven mammary cell migration
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Regulation of MAPKs by growth factors and receptor tyrosine kinases
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A module of negative feedback regulators defines growth factor signaling
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2005
Suppressors of cytokine signaling 4 and 5 regulate epidermal growth factor receptor signaling
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2004
LRIG1 restricts growth factor signaling by enhancing receptor ubiquitylation and degradation
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Tal, a Tsg101-specific E3 ubiquitin ligase, regulates receptor endocytosis and retrovirus budding
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