Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

STARCH: Copy number and clone inference from spatial transcriptomics data

(2020) Rebecca Elyanow et al.   PHYSICAL BIOLOGY

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data

(2019) George C. Linderman et al.   NATURE METHODS

Predicting cell populations in single cell mass cytometry data

(2019) Tamim Abdelaal et al.   CYTOMETRY PART A

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

(2019) Johanna Wagner et al.   CELL

Gene-expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ

(2019) Joseph W Foley et al.   GENOME RESEARCH

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

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

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

The role of PD-L1 expression as a predictive biomarker: an analysis of all US Food and Drug Administration (FDA) approvals of immune checkpoint inhibitors

(2019) Andrew A. Davis et al.   Journal for ImmunoTherapy of Cancer

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

(2018) Elham Azizi et al.   CELL

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Single Cell Transcriptomics of Pancreatic Cancer Precursors Demonstrates Epithelial and Microenvironmental Heterogeneity as an Early Event in Neoplastic Progression

(2018) Vincent Bernard et al.   CLINICAL CANCER RESEARCH

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline

(2016) Hao Chen et al.   PLoS Computational Biology

Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium

(2016) Greg Finak et al.   Scientific Reports

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

Methods for discovery and characterization of cell subsets in high dimensional mass cytometry data

(2015) Kirsten E. Diggins et al.   METHODS

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Myc and mTOR converge on a common node in protein synthesis control that confers synthetic lethality in Myc-driven cancers

(2013) M. Pourdehnad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE