Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

Stem cell-associated heterogeneity in Glioblastoma results from intrinsic tumor plasticity shaped by the microenvironment

(2019) Anne Dirkse et al.   Nature Communications

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

(2019) Matteo Ligorio et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

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

(2019) Ela Elyada et al.   Cancer Discovery

Toward Minimal Residual Disease-Directed Therapy in Melanoma

(2018) Florian Rambow et al.   CELL

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

(2018) Mariella G. Filbin et al.   SCIENCE

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

(2018) Emelie Berglund et al.   Nature Communications

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics

(2018) Anna Lundmark et al.   Scientific Reports

The Contribution of Non-Professional Antigen-Presenting Cells to Immunity and Tolerance in the Liver

(2018) Christina Mehrfeld et al.   Frontiers in Immunology

Epithelial MHC Class II Expression and Its Role in Antigen Presentation in the Gastrointestinal and Respiratory Tracts

(2018) Jonathan E. Wosen et al.   Frontiers in Immunology

MS4A4A: a novel cell surface marker for M2 macrophages and plasma cells

(2017) Ratna Sanyal et al.   IMMUNOLOGY AND CELL BIOLOGY

Distinct populations of inflammatory fibroblasts and myofibroblasts in pancreatic cancer

(2017) Daniel Öhlund et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The heterogeneity of tumor-infiltrating CD8+ T cells in metastatic melanoma distorts their quantification

(2017) Joseph M. Obeid et al.   MELANOMA RESEARCH

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Quantitative mRNA imaging throughout the entire Drosophila brain

(2017) Xi Long et al.   NATURE METHODS

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

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 Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer

(2017) Paul Savage et al.   Cell Reports

JunB promotes cell invasion, migration and distant metastasis of head and neck squamous cell carcinoma

(2016) Hiroshi Hyakusoku et al.   JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Understanding the Mysterious M2 Macrophage through Activation Markers and Effector Mechanisms

(2015) Tamás Rőszer   MEDIATORS OF INFLAMMATION

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells

(2015) Devon A. Lawson et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Cancer-Associated Fibroblasts: Their Characteristics and Their Roles in Tumor Growth

(2015) Kazuyoshi Shiga et al.   Cancers

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

A decade of discovery in cancer genomics

(2014) Kenneth Offit   Nature Reviews Clinical Oncology

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Carbonic anhydrase IX, a hypoxia-induced catalytic component of the pH regulating machinery in tumors

(2014) Olga Sedlakova   Frontiers in Physiology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS