Cell type-specific inference of differential expression in spatial transcriptomics

Cell2location maps fine-grained cell types in spatial transcriptomics

(2022) Vitalii Kleshchevnikov et al.   NATURE BIOTECHNOLOGY

A single-cell atlas of non-haematopoietic cells in human lymph nodes and lymphoma reveals a landscape of stromal remodelling

(2022) Yoshiaki Abe et al.   NATURE CELL BIOLOGY

Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer’s disease

(2021) Akira Sobue et al.   Acta Neuropathologica Communications

Robust decomposition of cell type mixtures in spatial transcriptomics

(2021) Dylan M. Cable et al.   NATURE BIOTECHNOLOGY

Evolutionary dynamics at the tumor edge reveal metabolic imaging biomarkers

(2021) Juan Jiménez-Sánchez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

(2021) Shahar Alon et al.   SCIENCE

Spatial transcriptomics at subspot resolution with BayesSpace

(2021) Edward Zhao et al.   NATURE BIOTECHNOLOGY

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues

(2021) Tongtong Zhao et al.   NATURE

A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types

(2021) Velina Kozareva et al.   NATURE

Cell segmentation in imaging-based spatial transcriptomics

(2021) Viktor Petukhov et al.   NATURE BIOTECHNOLOGY

Dissecting mammalian spermatogenesis using spatial transcriptomics

(2021) Haiqi Chen et al.   Cell Reports

Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease

(2020) Yingyue Zhou et al.   NATURE MEDICINE

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

Cellular and molecular properties of neural progenitors in the developing mammalian hypothalamus

(2020) Xin Zhou et al.   Nature Communications

Computerized Spermatogenesis Staging (CSS) of Mouse Testis Sections via Quantitative Histomorphological Analysis

(2020) Jun Xu et al.   MEDICAL IMAGE ANALYSIS

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

(2020) Alma Andersson et al.   Communications Biology

APOE and Alzheimer's disease: advances in genetics, pathophysiology, and therapeutic approaches

(2020) Alberto Serrano-Pozo et al.   LANCET NEUROLOGY

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

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

Microglial Progranulin: Involvement in Alzheimer’s Disease and Neurodegenerative Diseases

(2019) Anarmaa Mendsaikhan et al.   Cells

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Opposite microglial activation stages upon loss of PGRN or TREM2 result in reduced cerebral glucose metabolism

(2019) Julia K Götzl et al.   EMBO Molecular Medicine

Peritumoral Monocytes Induce Cancer Cell Autophagy to Facilitate the Progression of Human Hepatocellular Carcinoma

(2018) Dong-Ping Chen et al.   Autophagy

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq

(2018) Christopher Daniel Green et al.   DEVELOPMENTAL CELL

Human germinal center transcriptional programs are de-synchronized in B cell lymphoma

(2018) Pierre Milpied et al.   NATURE IMMUNOLOGY

New insights into the mechanisms of epithelial–mesenchymal transition and implications for cancer

(2018) Anushka Dongre et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

In vivo loss-of-function screens identify KPNB1 as a new druggable oncogene in epithelial ovarian cancer

(2017) Michiko Kodama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

NF-kappaB Is Involved in the Regulation of EMT Genes in Breast Cancer Cells

(2017) Bruno R. B. Pires et al.   PLoS One

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes

(2016) Roman A Romanov et al.   NATURE NEUROSCIENCE

Complement and microglia mediate early synapse loss in Alzheimer mouse models

(2016) S. Hong et al.   SCIENCE

Targeting the CCL2-CCR2 signaling axis in cancer metastasis

(2016) Su Yin Lim et al.   Oncotarget

Progranulin protects against amyloid β deposition and toxicity in Alzheimer's disease mouse models

(2014) S Sakura Minami et al.   NATURE MEDICINE

TMEM106B expression is reduced in Alzheimer’s disease brains

(2014) Jun-ichi Satoh et al.   Alzheimers Research & Therapy

Retinoic acid signaling in Sertoli cells regulates organization of the blood-testis barrier through cyclical changes in gene expression

(2012) K. Hasegawa et al.   DEVELOPMENT

Attenuating astrocyte activation accelerates plaque pathogenesis in APP/PS1 mice

(2012) Andrew W. Kraft et al.   FASEB JOURNAL

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Gene set enrichment analysis made simple

(2010) Rafael A Irizarry et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS