Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

(2017) James W. Nelson et al.   MOLECULAR CELL

Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity

(2017) Zasha Weinberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and analysis of integrons and cassette arrays in bacterial genomes

(2016) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

TheyjdFriboswitch candidate regulates gene expression by binding diverse azaaromatic compounds

(2016) Sanshu Li et al.   RNA

Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

(2016) D. Dar et al.   SCIENCE

The role of mRNA structure in bacterial translational regulation

(2016) Michelle M. Meyer   Wiley Interdisciplinary Reviews-RNA

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

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

Mn 2+ -Sensing Mechanisms of yybP-ykoY Orphan Riboswitches

(2015) Ian R. Price et al.   MOLECULAR CELL

An Ancient Riboswitch Class in Bacteria Regulates Purine Biosynthesis and One-Carbon Metabolism

(2015) Peter B. Kim et al.   MOLECULAR CELL

The Ubiquitous yybP-ykoY Riboswitch Is a Manganese-Responsive Regulatory Element

(2015) Michael Dambach et al.   MOLECULAR CELL

Bacterial Riboswitches Cooperatively Bind Ni 2+ or Co 2+ Ions and Control Expression of Heavy Metal Transporters

(2015) Kazuhiro Furukawa et al.   MOLECULAR CELL

New classes of self-cleaving ribozymes revealed by comparative genomics analysis

(2015) Zasha Weinberg et al.   Nature Chemical Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

RNA reflections: converging on Hfq

(2015) Susan Gottesman et al.   RNA

Chemistry and Biology of Self-Cleaving Ribozymes

(2015) Randi M. Jimenez et al.   TRENDS IN BIOCHEMICAL SCIENCES

Computational analysis of riboswitch-based regulation

(2014) Eric I. Sun et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Structural, Functional, and Taxonomic Diversity of Three PreQ1 Riboswitch Classes

(2014) Phillip J. McCown et al.   CHEMISTRY & BIOLOGY

CDD: NCBI's conserved domain database

(2014) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Gene regulation by structured mRNA elements

(2014) Andreas Wachter   TRENDS IN GENETICS

Riboswitches in eubacteria sense the second messenger c-di-AMP

(2013) James W Nelson et al.   Nature Chemical Biology

IMG/M 4 version of the integrated metagenome comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

GraphClust: alignment-free structural clustering of local RNA secondary structures

(2012) Steffen Heyne et al.   BIOINFORMATICS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

RNIE: genome-wide prediction of bacterial intrinsic terminators

(2011) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Bacterial aptamers that selectively bind glutamine

(2011) Tyler D. Ames et al.   RNA Biology

RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data

(2011) S. Washietl et al.   RNA

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride

(2011) J. L. Baker et al.   SCIENCE

Discovery and Structure Determination of the Orphan Enzyme Isoxanthopterin Deaminase,

(2010) Richard S. Hall et al.   BIOCHEMISTRY

A Eubacterial Riboswitch Class That Senses the Coenzyme Tetrahydrofolate

(2010) Tyler D. Ames et al.   CHEMISTRY & BIOLOGY

An Allosteric Self-Splicing Ribozyme Triggered by a Bacterial Second Messenger

(2010) E. R. Lee et al.   SCIENCE

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

(2010) Zasha Weinberg et al.   GENOME BIOLOGY

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes

(2009) A. Moura et al.   BIOINFORMATICS

Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis

(2009) Zasha Weinberg et al.   NATURE

FINDING NON-CODING RNAs THROUGH GENOME-SCALE CLUSTERING

(2009) HUEI-HUN TSENG et al.   Journal of Bioinformatics and Computational Biology

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS