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

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

Visualizing the spatial gene expression organization in the brain through non-linear similarity embeddings

(2015) Ahmed Mahfouz et al.   METHODS

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

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

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

(2014) S. Anders et al.   BIOINFORMATICS

Single-molecule mRNA detection and counting in mammalian tissue

(2013) Anna Lyubimova et al.   Nature Protocols

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

(2013) Paul Igor Costea et al.   PLoS One

Sequencing mRNA from Cryo-Sliced Drosophila Embryos to Determine Genome-Wide Spatial Patterns of Gene Expression

(2013) Peter A. Combs et al.   PLoS One

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Increased Throughput by Parallelization of Library Preparation for Massive Sequencing

(2010) Sverker Lundin et al.   PLoS One

Axl is an essential epithelial-to-mesenchymal transition-induced regulator of breast cancer metastasis and patient survival

(2009) C. Gjerdrum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS