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

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

(2015) Lars Barquist et al.   Annual Review of Genetics

Lacking alignments? The next-generation sequencing mapper segemehl revisited

(2014) Christian Otto et al.   BIOINFORMATICS

READemption--a tool for the computational analysis of deep-sequencing-based transcriptome data

(2014) K. U. Forstner et al.   BIOINFORMATICS

TheSalmonella Typhimurium effector protein SopE transiently localizes to the early SCV and contributes to intracellular replication

(2014) Pascale Vonaesch et al.   CELLULAR MICROBIOLOGY

MicL, a new  E-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein

(2014) M. S. Guo et al.   GENES & DEVELOPMENT

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

An RNA Degradation Machine Sculpted by Ro Autoantigen and Noncoding RNA

(2013) Xinguo Chen et al.   CELL

An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

(2013) Carsten Kröger et al.   Cell Host & Microbe

Complex transcriptional and post-transcriptional regulation of an enzyme for lipopolysaccharide modification

(2013) Kyung Moon et al.   MOLECULAR MICROBIOLOGY

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Simultaneous Transcriptional Profiling of Bacteria and Their Host Cells

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

The lipopolysaccharide modification regulator PmrA limitsSalmonellavirulence by repressing the type three-secretion system Spi/Ssa

(2013) Jeongjoon Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals

(2013) Roy R. Chaudhuri et al.   PLoS Genetics

Salmonella Modulation of Host Cell Gene Expression Promotes Its Intracellular Growth

(2013) Sebastian Hannemann et al.   PLoS Pathogens

The Salmonella Type III Effector SspH2 Specifically Exploits the NLR Co-chaperone Activity of SGT1 to Subvert Immunity

(2013) Amit P. Bhavsar et al.   PLoS Pathogens

Nuclear IL-33 is a transcriptional regulator of NF-κB p65 and induces endothelial cell activation

(2012) Yeon-Sook Choi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

SOCS3 in immune regulation of inflammatory bowel disease and inflammatory bowel disease-related cancer

(2012) Yi Li et al.   CYTOKINE & GROWTH FACTOR REVIEWS

An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs

(2012) Yanjie Chao et al.   EMBO JOURNAL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Dual RNA-seq of pathogen and host

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

The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair

(2012) K. Papenfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

(2012) C. Kroger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamics ofSalmonellasmall RNA expression in non-growing bacteria located inside eukaryotic cells

(2012) Álvaro D. Ortega et al.   RNA Biology

Analysis of the host microRNA response toSalmonellauncovers the control of major cytokines by thelet-7family

(2011) Leon N Schulte et al.   EMBO JOURNAL

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

A Salmonella Small Non-Coding RNA Facilitates Bacterial Invasion and Intracellular Replication by Modulating the Expression of Virulence Factors

(2011) Hao Gong et al.   PLoS Pathogens

Salmonella – At Home in the Host Cell

(2011) Preeti Malik-Kale et al.   Frontiers in Microbiology

Two antisense RNAs target the transcriptional regulator CsgD to inhibit curli synthesis

(2010) Erik Holmqvist et al.   EMBO JOURNAL

The primary transcriptome of the major human pathogen Helicobacter pylori

(2010) Cynthia M. Sharma et al.   NATURE

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets

(2009) J. W. Nicol et al.   BIOINFORMATICS

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

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

Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

(2009) Kai Papenfort et al.   MOLECULAR MICROBIOLOGY

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

(2009) Rotem Sorek et al.   NATURE REVIEWS GENETICS

CELL BIOLOGY: Moonlighting in Mitochondria

(2009) M. G. Myers Jr.   SCIENCE

Mutations in theSalmonella entericaserovar Choleraesuis cAMP-receptor protein gene lead to functional defects in the SPI-1 Type III secretion system

(2009) Zeng-Weng Chen et al.   VETERINARY RESEARCH

Salmonella Typhimurium Type III Secretion Effectors Stimulate Innate Immune Responses in Cultured Epithelial Cells

(2009) Vincent M. Bruno et al.   PLoS Pathogens

Analysis of Pools of Targeted Salmonella Deletion Mutants Identifies Novel Genes Affecting Fitness during Competitive Infection in Mice

(2009) Carlos A. Santiviago et al.   PLoS Pathogens

Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium

(2009) Hyunjin Yoon et al.   PLoS Pathogens

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

During infection of epithelial cells Salmonella enterica serovar Typhimurium undergoes a time-dependent transcriptional adaptation that results in simultaneous expression of three type 3 secretion systems

(2008) I. Hautefort et al.   CELLULAR MICROBIOLOGY

The PhoQ histidine kinases ofSalmonellaandPseudomonasspp. are structurally and functionally different: evidence that pH and antimicrobial peptide sensing contribute to mammalian pathogenesis

(2008) Lynne R. Prost et al.   MOLECULAR MICROBIOLOGY

Small RNAs encoded within genetic islands of Salmonella typhimurium show host-induced expression and role in virulence

(2008) Gilly Padalon-Brauch et al.   NUCLEIC ACIDS RESEARCH

The 5′ end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator

(2008) Maude Guillier et al.   NUCLEIC ACIDS RESEARCH

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq

(2008) Alexandra Sittka et al.   PLoS Genetics