A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling

Functional heterogeneity of lymphocytic patterns in primary melanoma dissected through single-cell multiplexing

(2020) Francesca Maria Bosisio et al.   eLife

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

(2019) Robert M. Samstein et al.   NATURE GENETICS

Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches

(2019) Svetoslav Chakarov et al.   SCIENCE

Colonic epithelial cell diversity in health and inflammatory bowel disease

(2019) Kaushal Parikh et al.   NATURE

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity

(2019) Peter van Galen et al.   CELL

B Cell Responses: Cell Interaction Dynamics and Decisions

(2019) Jason G. Cyster et al.   CELL

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Single-cell RNA-seq highlights intra-tumoral heterogeneity and malignant progression in pancreatic ductal adenocarcinoma

(2019) Junya Peng et al.   CELL RESEARCH

Resolving medulloblastoma cellular architecture by single-cell genomics

(2019) Volker Hovestadt et al.   NATURE

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

(2019) Ela Elyada et al.   Cancer Discovery

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

(2019) Allen W. Zhang et al.   NATURE METHODS

The genomic landscape of nonsmall cell lung carcinoma in never smokers

(2019) Bram Boeckx et al.   INTERNATIONAL JOURNAL OF CANCER

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

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

(2018) Jan P. Böttcher et al.   CELL

A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain

(2018) Kristofer Davie et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

Endothelial Cell Metabolism

(2018) Guy Eelen et al.   PHYSIOLOGICAL REVIEWS

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

(2018) James Kinchen et al.   CELL

Hyaluronan Receptor LYVE-1-Expressing Macrophages Maintain Arterial Tone through Hyaluronan-Mediated Regulation of Smooth Muscle Cell Collagen

(2018) Hwee Ying Lim et al.   IMMUNITY

Ovarian stromal cells as a source of cancer-associated fibroblasts in human epithelial ovarian cancer: A histopathological study

(2018) Masayoshi Fujisawa et al.   PLoS One

NKG2A Blockade Potentiates CD8 T Cell Immunity Induced by Cancer Vaccines

(2018) Nadine van Montfoort et al.   CELL

Anti-NKG2A mAb Is a Checkpoint Inhibitor that Promotes Anti-tumor Immunity by Unleashing Both T and NK Cells

(2018) Pascale André et al.   CELL

Identity Noise and Adipogenic Traits Characterize Dermal Fibroblast Aging

(2018) Marion Claudia Salzer et al.   CELL

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

High-Dimensional Single-Cell Analysis Identifies Organ-Specific Signatures and Conserved NK Cell Subsets in Humans and Mice

(2018) Adeline Crinier et al.   IMMUNITY

Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis

(2018) Chamith Y. Fonseka et al.   Science Translational Medicine

Regulating Innate and Adaptive Immunity for Controlling SIV Infection by 25-Hydroxycholesterol

(2018) Tongjin Wu et al.   Frontiers in Immunology

Folate deficiency affects dendritic cell function and subsequent T helper cell differentiation

(2017) Chi-Heng Wu et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

Mesothelial-to-mesenchymal transition as a possible therapeutic target in peritoneal metastasis of ovarian cancer

(2017) Angela Rynne-Vidal et al.   JOURNAL OF PATHOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Unsupervised High-Dimensional Analysis Aligns Dendritic Cells across Tissues and Species

(2016) Martin Guilliams et al.   IMMUNITY

Access of protective antiviral antibody to neuronal tissues requires CD4 T-cell help

(2016) Norifumi Iijima et al.   NATURE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Tissue-specific and convergent metabolic transformation of cancer correlates with metastatic potential and patient survival

(2016) Edoardo Gaude et al.   Nature Communications

Recommendations for myeloid-derived suppressor cell nomenclature and characterization standards

(2016) Vincenzo Bronte et al.   Nature Communications

Aldehyde dehydrogenase 2 inhibits inflammatory response and regulates atherosclerotic plaque

(2016) Chang Pan et al.   Oncotarget

Expression of the innate immune receptor LILRB5 on monocytes is associated with mycobacteria exposure

(2016) Louise E. Hogan et al.   Scientific Reports

Myeloid-derived suppressor cells in the tumor microenvironment: expect the unexpected

