A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes

Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions

(2016) Alexander J. Westermann et al.   NATURE

Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions

(2015) Laura A. L. Dillon et al.   BMC GENOMICS

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

The co-transcriptome of uropathogenicEscherichia coli-infected mouse macrophages reveals new insights into host-pathogen interactions

(2015) Charalampos Harris Mavromatis et al.   CELLULAR MICROBIOLOGY

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

(2015) Thorsten Bischler et al.   METHODS

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk

(2015) B. Baddal et al.   mBio

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data

(2015) Sylvie Schulze et al.   Frontiers in Microbiology

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

A Transcriptomic Network Identified in Uninfected Macrophages Responding to Inflammation Controls Intracellular Pathogen Survival

(2013) Lynette Beattie et al.   Cell Host & Microbe

Simultaneous Transcriptome Analysis of Sorghum and Bipolaris sorghicola by Using RNA-seq in Combination with De Novo Transcriptome Assembly

(2013) Takayuki Yazawa et al.   PLoS One

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

(2013) Michael S. Humphrys et al.   PLoS One

How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?

(2012) Brian J Haas et al.   BMC GENOMICS

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Simultaneous RNA-Seq Analysis of a Mixed Transcriptome of Rice and Blast Fungus Interaction

(2012) Yoshihiro Kawahara et al.   PLoS One

An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells

(2012) Lanay Tierney et al.   Frontiers in Microbiology

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis

(2010) Matthew P. R. Berry et al.   NATURE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY