Dana Pe'er
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Computer Science Biology
Dana Pe'er's Degrees
- PhD Computer Science Stanford University
- Bachelors Computer Science Tel Aviv University
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Why Is Dana Pe'er Influential?
(Suggest an Edit or Addition)According to Wikipedia, Dana Pe'er , Chair and Professor in Computational and Systems Biology Program at Sloan Kettering Institute is a researcher in computational systems biology. A Howard Hughes Medical Institute Investigator since 2021, she was previously a professor at Columbia Department of Biological Sciences. Pe'er's research focuses on understanding the organization, function and evolution of molecular networks, particularly how genetic variations alter the regulatory network and how these genetic variations can cause cancer.
Dana Pe'er's Published Works
Published Works
- Using Bayesian networks to analyze expression data (2000) (3562)
- Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum (2011) (2059)
- SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues (2020) (1833)
- Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data (2003) (1826)
- SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes (2020) (1723)
- Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data (2005) (1633)
- Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis (2015) (1454)
- viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia (2013) (1395)
- The Human Cell Atlas (2017) (1285)
- Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment (2018) (1054)
- Recovering Gene Interactions from Single-Cell Data Using Data Diffusion (2018) (950)
- Distinct Cellular Mechanisms Underlie Anti-CTLA-4 and Anti-PD-1 Checkpoint Blockade (2017) (819)
- Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses (2017) (791)
- Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development (2014) (787)
- Chromosomal instability drives metastasis through a cytosolic DNA response (2017) (766)
- An Immune Atlas of Clear Cell Renal Cell Carcinoma (2017) (655)
- Learning Bayesian Network Structure from Massive Datasets: The "Sparse Candidate" Algorithm (1999) (649)
- Inferring subnetworks from perturbed expression profiles (2001) (615)
- Normalization of mass cytometry data with bead standards (2013) (568)
- Toward understanding and exploiting tumor heterogeneity (2015) (557)
- Wishbone identifies bifurcating developmental trajectories from single-cell data (2016) (507)
- An Integrated Approach to Uncover Drivers of Cancer (2010) (472)
- Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm (2015) (399)
- Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance (2016) (350)
- High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis (2009) (307)
- PD-1 Blockade Expands Intratumoral Memory T Cells (2016) (288)
- Characterization of cell fate probabilities in single-cell data with Palantir (2019) (257)
- Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity (2019) (247)
- The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution (2020) (234)
- Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands (2015) (208)
- Learning a Prior on Regulatory Potential from eQTL Data (2009) (206)
- The emergent landscape of the mouse gut endoderm at single-cell resolution (2019) (205)
- Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19 (2020) (205)
- Regenerative lineages and immune-mediated pruning in lung cancer metastasis (2019) (203)
- Conditional density-based analysis of T cell signaling in single-cell data (2014) (200)
- Epigenomic‐Guided Mass Cytometry Profiling Reveals Disease‐Specific Features of Exhausted CD8 T Cells (2018) (196)
- Bayesian Network Analysis of Signaling Networks: A Primer (2005) (181)
- Principles and Strategies for Developing Network Models in Cancer (2011) (181)
- Combination anti–CTLA-4 plus anti–PD-1 checkpoint blockade utilizes cellular mechanisms partially distinct from monotherapies (2019) (179)
- Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma (2019) (177)
- Lineage plasticity in cancer: a shared pathway of therapeutic resistance (2020) (177)
- Concurrent RB1 and TP53 alterations define a subset of EGFR-mutant lung cancers at risk for histologic transformation and inferior clinical outcomes. (2019) (177)
- Learning Module Networks (2002) (175)
- CellRank for directed single-cell fate mapping (2020) (169)
- Tumor Analyses Reveal Squamous Transformation and Off-Target Alterations As Early Resistance Mechanisms to First-line Osimertinib in EGFR-Mutant Lung Cancer (2020) (153)
- Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification (2006) (142)
- MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data (2017) (135)
- A single-cell atlas of the human healthy airways (2019) (124)
- Regenerative potential of prostate luminal cells revealed by single-cell analysis (2020) (121)
- Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation. (2017) (120)
- Modulatory profiling identifies mechanisms of small molecule-induced cell death (2011) (107)
- Scalable microfluidics for single-cell RNA printing and sequencing (2015) (107)
- L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer (2020) (96)
- Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data (2016) (96)
- Mapping Differentiation under Mixed Culture Conditions Reveals a Tunable Continuum of T Cell Fates (2013) (95)
- Trajectories of cell-cycle progression from fixed cell populations (2015) (92)
- Cancer cells deploy lipocalin-2 to collect limiting iron in leptomeningeal metastasis (2020) (92)
- Environmental Stresses Disrupt Telomere Length Homeostasis (2013) (91)
- Integration of Genomic Data Enables Selective Discovery of Breast Cancer Drivers (2014) (87)
- Minreg: Inferring an active regulator set (2002) (86)
- Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. (2021) (78)
- A gene-environment induced epigenetic program initiates tumorigenesis (2021) (74)
- Fully defined human pluripotent stem cell-derived microglia and tri-culture system model C3 production in Alzheimer’s disease (2021) (74)
- Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation. (2019) (70)
- Integrated Single-Cell Atlas of Endothelial Cells of the Human Lung (2020) (70)
- Genotype-Environment Interactions Reveal Causal Pathways That Mediate Genetic Effects on Phenotype (2013) (68)
- A Single-cell Atlas of the Human Healthy Airways. (2020) (67)
- Modularity and interactions in the genetics of gene expression (2009) (65)
- The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland (2014) (62)
- Negative Co‐stimulation Constrains T Cell Differentiation by Imposing Boundaries on Possible Cell States (2019) (60)
- A roadmap for the Human Developmental Cell Atlas (2021) (57)
- The Human Cell Atlas White Paper (2018) (55)
- RHPN2 drives mesenchymal transformation in malignant glioma by triggering RhoA activation. (2013) (54)
- Single-cell mass cytometry of TCR signaling: Amplification of small initial differences results in low ERK activation in NOD mice (2014) (53)
- JISTIC: Identification of Significant Targets in Cancer (2010) (53)
- Harnessing gene expression to identify the genetic basis of drug resistance (2009) (49)
- NFkB disrupts tissue polarity in 3D by preventing integration of microenvironmental signals (2013) (44)
- Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells. (2019) (41)
- Detection of minimal residual disease in B lymphoblastic leukemia using viSNE (2015) (40)
- MinReg: A Scalable Algorithm for Learning Parsimonious Regulatory Networks in Yeast and Mammals (2006) (39)
- An integrated cell atlas of the human lung in health and disease (2022) (39)
- Bayesian Inference for Single-cell Clustering and Imputing (2017) (38)
- Spatial CRISPR genomics identifies regulators of the tumor microenvironment (2022) (37)
- Single-Cell Transcriptomics Reveals Early Emergence of Liver Parenchymal and Non-parenchymal Cell Lineages (2020) (34)
- The onset of p53 loss of heterozygosity is differentially induced in various stem cell types and may involve the loss of either allele (2014) (31)
- Learning Signaling Network Structures with Sparsely Distributed Data (2009) (31)
- Frontiers in cancer immunotherapy—a symposium report (2020) (29)
- A unified atlas of CD8 T cell dysfunctional states in cancer and infection. (2021) (28)
- Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology (2022) (28)
- Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling (2022) (28)
- Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma. (2015) (28)
- CD49b defines functionally mature Treg cells that survey skin and vascular tissues (2018) (26)
- A unified atlas of CD8 T cell dysfunctional states in cancer and infection (2020) (26)
- PhenoGraph and viSNE facilitate the identification of abnormal T‐cell populations in routine clinical flow cytometric data (2018) (25)
- Tissue-based molecular and histological landscape of acquired resistance to osimertinib given initially or at relapse in patients with EGFR-mutant lung cancers. (2019) (24)
- SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes (2020) (24)
- Module Networks : Discovering Regulatory Modules and their Condition Specific Regulators from Gene Expression Data (2003) (22)
- MITI minimum information guidelines for highly multiplexed tissue images (2021) (22)
- Adult Human Glioblastomas Harbor Radial Glia-like Cells (2020) (22)
- Chronic lung diseases are associated with gene expression programs favoring SARS-CoV-2 entry and severity (2021) (21)
- Engineering γδT cells limits tonic signaling associated with chimeric antigen receptors (2019) (20)
- Radiotherapy orchestrates natural killer cell dependent antitumor immune responses through CXCL8 (2022) (18)
- Single-Cell Immune Map of Breast Carcinoma Reveals Diverse Phenotypic States Driven by the Tumor Microenvironment (2017) (18)
- Lymphatics act as a signaling hub to regulate intestinal stem cell activity. (2022) (16)
- Palantir characterizes cell fate continuities in human hematopoiesis (2018) (15)
- Learning time-varying information flow from single-cell epithelial to mesenchymal transition data (2018) (15)
- Single-cell Map of Diverse Immune Phenotypes Driven by the Tumor Microenvironment (2018) (13)
- Sparcle: assigning transcripts to cells in multiplexed images (2021) (12)
- Context Sensitive Modeling of Cancer Drug Sensitivity (2015) (12)
- Inference of modules associated to eQTLs (2012) (12)
- SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data (2022) (11)
- Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy (2020) (11)
- Author response: The Human Cell Atlas (2017) (10)
- A Nonparametric Multi-view Model for Estimating Cell Type-Specific Gene Regulatory Networks (2019) (8)
- Notch3 signaling promotes tumor cell adhesion and progression in a murine epithelial ovarian cancer model (2020) (7)
- 1 PD-1 blockade expands intratumoral T memory cells (2016) (6)
- Charting the emergent organotypic landscape of the mammalian gut endoderm at single-cell resolution (2018) (6)
- Using systems and structure biology tools to dissect cellular phenotypes (2012) (6)
- Learning Edge Rewiring in EMT From Single Cell Data (2017) (5)
- Stag1 and Stag2 regulate cell fate decisions in hematopoiesis through non-redundant topological control (2019) (5)
- Perturb-map enables CRISPR genomics with spatial resolution and identifies regulators of tumor immune composition (2021) (4)
- A lymphatic-stem cell interactome regulates intestinal stem cell activity (2022) (3)
- MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis (2022) (3)
- Adult Human Glioblastomas Harbor Radial Glia-like Cells (2020) (3)
- Tumor heterogeneity. (2021) (3)
- SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data. (2023) (2)
- Counterfactual Hypothesis Testing of Tumor Microenvironment Scenarios Through Semantic Image Synthesis (2020) (2)
- Abstract NG03: Chromosomal instability promotes metastasis through a cytosolic DNA response (2018) (2)
- Abstract 432: BIN3 is a novel 8p21 tumor suppressor gene that regulates the attachment checkpoint in epithelial cells (2014) (2)
- Author Correction: Characterization of cell fate probabilities in single-cell data with Palantir (2019) (2)
- Single cell profiling reveals novel tumor and myeloid subpopulations in small cell lung cancer (2020) (2)
- Single Cell Trajectory Detection Orders Hallmarks of Early Human B Cell Development (2012) (2)
- Negative costimulation constrains T cell differentiation (2018) (2)
- Human Developmental Cell Atlas: milestones achieved and the roadmap ahead (2020) (2)
- Abstract 592: Distinct cellular mechanisms mediate anti-CTLA-4 and anti-PD-1 checkpoint blockade (2017) (2)
- Author Correction: L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer (2020) (2)
- OA07.01 Signatures of Plasticity and Immunosuppression in a Single-Cell Atlas of Human Small Cell Lung Cancer (2021) (2)
- Dynamic structural cell responses in the thymus to acute injury, regeneration, and age (2021) (2)
- Multilineage plasticity in prostate cancer through expansion of stem–like luminal epithelial cells with elevated inflammatory signaling (2021) (2)
- From gene expression to molecular pathways (מביטוי גנים למסלולים מולקולריים.) (2003) (1)
- Comprehensive Single-Cell RNA-Sequencing Mapping of Primary Acute Myeloid Leukemias and Profiling of NPM1-Mutated Cells (2018) (1)
- STING inhibits the reactivation of dormant metastasis in lung adenocarcinoma (2023) (1)