(2015) Douglas Marvel et al.   JOURNAL OF CLINICAL INVESTIGATION

Ly6h Regulates Trafficking of Alpha7 Nicotinic Acetylcholine Receptors and Nicotine-Induced Potentiation of Glutamatergic Signaling

(2015) C. A. Puddifoot et al.   JOURNAL OF NEUROSCIENCE

Understanding the Mysterious M2 Macrophage through Activation Markers and Effector Mechanisms

(2015) Tamás Rőszer   MEDIATORS OF INFLAMMATION

Phenotypic and Functional Delineation of Murine CX3CR1+ Monocyte-Derived Cells in Ovarian Cancer

(2015) Kevin M. Hart et al.   NEOPLASIA

B-cell-intrinsic STAT6 signaling controls germinal center formation

(2014) Adriana Turqueti-Neves et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Generation of memory B cells inside and outside germinal centers

(2014) Toshitada Takemori et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Purinergic inhibitory regulation of murine detrusor muscles mediated by PDGFRα+interstitial cells

(2014) Haeyeong Lee et al.   JOURNAL OF PHYSIOLOGY-LONDON

Diversification of TAM receptor tyrosine kinase function

(2014) Anna Zagórska et al.   NATURE IMMUNOLOGY

IGFBP7, a novel tumor stroma marker, with growth-promoting effects in colon cancer through a paracrine tumor–stroma interaction

(2014) C Rupp et al.   ONCOGENE

Langerhans cells are generated by two distinct PU.1-dependent transcriptional networks

(2013) Michaël Chopin et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The Wilms’ tumor gene (WT1) regulates E-cadherin expression and migration of prostate cancer cells

(2013) Adina Brett et al.   Molecular Cancer

Limited expression of APRIL and its receptors prior to intestinal IgA plasma cell development during human infancy

(2013) C E Gustafson et al.   Mucosal Immunology

Minireview: Roles of the Forkhead Transcription Factor FOXL2 in Granulosa Cell Biology and Pathology

(2011) Margareta D. Pisarska et al.   ENDOCRINOLOGY

The chemokine CCL18 causes maturation of cultured monocytes to macrophages in the M2 spectrum

(2011) Ingrid U. Schraufstatter et al.   IMMUNOLOGY

Enhanced Activity of Transforming Growth Factor β1 (TGF-β1) Bound to Cartilage Oligomeric Matrix Protein

(2011) Dominik R. Haudenschild et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

EGFL6 Promotes Endothelial Cell Migration and Angiogenesis through the Activation of Extracellular Signal-regulated Kinase

(2011) Shek Man Chim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

EBI2 Operates Independently of but in Cooperation with CXCR5 and CCR7 To Direct B Cell Migration and Organization in Follicles and the Germinal Center

(2011) D. Gatto et al.   JOURNAL OF IMMUNOLOGY

IFN-  Directly Promotes Programmed Cell Death-1 Transcription and Limits the Duration of T Cell-Mediated Immunity

(2011) S. Terawaki et al.   JOURNAL OF IMMUNOLOGY

Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene

(2010) F M Buffa et al.   BRITISH JOURNAL OF CANCER

The von Hippel–Lindau Chuvash mutation promotes pulmonary hypertension and fibrosis in mice

(2010) Michele M. Hickey et al.   JOURNAL OF CLINICAL INVESTIGATION

Tumor-reactive CD4+T cells develop cytotoxic activity and eradicate large established melanoma after transfer into lymphopenic hosts

(2010) Sergio A. Quezada et al.   JOURNAL OF EXPERIMENTAL MEDICINE

A functional role for the ‘fibroblast-like cells’ in gastrointestinal smooth muscles

(2010) Masaaki Kurahashi et al.   JOURNAL OF PHYSIOLOGY-LONDON

Transcriptional profiling reveals developmental relationship and distinct biological functions of CD16+ and CD16- monocyte subsets

(2009) Petronela Ancuta et al.   BMC GENOMICS

CD8+ T lymphocyte mobilization to virus-infected tissue requires CD4+ T-cell help

(2009) Yusuke Nakanishi et al.   NATURE

Transcriptional diversity during monocyte to macrophage differentiation

(2008) Hongtao Liu et al.   IMMUNOLOGY LETTERS