Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

[1]  J. Hartigan,et al.  The Dip Test of Unimodality , 1985 .

[2]  A. Bhattacharyya On a Geometrical Representation of Probability Distributions and its use in Statistical Inference. , 1990 .

[3]  Tony Jebara,et al.  Probability Product Kernels , 2004, J. Mach. Learn. Res..

[4]  Ann B. Lee,et al.  Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Tilman Brummer,et al.  Positive regulation of immune cell function and inflammatory responses by phosphatase PAC-1 , 2006, Nature Immunology.

[6]  T. Tao,et al.  On random ±1 matrices: Singularity and determinant , 2006 .

[7]  Terence Tao,et al.  On random plus/minus 1 matrices: Singularity and determinant , 2006, Random Struct. Algorithms.

[8]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .

[9]  Carl E. Rasmussen,et al.  Dirichlet Process Gaussian Mixture Models: Choice of the Base Distribution , 2010, Journal of Computer Science and Technology.

[10]  A. Giaccia,et al.  Hypoxia, inflammation, and the tumor microenvironment in metastatic disease , 2010, Cancer and Metastasis Reviews.

[11]  N. Friedman,et al.  Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis , 2011, Cell.

[12]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[13]  A. Rudensky,et al.  Regulatory T cells: mechanisms of differentiation and function. , 2012, Annual review of immunology.

[14]  B. Faircloth,et al.  Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels , 2012, PloS one.

[15]  Sean C. Bendall,et al.  Normalization of mass cytometry data with bead standards , 2013, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[16]  A. Mantovani,et al.  Tumor-Associated Macrophages as a Paradigm of Macrophage Plasticity, Diversity, and Polarization: Lessons and Open Questions , 2013, Arteriosclerosis, thrombosis, and vascular biology.

[17]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[18]  Sean C. Bendall,et al.  viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia , 2013, Nature Biotechnology.

[19]  S. Gordon,et al.  The M1 and M2 paradigm of macrophage activation: time for reassessment , 2014, F1000prime reports.

[20]  C. Benoist,et al.  Treg cells expressing the coinhibitory molecule TIGIT selectively inhibit proinflammatory Th1 and Th17 cell responses. , 2014, Immunity.

[21]  Will Liao,et al.  The cellular and molecular origin of tumor-associated macrophages , 2014, Science.

[22]  I. Amit,et al.  Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types , 2014, Science.

[23]  Sean C. Bendall,et al.  Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis , 2015, Cell.

[24]  Andrew Menzies,et al.  Subclonal diversification of primary breast cancer revealed by multiregion sequencing , 2015, Nature Medicine.

[25]  Eli R. Zunder,et al.  Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm , 2015, Nature Protocols.

[26]  Fabian J. Theis,et al.  Diffusion maps for high-dimensional single-cell analysis of differentiation data , 2015, Bioinform..

[27]  F. Geissmann,et al.  The development and maintenance of resident macrophages , 2015, Nature Immunology.

[28]  C. Drake,et al.  Immune checkpoint blockade: a common denominator approach to cancer therapy. , 2015, Cancer cell.

[29]  S. Loi,et al.  Relevance of tumor-infiltrating lymphocytes in breast cancer , 2015, BMC Medicine.

[30]  Allon M. Klein,et al.  Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells , 2015, Cell.

[31]  Rona S. Gertner,et al.  Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity , 2015, Cell.

[32]  E. Wherry,et al.  Molecular and cellular insights into T cell exhaustion , 2015, Nature Reviews Immunology.

[33]  E. Wherry,et al.  Overcoming T cell exhaustion in infection and cancer. , 2015, Trends in immunology.

[34]  M. Pittet,et al.  The role of myeloid cells in cancer therapies , 2016, Nature Reviews Cancer.

[35]  T. Schumacher,et al.  Neoantigen landscape dynamics during human melanoma–T cell interactions , 2016, Nature.

[36]  Ludmila V. Danilova,et al.  Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures , 2016, Genome Biology.

[37]  Sandhya Prabhakaran,et al.  Dirichlet Process Mixture Model for Correcting Technical Variation in Single-Cell Gene Expression Data , 2016, ICML.

[38]  Aviv Regev,et al.  A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells , 2016, Cell.

[39]  Charles H. Yoon,et al.  Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.

[40]  A. Rudensky,et al.  Hallmarks of Tissue-Resident Lymphocytes , 2016, Cell.

[41]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[42]  G. Plitas,et al.  Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. , 2016, Immunity.

[43]  Harini Veeraraghavan,et al.  Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient , 2017, Cell.

[44]  Andrea Sottoriva,et al.  Between-Region Genetic Divergence Reflects the Mode and Tempo of Tumor Evolution , 2017, Nature Genetics.

[45]  Boxi Kang,et al.  Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing , 2017, Cell.

[46]  A. Kriegstein,et al.  Single-cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment , 2017, Genome Biology.

[47]  Michael B. Stadler,et al.  An Immune Atlas of Clear Cell Renal Cell Carcinoma , 2017, Cell.

[48]  S. Sakaguchi,et al.  Regulatory T cells in cancer immunotherapy , 2016, Cell Research.

[49]  Christina S. Leslie,et al.  Chromatin states define tumor-specific T cell dysfunction and reprogramming , 2017, Nature.

[50]  Allon M. Klein,et al.  Single-cell barcoding and sequencing using droplet microfluidics , 2016, Nature Protocols.

[51]  Benjamin D. Greenbaum,et al.  Innate Immune Landscape in Early Lung Adenocarcinoma by Paired Single-Cell Analyses , 2017, Cell.

[52]  Allon M Klein,et al.  Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR , 2018, Nature Immunology.