- Signatures of plasticity and immunosuppression in a single-cell atlas of human small cell lung cancer. (2021) (1)
- Abstract B70: Conexic: A Bayesian framework to detect drivers and their function uncovers an endosomal signature in melanoma (2009) (1)
- Chromosome 9p21.3 Coordinates Cell Intrinsic and Extrinsic Tumor Suppression (2022) (1)
- Publisher Correction: Lineage plasticity in cancer: a shared pathway of therapeutic resistance (2020) (1)
- Can CAD cure cancer? (2013) (1)
- Broadening horizons: holistic viewpoints from the Biology of Genomes (2014) (1)
- ETMM-03. CANCER CELLS DEPLOY LIPOCALIN- 2 TO COLLECT LIMITING IRON IN LEPTOMENINGEAL METASTASIS (2021) (1)
- Analysis of signaling pathways in human T-cells using Bayesian network modeling of single cell data (2004) (1)
- Reversal of lineage plasticity in RB1/TP53-deleted prostate cancer through FGFR and Janus kinase inhibition (2021) (1)
- Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics (2021) (1)
- Supervised discovery of interpretable gene programs from single-cell data (2022) (1)
- Reconstructing a Genotype-Phenotype Map In Chronic Lymphocytic Leukemia (2013) (1)
- Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities (2023) (0)
- Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas (2022) (0)
- Dimensionality Reduction Reveals Distinct Shapes of Normal and Malignant Hematopoietic Cell Populations (2012) (0)
- Abstract B016: Quantifying and dissecting pancreatic cancer cell phenotypic plasticity using lineage tracing, single-cell multiomics and CRISPR perturbations reveals novel regulators of plastic states (2022) (0)
- Mapping the Evolution of T Cell Transcriptional States during DLI Response and Resistance Using Single-Cell Data (2018) (0)
- Lineage plasticity is a well–established mechanism of resistance to targeted therapies in lung and prostate cancer, where tumors transition from adenocarcinoma to small–cell or neuroendocrine carcinoma. Through single–cell analysis of a cohort of heavily–treated castration–resistant human prostate c (2021) (0)
- The covariance environment defines cellular niches for spatial inference (2023) (0)
- Protocol to dissociate, process, and analyze the human lung tissue using single-cell RNA-seq (2022) (0)
- Abstract 4990: Regenerative origin of colorectal metastasis stem cells (2018) (0)
- Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling (2022) (0)
- Scalable microfluidics for single-cell RNA printing and sequencing (2015) (0)
- Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs new combination cancer therapy strategies. (2023) (0)
- Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma (2019) (0)
- Abstract 1728: Single cell RNA-seq analysis reveals a role of pro-inflammatory tumor-associated macrophages in driving prostate cancer progression (2022) (0)
- Compositional and architectural characterization of high-grade serous ovarian carcinomas using single cell technologies and multiplex microscopy (2020) (0)
- Abstract 6421: Molecular profiles and single cell analysis identify immunogenic pancreatic ductal adenocarcinoma (iPDAC) (2023) (0)
- Abstract 2200: Multilineage plasticity in prostate cancer through expansion of stem-like luminal epithelial cells with elevated inflammatory signaling (2022) (0)
- Characterization of cell fate probabilities in single-cell data with Palantir (2019) (0)
- Modeling collective cell behavior in cancer: Perspectives from an interdisciplinary conversation. (2023) (0)
- Leptomeningeal anti-tumor immunity follows unique signaling principles (2023) (0)
- Abstract A26: Multi-Reg: An integrative parallel approach to uncover drivers of cancer (2011) (0)
- Distinct tumor architectures for metastatic colonization of the brain (2023) (0)
- NCMP-05. DECODING THE IMMUNE SYSTEM RESPONSE TO LEPTOMENINGEAL METASTASIS (2020) (0)
- Abstract A25: Cytometric atlas of the human breast: Comprehensive characterization reveals 12 distinct cell populations (2016) (0)
- Abstract A54: A cellular and molecular atlas of the human breast for dissecting mechanisms of cell and tissue function (2018) (0)
- Single Cell T Cell Maps of Donor Lymphocyte Infusion (DLI) Response and Resistance (2019) (0)
- A network approach to understanding drug resistance (235.2) (2014) (0)
- Measuring Signaling and R NA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NFk B Activation Graphical Abstract Highlights (2017) (0)
- P1.14-06 Tissue-Based Molecular and Histologic Landscape of Acquired Resistance to Osimertinib in Patients with EGFR-Mutant Lung Cancers (2019) (0)
- Abstract IA14: An atlas of the tumor immune ecosystem (2018) (0)
- Abstract 3178: Deep sequencing of immunophenotypically distinct subsets in acute myeloid leukemia reveals reservoirs of genetically distinct subclones along a conserved differentiation trajectory. (2013) (0)
- Abstract IA24: Computational dissection of phenotypic and functional heterogeneity in cancer (2015) (0)
- Sachs Single-Cell Data Causal Protein-Signaling Networks Derived from Multiparameter (2014) (0)
- epithelium in the involuting mammary gland cluster orchestrates remodeling of the miR-424 ( 322 ) / 503 The Material Supplemental (2014) (0)
- Abstract S1-06: The miR-424/503 cluster is a breast cancer tumor suppressor with a role in chemoresistance (2016) (0)
- Abstract A32: Computational dissection of phenotypic and functional heterogeneity in acute myeloid leukemia. (2015) (0)
- Abstract 1167: Single-cell transcriptomic profiling of SCLC transformation reveals increased intratumoral diversity of variant and non-neuroendocrine subtypes (2023) (0)
- Abstract P2-06-02: BIN3 is an 8p21 tumor suppressor regulating the epithelial attachment checkpoint (2016) (0)
- Abstract IA30: Towards rationale therapy: Dealing with intertumor and intratumor heterogeneity (2013) (0)
- Signaling and Immunophenotypic Diversity in Pediatric Acute Myeloid Leukemia As Defined by 31-Parameter Single-Cell Mass Cytometry (2011) (0)
- Abstract A12: L1CAM defines the regenerative origin of metastasis initiating cells in colorectal cancer (2020) (0)
- Abstract 5722: Acquired stemness by luminal cells (2020) (0)
- Abstract 977: Phenotypic analysis of single-cell breast cancer inhibition data reveals insights into EMT (2017) (0)
- Abstract 3168: Helios identifies novel oncogenes in breast cancer by integrating genomic characterization of primary tumors and functional shRNA-screens. (2013) (0)
- Stag2 Regulates Hematopoietic Differentiation and Self-Renewal through Alterations in Gene Expression and Topological Control (2019) (0)
- Abstract PO-134: Identification of the cells of origin and tumor heterogeneity in neuroendocrine prostate cancer (NEPC) by single-cell analysis (2020) (0)
- Abstract SY17-02: A systems approach to understanding tumor specific drug response (2011) (0)
- Multiparameter mass cytometry of T cell development and selection (2016) (0)
- Interferon a / b Enhances t he Cytotoxic Response of MEK Inhibition in Melanoma Graphical (2015) (0)
- Exploring Cellular Protein Localization Through Semantic Image Synthesis (2019) (0)
- Abstract 5236: Novel network analysis framework identifies context-specific drug combinations in melanoma. (2013) (0)
- Molecular and Cellular Pathobiology RHPN 2 Drives Mesenchymal Transformation in Malignant Glioma by Triggering RhoA Activation (2013) (0)
- Abstract 3371: Mapping the evolution of T cell states during DLI response and resistance using single-cell data and computational tools (2019) (0)
- Mixed-Layer Deep Modeling of Genotypes and Cross-Tissue Expression Uncovers Trans-Eqtls (2017) (0)
- Regenerative lineages and immune-mediated pruning in lung cancer metastasis (2020) (0)
- Gradient Estimation for Binary Latent Variables via Gradient Variance Clipping (2022) (0)
- The emergent landscape of the mouse gut endoderm at single-cell resolution (2019) (0)
- Abstract NG05: Multi-omic approaches to study the role of plasticity in therapy resistance and metastasis in lung cancer (2023) (0)
- Cross-platform dataset of multiplex fluorescent cellular object image annotations (2023) (0)
- Abstract C012: Dissecting the reorganization of pancreatic tumor microenvironments after radiation and immunotherapy reveals insights into immunotherapy resistance (2022) (0)
- Age-related epithelial defects limit thymic function and regeneration (2023) (0)
- Abstract 279: Optimal tumor metastatic gene programs in pancreatic cancer (2022) (0)
- Abstract 1594: Reversal of lineage plasticity in RB1/TP53-deleted prostate cancer through FGFR and Janus kinase inhibition (2022) (0)
- Systematic comparison of pancreatic ductal adenocarcinoma models identifies a conserved highly plastic basal cell state. (2022) (0)
- Effect of Janus kinase (JAK) signaling inhibition on lineage plasticity and drug sensitivity in castrate resistant prostate cancer. (2023) (0)
- SPOT: Spatial Optimal Transport for Analyzing Cellular Microenvironments (2022) (0)
- LMD-16. Choroid plexus orchestrates anti-cancer immunity in leptomeninges (2021) (0)
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