Mapping the small RNA interactome in bacteria using RIL-seq

ProQ/FinO-domain proteins: another ubiquitous family of RNA matchmakers?

(2017) Mikolaj Olejniczak et al.   MOLECULAR MICROBIOLOGY

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E

(2016) Shafagh A Waters et al.   EMBO JOURNAL

Global Mapping of Small RNA-Target Interactions in Bacteria

(2016) Sahar Melamed et al.   MOLECULAR CELL

GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation

(2016) Kook Han et al.   Nature Microbiology

A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise

(2015) David Lalaouna et al.   MOLECULAR CELL

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

(2015) Alexander A Shishkin et al.   NATURE METHODS

miRNA–target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity

(2015) Michael J. Moore et al.   Nature Communications

Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions

(2014) Stefanie Grosswendt et al.   MOLECULAR CELL

Revisiting the coding potential of theE. coligenome through Hfq co-immunoprecipitation

(2014) Ivana Bilusic et al.   RNA Biology

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

(2013) Aleksandra Helwak et al.   CELL

In vivo mapping of RNA–RNA interactions in Staphylococcus aureus using the endoribonuclease III

(2013) Efthimia Lioliou et al.   METHODS

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

(2012) Yanjie Chao et al.   EMBO JOURNAL

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Post-Transcriptional Regulation of Gene Expression in Yersinia Species

(2012) Chelsea A. Schiano et al.   Frontiers in Cellular and Infection Microbiology

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

(2008) Alexandra Sittka et al.   PLoS Genetics