A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

SciBet as a portable and fast single cell type identifier

(2020) Chenwei Li et al.   Nature Communications

Proline Metabolism in Tumor Growth and Metastatic Progression

(2020) Cristina D'Aniello et al.   Frontiers in Oncology

An entropy-based metric for assessing the purity of single cell populations

(2020) Baolin Liu et al.   Nature Communications

Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing

(2020) Ashley Maynard et al.   CELL

Onco-fetal Reprogramming of Endothelial Cells Drives Immunosuppressive Macrophages in Hepatocellular Carcinoma

(2020) Ankur Sharma et al.   CELL

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

(2019) Moshe Sade-Feldman et al.   CELL

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

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

(2019) Svetoslav Chakarov et al.   SCIENCE

Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity

(2019) Mikhail Binnewies et al.   CELL

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

ZEBs: Novel Players in Immune Cell Development and Function

(2019) Charlotte L. Scott et al.   TRENDS IN IMMUNOLOGY

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

(2019) Samuel L. Wolock 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

Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells

(2019) Charles-Antoine Dutertre et al.   IMMUNITY

Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity

(2019) Chrysothemis C. Brown et al.   CELL

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

Myeloid immunosuppression and immune checkpoints in the tumor microenvironment

(2019) Kyohei Nakamura et al.   Cellular & Molecular Immunology

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

CXCL9, CXCL10, CXCL11/CXCR3 axis for immune activation – A target for novel cancer therapy

(2018) Ryuma Tokunaga et al.   CANCER TREATMENT REVIEWS

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

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

(2018) Elham Azizi et al.   CELL

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

(2018) Xinyi Guo et al.   NATURE MEDICINE

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

RARα supports the development of Langerhans cells and langerin-expressing conventional dendritic cells

(2018) Seika Hashimoto-Hill et al.   Nature Communications

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Identification of CMTM6 and CMTM4 as PD-L1 protein regulators

(2017) Riccardo Mezzadra et al.   NATURE

CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity

(2017) Marian L. Burr et al.   NATURE

Toil enables reproducible, open source, big biomedical data analyses

(2017) John Vivian et al.   NATURE BIOTECHNOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Crosstalk between Regulatory T Cells and Tumor-Associated Dendritic Cells Negates Anti-tumor Immunity in Pancreatic Cancer

(2017) Jung-Eun Jang et al.   Cell Reports

TGF-β1-induced transcription factor networks in Langerhans cell development and maintenance

(2016) X. Zhang et al.   ALLERGY

Mast cells as therapeutic target in cancer

(2016) Domenico Ribatti   EUROPEAN JOURNAL OF PHARMACOLOGY

Mast cells and basophils in inflammatory and tumor angiogenesis and lymphangiogenesis

(2016) Gianni Marone et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

BTLA + Dendritic Cells: The Regulatory T Cell Force Awakens

(2016) Thomas Simon et al.   IMMUNITY

Expansion and Activation of CD103 + Dendritic Cell Progenitors at the Tumor Site Enhances Tumor Responses to Therapeutic PD-L1 and BRAF Inhibition

(2016) Hélène Salmon et al.   IMMUNITY

Tumour-specific proline vulnerability uncovered by differential ribosome codon reading

(2016) Fabricio Loayza-Puch et al.   NATURE

New insights into the multidimensional concept of macrophage ontogeny, activation and function

(2016) Florent Ginhoux et al.   NATURE IMMUNOLOGY

The Receptor Tyrosine Kinase AXL in Cancer Progression

(2016) Erinn Rankin et al.   Cancers

Mast-Cell-Derived TNF Amplifies CD8+ Dendritic Cell Functionality and CD8+ T Cell Priming

(2015) Jan Dudeck et al.   Cell Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities

(2014) David Gosselin et al.   CELL

Human macrophage polarization in vitro: Maturation and activation methods compared

(2014) Daphne Y.S. Vogel et al.   IMMUNOBIOLOGY

Macrophage heterogeneity in tissues: phenotypic diversity and functions

(2014) Siamon Gordon et al.   IMMUNOLOGICAL REVIEWS

Dendritic Cells: Master Regulators of the Immune Response

(2013) I. Mellman   Cancer Immunology Research

Mast cells as novel mediators of reproductive processes

(2013) Katja Woidacki et al.   Frontiers in Immunology

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Effectors and memories: Bcl-6 and Blimp-1 in T and B lymphocyte differentiation

(2010) Shane Crotty et al.   NATURE IMMUNOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Muc4/MUC4 functions and regulation in cancer

(2009) Kermit L Carraway et al.   Future Oncology