SpatialDE: identification of spatially variable genes

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

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

(2016) Sheel Shah et al.   NEURON

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) P. L. Stahl et al.   SCIENCE

Quantitative approaches for investigating the spatial context of gene expression

(2016) Je H. Lee   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs

(2016) Mélanie A. Eckersley-Maslin et al.   Cell Reports

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

(2016) Nick D.L. Owens et al.   Cell Reports

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

(2016) Iain C. Macaulay et al.   Cell Reports

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich et al.   CELL

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

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

(2014) Tarmo Äijö et al.   BIOINFORMATICS

Genome-wide RNA Tomography in the Zebrafish Embryo

(2014) Jan Philipp Junker et al.   CELL

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

(2014) Jean-Baptiste Pettit et al.   PLoS Computational Biology

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Cancer: Destiny from density

(2012) Victoria L. Seewaldt   NATURE

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression

(2011) Alfredo A Kalaitzis et al.   BMC BIOINFORMATICS

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series

(2010) Oliver Stegle et al.   JOURNAL OF COMPUTATIONAL BIOLOGY