XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment

Trajectory-based differential expression analysis for single-cell sequencing data

(2020) Koen Van den Berge et al.   Nature Communications

Transcriptome profiling of human thymic CD4+ and CD8+ T cells compared to primary peripheral T cells

(2020) Hanna Helgeland et al.   BMC GENOMICS

Interplay between mesenchymal stem cell and tumor and potential application

(2020) Qing Wang et al.   Human Cell

Protein kinase G1 regulates bone regeneration and rescues diabetic fracture healing

(2020) Nadine Schall et al.   JCI Insight

Regulatory T cell control of systemic immunity and immunotherapy response in liver metastasis

(2020) James C. Lee et al.   Science Immunology

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation

(2019) Marta Joana Costa Jordão et al.   SCIENCE

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges

(2019) Mario L. Suvà et al.   MOLECULAR CELL

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

PD-L1 on host cells is essential for PD-L1 blockade–mediated tumor regression

(2018) Haidong Tang et al.   JOURNAL OF CLINICAL INVESTIGATION

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Nitric oxide and cyclic GMP functions in bone

(2018) Hema Kalyanaraman et al.   NITRIC OXIDE-BIOLOGY AND CHEMISTRY

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution

(2018) Mirjana Efremova et al.   Nature Communications

A practical solution for preserving single cells for RNA sequencing

(2018) Moustafa Attar et al.   Scientific Reports

Systematic identification of the key candidate genes in breast cancer stroma

(2018) Yanxia Wang et al.   CELLULAR & MOLECULAR BIOLOGY LETTERS

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

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The Cytokine TGF-β Promotes the Development and Homeostasis of Alveolar Macrophages

(2017) Xueyang Yu et al.   IMMUNITY

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

(2017) Sheel Shah et al.   NEURON

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

The relationship between stromal cell derived SPARC in human gastric cancer tissue and its clinicopathologic significance

(2017) Yi Gao et al.   Oncotarget

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

(2016) P. L. Stahl et al.   SCIENCE

Cell surface heparan sulfate proteoglycans as novel markers of human neural stem cell fate determination

(2016) Lotta E. Oikari et al.   Stem Cell Research

Complement inhibitor CSMD1 acts as tumor suppressor in human breast cancer

(2016) Astrid Escudero-Esparza et al.   Oncotarget

Immune Checkpoint Blockade to Improve Tumor Infiltrating Lymphocytes for Adoptive Cell Therapy

(2016) Krithika N. Kodumudi et al.   PLoS One

Epithelial-derived IL-18 regulates Th17 cell differentiation and Foxp3+ Treg cell function in the intestine

(2015) O J Harrison et al.   Mucosal Immunology

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

Down-regulation of the zinc-finger homeobox protein TSHZ2 releases GLI1 from the nuclear repressor complex to restore its transcriptional activity during mammary tumorigenesis

(2015) Miho Riku et al.   Oncotarget

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

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

(2014) A. P. Patel et al.   SCIENCE

PKC-theta-mediated signal delivery from the TCR/CD28 surface receptors

(2012) Noah Isakov et al.   Frontiers in Immunology

Metastatic Outgrowth Encompasses COL-I, FN1, and POSTN Up-Regulation and Assembly to Fibrillar Networks Regulating Cell Adhesion, Migration, and Growth

(2010) Johanna Soikkeli et al.   AMERICAN JOURNAL OF PATHOLOGY

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS