Accessibility and conservation: General features of bacterial small RNA–mRNA interactions?

Global or local? Predicting secondary structure and accessibility in mRNAs

(2012) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

RNA Accessibility in cubic time

(2011) Stephan H Bernhart et al.   Algorithms for Molecular Biology

The sufficient minimal set of miRNA seed types

(2011) Daniel C. Ellwanger et al.   BIOINFORMATICS

Fast accessibility-based prediction of RNA–RNA interactions

(2011) Hakim Tafer et al.   BIOINFORMATICS

Accessibility and Evolutionary Conservation Mark Bacterial Small-RNA Target-Binding Regions

(2011) A. Peer et al.   JOURNAL OF BACTERIOLOGY

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA

(2011) Cynthia M. Sharma et al.   MOLECULAR MICROBIOLOGY

Hfq and its constellation of RNA

(2011) Jörg Vogel et al.   NATURE REVIEWS MICROBIOLOGY

The small RNA SgrS controls sugar–phosphate accumulation by regulating multiple PTS genes

(2011) Jennifer B. Rice et al.   NUCLEIC ACIDS RESEARCH

Fast prediction of RNA-RNA interaction

(2010) Raheleh Salari et al.   Algorithms for Molecular Biology

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

(2010) Stefan E Seemann et al.   Algorithms for Molecular Biology

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica

(2010) Roberto Balbontín et al.   MOLECULAR MICROBIOLOGY

Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA

(2010) K. Papenfort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A small RNA promotes siderophore production through transcriptional and metabolic remodeling

(2010) H. Salvail et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational prediction of sRNAs and their targets in bacteria

(2010) Rolf Backofen et al.   RNA Biology

sRNATarBase: A comprehensive database of bacterial sRNA targets verified by experiments

(2010) Y. Cao et al.   RNA

Bacterial Small RNA Regulators: Versatile Roles and Rapidly Evolving Variations

(2010) S. Gottesman et al.   Cold Spring Harbor Perspectives in Biology

Partition function and base pairing probabilities for RNA–RNA interaction prediction

(2009) Fenix W. D. Huang et al.   BIOINFORMATICS

A partition function algorithm for interacting nucleic acid strands

(2009) Hamidreza Chitsaz et al.   BIOINFORMATICS

Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1

(2009) Andreas S. Richter et al.   BIOINFORMATICS

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Experimental approaches for the discovery and characterization of regulatory small RNA

(2009) Cynthia Mira Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

Small RNA-induced differential degradation of the polycistronic mRNA iscRSUA

(2009) Guillaume Desnoyers et al.   EMBO JOURNAL

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

(2009) Kai Papenfort et al.   MOLECULAR MICROBIOLOGY

The transcription unit architecture of the Escherichia coli genome

(2009) Byung-Kwan Cho et al.   NATURE BIOTECHNOLOGY

Non-coding RNA annotation of the genome of Trichoplax adhaerens

(2009) J. Hertel et al.   NUCLEIC ACIDS RESEARCH

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Identification of Transcription Start Sites, Promoters and Transcription Factor Binding Sites in E. coli

(2009) Alfredo Mendoza-Vargas et al.   PLoS One

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Most mammalian mRNAs are conserved targets of microRNAs

(2008) R. C. Friedman et al.   GENOME RESEARCH

Small RNA Binding to 5′ mRNA Coding Region Inhibits Translational Initiation

(2008) Marie Bouvier et al.   MOLECULAR CELL

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

NCBI Reference Sequences: current status, policy and new initiatives

(2008) K. D. Pruitt 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