Image-based transcriptomics in thousands of single human cells at single-molecule resolution

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

(2013) Marshall J Levesque et al.   NATURE METHODS

Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions

(2012) Dev M. Bhatt et al.   CELL

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Single-cell analysis of population context advances RNAi screening at multiple levels

(2012) Berend Snijder et al.   Molecular Systems Biology

Transcriptome sequencing of single cells with Smart-Seq

(2012) Jillian J Goetz et al.   NATURE BIOTECHNOLOGY

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

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

(2012) Tamar Hashimshony et al.   Cell Reports

Single-Molecule mRNA Decay Measurements Reveal Promoter- Regulated mRNA Stability in Yeast

(2011) Tatjana Trcek et al.   CELL

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

CellClassifier: supervised learning of cellular phenotypes

(2009) Pauli Rämö et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE